------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by Los Alamos National Security, LLC at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- RESOLVE --- * * * * Statistical density modification * * Automated model-building * * * * For on-line help * * see "http://solve.lanl.gov" * * * * This software uses library routines from the * * CCP4 suite (http://www.ccp4.ac.uk) for which * * the author is very thankful! * ******************************************************* (version 2.15 of 20-Mar-2010) (size = 12) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" >workdir AutoBuild_run_1_/TEMP0 Work directory will be : AutoBuild_run_1_/TEMP0/ >outputdir AutoBuild_run_1_ Directory for STOPWIZARD will be AutoBuild_run_1_/ >freer_if_present Only writing out FreeR_flag if present >hklin image.mtz Data to be read from mtz file: image.mtz >labin FP=FP SIGFP=SIGFP PHIB=PHIM FOM=FOMM Current value of "LABIN" is: labin FP=FP SIGFP=SIGFP PHIB=PHIM FOM=FOMM >labin HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM Current value of "LABIN" is: labin FP=FP SIGFP=SIGFP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM >hklout image_only_dm.mtz Data to be written to mtz file: image_only_dm.mtz >solvent_content 0.47 Fraction of unit cell assumed to be solvent is: 0.4700000 >no_build Model will not be built >resolution 1.6096 500.0 Resolution range (A) is: 1.609600 to 500.0000 >ha_file NONE Heavy atom sites will be read from file: NONE The file does not exist...ignoring it >use_hist_prob Histogram-based method for solvent mask will be used >no_ha no_ha: heavy-atoms not written out in pdb files >new_ncs_group Ignoring new_ncs_group as no NCS read in yet About to start NCS group 1 >rota_matrix 1.0000 0.0000 0.0000 Starting NCS operator 1 The expectation for NCS operators is that they map from molecule j onto molecule 1.f This is what you get from lsqkab if molecule 1 is xyzin1 (reference) and molecule j is xyzin2 (working) You can input the inverse transformations if you also specify "invert" >rota_matrix 0.0000 1.0000 -0.0000 >rota_matrix 0.0000 0.0000 1.0000 >tran_orth 0.0000 -0.0000 -0.0000 >center_orth -5.6944 42.8323 65.7655 Center of mass of object 1 is near (orthogonal coordinates): -5.694400 42.83230 65.76550 >rota_matrix -1.0000 0.0042 0.0022 Starting NCS operator 2 >rota_matrix -0.0042 -1.0000 0.0037 >rota_matrix 0.0022 0.0036 1.0000 >tran_orth 82.2376 50.8440 -0.0732 >center_orth 88.1067 7.8821 65.6182 Center of mass of object 2 is near (orthogonal coordinates): 88.10670 7.882100 65.61820 >n_xyz 120 150 180 Grid units x y z: 120 150 180 >database 5 Entry in database of histograms to use: 5 >no_optimize_ncs Not optimizing NCS >spg_name_use P 1 21 1 Space group name for output PDB file only: P 1 21 1 >min_z_value_rho -3.0 Minimum z-value for a segment not matched to sequence: -3.000000 >no_create_free Will not create FREE (test) set >use_all_for_test Will use all data for testing solvent content and histograms >delta_phi 20.00 Angular grid (degrees) for image search: 20.00000 >dist_cut_base 3.0 Tolerance for base pairing (dist_cut_base): 3.000000 >free_id 0 Free R flag ID will be 0 >group_ca_length 4 Minimum # of residues in a group to keep= 4 >group_length 2 Minimum # of segments in a group to keep= 2 >n_random_frag 0 Number of random orientations of start/end of fragments: 0 All done with inputs New total number of NCS groups: 1 Copy to group 1 2 ------------------------------------------- Summary of NCS groups NCS GROUP 1 OPERATORS READ: 2 DOMAIN FILE: HA FILE: ------------------------------------------- Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB NONE All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 08-oct-14. Your license is good until 15-dec-96. Opened mtz file image.mtz Dataset 1 HKL_base HKL_base HKL_base 0 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 0.000000 Dataset 2 project crystal dataset 1 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Reading SG information from image.mtz Space group name: P21 Point group: PG2 Space group number : 4 Symmetry operators: 2 Number of columns: 13 H K L FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FWT PHWT Column assignments: PROGRAM INPUT_MTZ DATA# 1 H DATA# 2 K DATA# 3 L DATA# 4 FP : FP DATA# 5 PHIB : PHIM DATA# 6 FOM : FOMM DATA# 7 HLA : HLAM DATA# 8 HLB : HLBM DATA# 9 HLC : HLCM DATA# 10 HLD : HLDM DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP : SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 4 Dataset information for dataset number 2 and ID= 1 Dataset name:dataset Crystal name:crystal Project name:project Cell: 59.554001 79.206001 87.430000 90.000000 92.260002 90.000000 Wavelength: 1.000000 PHIB taken from column 6 FOM taken from column 7 Using HLA HLB HLC HLD coefficients Reading in SIGFP from column 5 No FreeR_flag read in or created Total of 84260 reflections read from file Guessing FreeR_flag corresponding to free reflections This can be set with free_id xx No freeR reflections at all Total of 0 of 84260 reflections in test set High-resolution limit of input phased data: 1.61 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 1.61 max: 1.61 Space group is 4 Using symmetry operations from input MTZ file Transformations from orthogonal to fractional and back: Orthogonal to fractional fractional x= 0.01679 X + -0.00000 Y + 0.00066 Z fractional y= 0.00000 X + 0.01263 Y + -0.00000 Z fractional z= 0.00000 X + 0.00000 Y + 0.01145 Z Fractional to orthogonal Orthogonal X= 59.55400 x + 0.00009 y + -3.44763 z Orthogonal Y= 0.00000 x + 79.20600 y + 0.00010 z Orthogonal Z= 0.00000 x + 0.00000 y + 87.36200 z Estimated # of atoms in au: 5748 Not separating out FREE set from other reflections for main cycles. Using all data. Expected resolution-corrected F at d = 2.9A : 772.557 Results of wilson scaling: Scale on I = 18.486 B-value = -5.240 Scaling data with value of 18.486 Reading model density histograms from /net/chevy/raid1/afonine/sources/solve_resolve/ext_ref_files/segments/rho.list Read total of 10 sets of density functions Highest value of ix, iy, iz in a.u: 119 149 90 nu nv nw: 120 150 180 Number of grid points in au: 1620000 Mean fom of this map was: 0.17 Copy to group 1 2 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 13.80 0.53 0.61 300 8.79 0.57 0.58 567 6.66 0.41 0.54 1149 5.26 0.48 0.49 2015 4.44 0.54 0.44 1983 3.90 0.51 0.40 1973 3.35 0.41 0.34 4306 3.00 0.30 0.29 4827 2.73 0.24 0.25 5554 2.53 0.21 0.21 5748 2.36 0.18 0.18 6812 2.19 0.16 0.15 4327 2.08 0.12 0.13 8211 1.97 0.10 0.11 8771 1.84 0.06 0.08 10931 1.74 0.04 0.06 9168 1.66 0.03 0.05 7618 Mean fom of this map was: 0.17 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Estimating optimal initial smoothing radius using the function: R=2.41 * (dmin**0.90) * (fom**-0.26) with dmin = 1.609600 and fom = 0.1748910 Leading to R= 5.820278 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_start" Setting final smoothing radius to 4.000000 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_finish" Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators -------------------------------------- Analysis of NCS for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0042 Y + 0.0022 Z + 82.4491 New Y-prime= 0.0042 X + -1.0000 Y + 0.0037 Z + 50.4966 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2900 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.11 7.88 65.62 and as input by user is, 88.11 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + 0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0042 Y + 0.0022 Z + 82.2376 New Y-prime= -0.0042 X + -1.0000 Y + 0.0037 Z + 50.8440 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0732 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0042 0.0022 rota_matrix -0.0042 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2376 50.8440 -0.0732 center_orth 88.1095 7.8844 65.6165 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.208 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- -------------------------------------- Adding extra mask cycle at beginning to get free estimates of solvent errors Adding extra mask cycle at beginning to get free estimates of NCS errors Solvent content will be 0.47 Using database entry 5 for histograms (" 3 A dehalogenase model ") Total mask cycles: 7 Total density modification mask cycles: 7 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 YES YES NO NO NO NO 10 2 NO NO NO NO YES NO 10 3 YES YES NO NO YES NO 10 4 YES YES NO NO YES NO 10 5 YES YES NO NO YES NO 10 6 YES YES NO NO YES NO 10 7 YES YES NO NO YES NO 10 Mask cycle 1 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 5.82 Using histogram-based mask Assuming this cycle is unbiased (no previous density modification) Plot 1 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 .......................................xxxxxxxxxxx . + xxxx . . + xxxx . . + xx . . + xx . . + x . . +x . p(protein) . x . 0.5 . + . . xx+ . . x + . . xx + . . xxxx + . . x + . . xxx + . 0.0 .xxxxxxxxxx.............+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0042 Y + 0.0022 Z + 82.4491 New Y-prime= 0.0042 X + -1.0000 Y + 0.0037 Z + 50.4966 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2900 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.11 7.88 65.62 and as input by user is, 88.11 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + 0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0042 Y + 0.0022 Z + 82.2376 New Y-prime= -0.0042 X + -1.0000 Y + 0.0037 Z + 50.8440 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0732 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0042 0.0022 rota_matrix -0.0042 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2376 50.8440 -0.0732 center_orth 88.1095 7.8844 65.6165 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.208 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.14727 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 3.91 95066 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.11 63677 17.3 2.90 231387 25.4 1.17 514760 33.4 1.01 805030 41.5 1.52 908023 49.2 1.41 524858 56.6 1.71 123538 63.3 2.68 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.41 which is very good. The fall-off of the overlap has a characteristic length of 7348.9 A which is a little surprising considering the distance between molecular centers of 43.1 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 51.9% of asymmetric unit used in NCS with 25.9% within molecule 1 and 25.9% in NCS-related molecules. Cutoff in used in identifying NCS = 0.99 Asymmetric unit of NCS contains 420169 points (plus the 95682 border points) which can be represented by 18285 continuous rows along x with mean length of 28.2 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.89 Final overall correlation of NCS is: 0.89 Refined NCS operators: Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0045 Y + 0.0022 Z + 82.4558 New Y-prime= 0.0045 X + -1.0000 Y + 0.0037 Z + 50.4985 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2898 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.11 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0045 Y + 0.0022 Z + 82.2274 New Y-prime= -0.0045 X + -1.0000 Y + 0.0037 Z + 50.8735 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0757 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0045 0.0022 rota_matrix -0.0045 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2274 50.8735 -0.0757 center_orth 88.1038 7.8844 65.6165 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.15047 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 3.91 95090 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.11 63677 17.3 2.90 231387 25.4 1.17 514760 33.4 1.01 805030 41.5 1.52 908023 49.2 1.40 524858 56.6 1.71 123538 63.3 2.68 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.41 which is very good. The fall-off of the overlap has a characteristic length of 7348.9 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 51.9% of asymmetric unit used in NCS with 25.9% within molecule 1 and 25.9% in NCS-related molecules. Cutoff in used in identifying NCS = 0.99 Asymmetric unit of NCS contains 420158 points (plus the 95287 border points) which can be represented by 18218 continuous rows along x with mean length of 28.3 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Saving phases and map as this is a test cycle. This is a cycle to estimate errors in solvent region. Solvent flattening omitted. Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: -1.78513e-09 Values of m, alpha, s Centric: 0.23111231844139474 0.1186674 0.2348899 Acentric: 0.17329066504681193 8.9316264E-02 0.1832907 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 2 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.05.................................................. . . . . . . . xxo . . . xx xx. . . ox x . . xx .x . p(rho) . x . x . . x . ox . . x . xxx . . x . oxxx . . x . oxxx . . xo . ooxx . . x . xxxoo . . xxo . xxxooooo . 0.0 xxxxxxxo..............................xxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 3 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.08.................................................. . . . . xx . . xox . . x. x . . x . x . . x . x . p(rho) . x . x . . x . x . . x . ox . . o . ox . . ox . x . . x . ox . . ox . xo . . ox . xoo . 0.0 xxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.89 RMS in NCS unit : 1: 0.63133126918933857 RMS in NCS unit : 2: 0.63108264207471232 Average RMS ncs in std crystal: 0.63120695948600769 Including ncs au 1 with rms of 0.63200406954032262 Including ncs au 2 with rms of 0.63185458917647441 RMS rho in NCS region: 0.63192933377827154 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.41 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.2689945 For NCS asym unit 1 the mean target rho is 0.029 +/- 0.631 and the mean uncertainty in it is 0.287 +/- 0.095 For NCS asym unit 2 the mean target rho is 0.031 +/- 0.631 and the mean uncertainty in it is 0.287 +/- 0.095 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.26 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.63 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.57 offset is -0.28 and sigma is a random variable with rms value of 0.26 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.17 0.23 0.17 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.34 0.35 0.34 81921 2331 84252 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.45 0.47 0.46 0.31 0.47 81928 4.6 0.48 0.84 0.85 0.75 0.20 0.85 4137 2.9 0.40 0.82 0.83 0.65 0.18 0.83 11903 2.3 0.21 0.61 0.63 0.55 0.24 0.63 16949 2.0 0.14 0.45 0.48 0.47 0.28 0.48 14217 1.7 0.06 0.23 0.26 0.36 0.35 0.26 24723 1.6 0.03 0.12 0.13 0.20 0.38 0.13 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.52 0.54 0.47 0.29 0.54 2332 4.6 0.43 0.77 0.79 0.64 0.31 0.79 345 2.9 0.39 0.76 0.77 0.57 0.29 0.77 496 2.3 0.22 0.59 0.61 0.49 0.24 0.61 534 2.0 0.14 0.41 0.43 0.46 0.24 0.43 358 1.7 0.06 0.22 0.25 0.30 0.21 0.25 471 1.6 0.03 0.11 0.12 0.16 0.22 0.12 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.45 0.47 0.46 0.31 0.47 84260 4.6 0.48 0.83 0.85 0.74 0.20 0.85 4482 2.9 0.40 0.81 0.82 0.64 0.19 0.82 12399 2.3 0.21 0.61 0.63 0.55 0.24 0.63 17483 2.0 0.14 0.45 0.48 0.47 0.28 0.48 14575 1.7 0.06 0.23 0.26 0.36 0.34 0.26 25194 1.6 0.03 0.12 0.13 0.20 0.37 0.13 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.47 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.31 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.69 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.83 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.34 0.84 42 0.30 0.84 10.73 507 0.68 0.82 60 0.59 0.82 7.75 1058 0.77 0.80 91 0.80 0.80 5.96 1884 0.81 0.77 131 0.78 0.77 4.77 1883 0.82 0.74 100 0.64 0.74 4.17 1899 0.66 0.71 74 0.59 0.71 3.58 4133 0.74 0.66 173 0.76 0.66 3.16 4651 0.70 0.62 176 0.73 0.62 2.86 5367 0.63 0.58 187 0.50 0.58 2.62 5570 0.61 0.55 178 0.53 0.55 2.44 6624 0.58 0.51 188 0.61 0.51 2.27 4223 0.43 0.47 104 0.53 0.47 2.15 8006 0.58 0.44 205 0.77 0.44 2.03 8584 0.36 0.41 187 0.32 0.41 1.91 10719 0.36 0.37 212 0.38 0.37 1.79 9039 0.25 0.34 129 0.20 0.34 1.70 7523 0.14 0.30 95 -0.01 0.30 1.61 Overall average CC: 0.48077902813697265 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.725 B-value to apply to Fc= 19.921 Overall R-factor for FC vs FP: 0.434 for 84260 reflections Writing overall R-factor of 0.434 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.57 0.73 81928 0.54 0.75 2332 0.57 0.74 84260 4.6 0.80 0.84 4137 0.68 0.78 345 0.79 0.84 4482 2.9 0.70 0.76 11903 0.61 0.75 496 0.70 0.76 12399 2.3 0.63 0.74 16949 0.56 0.75 534 0.63 0.74 17483 2.0 0.57 0.72 14217 0.51 0.75 358 0.57 0.72 14575 1.7 0.51 0.69 24723 0.42 0.69 471 0.50 0.69 25194 1.6 0.37 0.53 9999 0.30 0.46 128 0.37 0.52 10127 End of first cycle ____________________________________________________________ Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0251013 Values of m, alpha, s Centric: 0.54319501904066270 0.2959170 0.4559170 Acentric: 0.47032273832245713 0.2762582 0.4221936 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 4 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . ooooo . . . xxxxxo . . . xx xxx . . x xx . p(rho) . xx .xx . . xo . ox . . o . oxxx . . xo . oooxxx . . xo . ooxxx . . xxo . oooxxx . . xoo . oxxxxooooo . xxxxo . xxxxxoooooooo 0.0 ooo.......................................xxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 5 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.05.................................................. . . . . . . . ooxxxx . . oox .oxx . . ox . ox . . ox . oox . p(rho) . ox . o x . . ox . ooxx . . ox . ox . . x . ox . . ox . ox . . xx . xx . . xx . xxo . . xxo . xxooo . 0.0 xxxxxxxxo........................xxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.87 RMS in NCS unit : 1: 0.94453560682649573 RMS in NCS unit : 2: 0.94342187801242439 Average RMS ncs in std crystal: 0.94397875666618347 Including ncs au 1 with rms of 0.94532600229087183 Including ncs au 2 with rms of 0.94432887850886316 RMS rho in NCS region: 0.94482757193920019 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.87 Normalized rms error est from solvent/protein= 0.44 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4335486 For NCS asym unit 1 the mean target rho is 0.039 +/- 0.943 and the mean uncertainty in it is 0.453 +/- 0.133 For NCS asym unit 2 the mean target rho is 0.041 +/- 0.945 and the mean uncertainty in it is 0.453 +/- 0.133 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.42 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.47 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.67 offset is -0.47 and sigma is a random variable with rms value of 0.42 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.47 0.54 0.47 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.32 0.26 0.31 81916 2332 84248 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.39 0.42 0.53 0.35 0.42 81928 4.6 0.48 0.73 0.77 0.74 0.30 0.77 4137 2.9 0.40 0.72 0.75 0.68 0.26 0.75 11903 2.3 0.21 0.52 0.56 0.60 0.30 0.56 16949 2.0 0.14 0.39 0.43 0.56 0.32 0.43 14217 1.7 0.06 0.20 0.23 0.44 0.37 0.23 24723 1.6 0.03 0.10 0.11 0.29 0.39 0.11 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.44 0.47 0.50 0.33 0.47 2332 4.6 0.43 0.64 0.67 0.63 0.38 0.67 345 2.9 0.39 0.65 0.68 0.54 0.35 0.68 496 2.3 0.22 0.48 0.51 0.51 0.30 0.51 534 2.0 0.14 0.35 0.38 0.47 0.27 0.38 358 1.7 0.06 0.19 0.22 0.40 0.24 0.22 471 1.6 0.03 0.08 0.10 0.35 0.27 0.10 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.39 0.42 0.53 0.35 0.42 84260 4.6 0.48 0.72 0.76 0.73 0.31 0.76 4482 2.9 0.40 0.72 0.75 0.68 0.26 0.75 12399 2.3 0.21 0.52 0.56 0.60 0.30 0.56 17483 2.0 0.14 0.39 0.43 0.56 0.32 0.43 14575 1.7 0.06 0.20 0.23 0.44 0.36 0.23 25194 1.6 0.03 0.10 0.11 0.29 0.39 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.42 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.35 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.65 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.67 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.42 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.47 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.67 offset is -0.47 and sigma is a random variable with rms value of 0.42 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.47 0.54 0.47 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.24 0.19 0.24 81912 2332 84244 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.39 0.40 0.53 0.35 0.40 81928 4.6 0.48 0.73 0.75 0.74 0.30 0.75 4137 2.9 0.40 0.72 0.70 0.68 0.26 0.70 11903 2.3 0.21 0.52 0.53 0.60 0.30 0.53 16949 2.0 0.14 0.39 0.41 0.56 0.32 0.41 14217 1.7 0.06 0.20 0.23 0.44 0.37 0.23 24723 1.6 0.03 0.10 0.11 0.29 0.39 0.11 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.44 0.45 0.50 0.33 0.45 2332 4.6 0.43 0.64 0.66 0.63 0.38 0.66 345 2.9 0.39 0.65 0.64 0.54 0.35 0.64 496 2.3 0.22 0.48 0.49 0.51 0.30 0.49 534 2.0 0.14 0.35 0.37 0.47 0.27 0.37 358 1.7 0.06 0.19 0.21 0.40 0.24 0.21 471 1.6 0.03 0.08 0.10 0.35 0.27 0.10 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.39 0.40 0.53 0.35 0.40 84260 4.6 0.48 0.72 0.74 0.73 0.31 0.74 4482 2.9 0.40 0.72 0.70 0.68 0.26 0.70 12399 2.3 0.21 0.52 0.53 0.60 0.30 0.53 17483 2.0 0.14 0.39 0.41 0.56 0.32 0.41 14575 1.7 0.06 0.20 0.23 0.44 0.36 0.23 25194 1.6 0.03 0.10 0.11 0.29 0.39 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.40 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.35 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.65 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.67 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.59 0.95 42 0.20 0.95 10.73 507 0.90 0.94 60 0.83 0.94 7.75 1058 0.87 0.93 91 0.89 0.93 5.96 1884 0.89 0.90 131 0.87 0.90 4.77 1883 0.91 0.88 100 0.89 0.88 4.17 1899 0.88 0.86 74 0.87 0.86 3.58 4133 0.87 0.82 173 0.86 0.82 3.16 4651 0.83 0.79 176 0.82 0.79 2.86 5367 0.80 0.76 187 0.75 0.76 2.62 5570 0.79 0.73 178 0.81 0.73 2.44 6624 0.77 0.70 188 0.75 0.70 2.27 4223 0.73 0.67 104 0.80 0.67 2.15 8006 0.77 0.64 205 0.82 0.64 2.03 8584 0.62 0.61 187 0.65 0.61 1.91 10719 0.56 0.57 212 0.62 0.57 1.79 9039 0.44 0.54 129 0.34 0.54 1.70 7523 0.30 0.51 95 0.23 0.51 1.61 Overall average CC: 0.66896006611847636 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.296 B-value to apply to Fc= 13.558 Overall R-factor for FC vs FP: 0.357 for 84260 reflections Writing overall R-factor of 0.357 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.69 0.87 81928 0.65 0.88 2332 0.69 0.87 84260 4.6 0.86 0.93 4137 0.79 0.92 345 0.86 0.93 4482 2.9 0.81 0.90 11903 0.68 0.87 496 0.80 0.90 12399 2.3 0.76 0.88 16949 0.68 0.89 534 0.76 0.88 17483 2.0 0.71 0.87 14217 0.62 0.89 358 0.71 0.87 14575 1.7 0.62 0.81 24723 0.57 0.85 471 0.62 0.81 25194 1.6 0.49 0.68 9999 0.44 0.78 128 0.49 0.68 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.42 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.47 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.67 offset is -0.47 and sigma is a random variable with rms value of 0.42 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.40 0.45 0.40 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.06 0.05 0.06 81915 2332 84247 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.37 0.41 0.57 0.36 0.41 81928 4.6 0.48 0.72 0.76 0.80 0.31 0.76 4137 2.9 0.40 0.70 0.72 0.77 0.28 0.72 11903 2.3 0.21 0.50 0.54 0.69 0.31 0.54 16949 2.0 0.14 0.37 0.41 0.60 0.33 0.41 14217 1.7 0.06 0.19 0.22 0.46 0.37 0.22 24723 1.6 0.03 0.09 0.11 0.29 0.40 0.11 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.43 0.46 0.53 0.34 0.46 2332 4.6 0.43 0.64 0.66 0.65 0.38 0.66 345 2.9 0.39 0.65 0.66 0.62 0.35 0.66 496 2.3 0.22 0.48 0.51 0.61 0.30 0.51 534 2.0 0.14 0.34 0.37 0.49 0.28 0.37 358 1.7 0.06 0.18 0.21 0.37 0.25 0.21 471 1.6 0.03 0.07 0.09 0.27 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.38 0.41 0.57 0.36 0.41 84260 4.6 0.48 0.72 0.75 0.79 0.31 0.75 4482 2.9 0.40 0.70 0.72 0.76 0.28 0.72 12399 2.3 0.21 0.50 0.53 0.69 0.31 0.53 17483 2.0 0.14 0.37 0.41 0.59 0.33 0.41 14575 1.7 0.06 0.19 0.22 0.45 0.37 0.22 25194 1.6 0.03 0.09 0.11 0.29 0.40 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.41 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.36 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.64 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 8.69 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 255 0.56 1.00 42 0.25 1.00 10.73 507 0.89 0.99 60 0.82 0.99 7.75 1058 0.89 0.97 91 0.91 0.97 5.96 1884 0.92 0.95 131 0.89 0.95 4.77 1883 0.94 0.93 100 0.92 0.93 4.17 1899 0.89 0.90 74 0.88 0.91 3.58 4133 0.92 0.87 173 0.91 0.87 3.16 4651 0.89 0.83 176 0.89 0.83 2.86 5367 0.86 0.80 187 0.83 0.80 2.62 5570 0.85 0.77 178 0.85 0.77 2.44 6624 0.83 0.74 188 0.83 0.74 2.27 4223 0.74 0.70 104 0.82 0.70 2.15 8006 0.81 0.68 205 0.86 0.68 2.03 8584 0.66 0.65 187 0.71 0.65 1.91 10719 0.60 0.60 212 0.60 0.60 1.79 9039 0.46 0.57 129 0.32 0.57 1.70 7523 0.31 0.53 95 0.16 0.54 1.61 Overall average CC: 0.70723515859776498 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.579 B-value to apply to Fc= 13.202 Overall R-factor for FC vs FP: 0.334 for 84257 reflections Writing overall R-factor of 0.334 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.71 0.88 81928 0.65 0.89 2332 0.70 0.88 84260 4.6 0.87 0.93 4137 0.77 0.93 345 0.86 0.93 4482 2.9 0.83 0.91 11903 0.70 0.88 496 0.83 0.91 12399 2.3 0.78 0.90 16949 0.70 0.91 534 0.78 0.90 17483 2.0 0.72 0.88 14217 0.59 0.89 358 0.72 0.88 14575 1.7 0.63 0.82 24723 0.53 0.84 471 0.63 0.82 25194 1.6 0.51 0.70 9999 0.47 0.75 128 0.50 0.70 10127 Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0257364 Values of m, alpha, s Centric: 0.45875777945162072 0.2452547 0.4052547 Acentric: 0.40533235323316624 0.2331994 0.3742659 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 6 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . oxxxo . . . ox xx . . . xx oxx . p(rho) . x oxx . . xxo oox . . oo .ooxx . . xo . oo xx . . xxo . oooxxx . . xxo . ooxxxx . . xx o . oxxxooooo . . xxooo . xxxxxoooooooooo 0.0 xxooo...................................xxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 7 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . ooxxx . . oxxo x . . o x .o x . . ox . ox . p(rho) . ox . oox . . ox . o x . . ox . oox . . oxx . ox . . x . ox . . x . xx . . xx . xoo . . xxo . xxooo . 0.0 xxxxxxxxxoo....................xxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.91 RMS in NCS unit : 1: 0.93367939471149175 RMS in NCS unit : 2: 0.92861105519416809 Average RMS ncs in std crystal: 0.93114522099494934 Including ncs au 1 with rms of 0.93457743294955864 Including ncs au 2 with rms of 0.92957887453754251 RMS rho in NCS region: 0.93208150452765426 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.39 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.3967609 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.929 and the mean uncertainty in it is 0.424 +/- 0.140 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.934 and the mean uncertainty in it is 0.424 +/- 0.140 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.36 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.93 and 0.42 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.66 offset is -0.51 and sigma is a random variable with rms value of 0.36 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.41 0.46 0.41 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.16 0.11 0.16 81918 2332 84250 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.44 0.43 0.46 0.32 0.43 81928 4.6 0.48 0.78 0.78 0.75 0.25 0.78 4137 2.9 0.40 0.78 0.75 0.64 0.21 0.75 11903 2.3 0.21 0.59 0.57 0.54 0.26 0.57 16949 2.0 0.14 0.45 0.45 0.45 0.28 0.45 14217 1.7 0.06 0.24 0.25 0.36 0.34 0.25 24723 1.6 0.03 0.12 0.12 0.24 0.38 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.50 0.49 0.48 0.30 0.49 2332 4.6 0.43 0.70 0.70 0.66 0.35 0.70 345 2.9 0.39 0.72 0.70 0.61 0.31 0.70 496 2.3 0.22 0.56 0.55 0.52 0.26 0.55 534 2.0 0.14 0.40 0.40 0.41 0.24 0.40 358 1.7 0.06 0.23 0.23 0.31 0.21 0.23 471 1.6 0.03 0.09 0.10 0.16 0.25 0.10 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.44 0.43 0.46 0.32 0.43 84260 4.6 0.48 0.78 0.77 0.74 0.26 0.77 4482 2.9 0.40 0.78 0.75 0.64 0.21 0.75 12399 2.3 0.21 0.59 0.57 0.54 0.26 0.57 17483 2.0 0.14 0.45 0.44 0.45 0.28 0.44 14575 1.7 0.06 0.24 0.25 0.36 0.34 0.25 25194 1.6 0.03 0.11 0.12 0.24 0.38 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.32 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.68 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.95 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 255 0.51 0.92 42 0.46 0.92 10.73 507 0.83 0.91 60 0.67 0.91 7.75 1058 0.87 0.89 91 0.90 0.89 5.96 1884 0.89 0.87 131 0.88 0.87 4.77 1883 0.89 0.85 100 0.83 0.85 4.17 1899 0.80 0.83 74 0.77 0.84 3.58 4133 0.84 0.80 173 0.86 0.80 3.16 4651 0.82 0.77 176 0.86 0.78 2.86 5367 0.79 0.75 187 0.70 0.75 2.62 5570 0.76 0.72 178 0.78 0.72 2.44 6624 0.74 0.69 188 0.78 0.69 2.27 4223 0.69 0.66 104 0.75 0.66 2.15 8006 0.75 0.64 205 0.84 0.64 2.03 8584 0.62 0.61 187 0.64 0.61 1.91 10719 0.58 0.58 212 0.58 0.58 1.79 9039 0.47 0.55 129 0.39 0.55 1.70 7523 0.34 0.51 95 0.17 0.51 1.61 Overall average CC: 0.66375479542429650 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.301 B-value to apply to Fc= 13.119 Overall R-factor for FC vs FP: 0.346 for 84257 reflections Writing overall R-factor of 0.346 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.62 0.80 81928 0.58 0.83 2332 0.62 0.81 84260 4.6 0.84 0.90 4137 0.78 0.90 345 0.83 0.90 4482 2.9 0.75 0.83 11903 0.65 0.83 496 0.75 0.83 12399 2.3 0.69 0.81 16949 0.62 0.84 534 0.69 0.82 17483 2.0 0.61 0.78 14217 0.53 0.80 358 0.61 0.78 14575 1.7 0.55 0.75 24723 0.43 0.77 471 0.55 0.75 25194 1.6 0.45 0.65 9999 0.27 0.64 128 0.45 0.65 10127 Minor cycle 4 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.025339 Values of m, alpha, s Centric: 0.49354728473394466 0.2661284 0.4261284 Acentric: 0.43225207185839426 0.2493512 0.3958017 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 8 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . o xxo . . . oxx xx . . . xx oxx . p(rho) . x oxx . . xx ooxx . . o .ooxx . . xo . oo xx . . xxo . oooxxx . . xxxo . ooxxx . . xx o . oxxxooooo . .xxxooo . xxxxxoooooooooo 0.0 xoooo...................................xxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 9 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . ooxxx . . o xxo x . . oxx oo x . . o x .oox . p(rho) . ox . ooxx . . oxx . o x . . o x . oo x . . ox . oxx . . x . ox . . xx . oxo . . x . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxo......................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.93 RMS in NCS unit : 1: 0.93142513534806926 RMS in NCS unit : 2: 0.92795520399867015 Average RMS ncs in std crystal: 0.92969018220901489 Including ncs au 1 with rms of 0.93230756252224112 Including ncs au 2 with rms of 0.92889933478844500 RMS rho in NCS region: 0.93060500893412823 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.3961323 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.928 and the mean uncertainty in it is 0.423 +/- 0.140 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.931 and the mean uncertainty in it is 0.423 +/- 0.140 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.93 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.57 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.15 0.09 0.15 81913 2332 84245 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.42 0.52 0.34 0.42 81928 4.6 0.48 0.75 0.77 0.77 0.28 0.77 4137 2.9 0.40 0.74 0.73 0.72 0.24 0.73 11903 2.3 0.21 0.54 0.55 0.63 0.28 0.55 16949 2.0 0.14 0.42 0.43 0.55 0.30 0.43 14217 1.7 0.06 0.22 0.24 0.42 0.35 0.24 24723 1.6 0.03 0.11 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.46 0.48 0.50 0.32 0.48 2332 4.6 0.43 0.66 0.68 0.65 0.37 0.68 345 2.9 0.39 0.67 0.67 0.57 0.34 0.67 496 2.3 0.22 0.52 0.53 0.54 0.27 0.53 534 2.0 0.14 0.37 0.39 0.51 0.26 0.39 358 1.7 0.06 0.21 0.23 0.34 0.23 0.23 471 1.6 0.03 0.07 0.09 0.25 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.42 0.52 0.34 0.42 84260 4.6 0.48 0.74 0.76 0.76 0.29 0.76 4482 2.9 0.40 0.74 0.73 0.71 0.25 0.73 12399 2.3 0.21 0.54 0.55 0.62 0.28 0.55 17483 2.0 0.14 0.42 0.43 0.55 0.30 0.43 14575 1.7 0.06 0.22 0.24 0.41 0.35 0.24 25194 1.6 0.03 0.11 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.42 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.30 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.93 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.57 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.15 0.09 0.15 81913 2332 84245 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.42 0.52 0.34 0.42 81928 4.6 0.48 0.75 0.77 0.77 0.28 0.77 4137 2.9 0.40 0.74 0.73 0.72 0.24 0.73 11903 2.3 0.21 0.54 0.55 0.63 0.28 0.55 16949 2.0 0.14 0.42 0.43 0.55 0.30 0.43 14217 1.7 0.06 0.22 0.24 0.42 0.35 0.24 24723 1.6 0.03 0.11 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.46 0.48 0.50 0.32 0.48 2332 4.6 0.43 0.66 0.68 0.65 0.37 0.68 345 2.9 0.39 0.67 0.67 0.57 0.34 0.67 496 2.3 0.22 0.52 0.53 0.54 0.27 0.53 534 2.0 0.14 0.37 0.39 0.51 0.26 0.39 358 1.7 0.06 0.21 0.23 0.34 0.23 0.23 471 1.6 0.03 0.07 0.09 0.25 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.42 0.52 0.34 0.42 84260 4.6 0.48 0.74 0.76 0.76 0.29 0.76 4482 2.9 0.40 0.74 0.73 0.71 0.25 0.73 12399 2.3 0.21 0.54 0.55 0.62 0.28 0.55 17483 2.0 0.14 0.42 0.43 0.55 0.30 0.43 14575 1.7 0.06 0.22 0.24 0.41 0.35 0.24 25194 1.6 0.03 0.11 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.42 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.30 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.57 0.99 42 0.28 0.99 10.73 507 0.89 0.98 60 0.80 0.98 7.75 1058 0.91 0.97 91 0.92 0.97 5.96 1884 0.93 0.95 131 0.90 0.95 4.77 1883 0.94 0.93 100 0.91 0.93 4.17 1899 0.89 0.91 74 0.89 0.91 3.58 4133 0.91 0.87 173 0.93 0.88 3.16 4651 0.89 0.85 176 0.88 0.85 2.86 5367 0.87 0.82 187 0.84 0.82 2.62 5570 0.86 0.79 178 0.86 0.79 2.44 6624 0.84 0.76 188 0.88 0.76 2.27 4223 0.79 0.73 104 0.84 0.73 2.15 8006 0.83 0.71 205 0.86 0.71 2.03 8584 0.72 0.68 187 0.77 0.68 1.91 10719 0.64 0.64 212 0.61 0.64 1.79 9039 0.52 0.61 129 0.38 0.61 1.70 7523 0.37 0.58 95 0.15 0.58 1.61 Overall average CC: 0.73559209058236463 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.435 B-value to apply to Fc= 13.035 Overall R-factor for FC vs FP: 0.317 for 84258 reflections Writing overall R-factor of 0.317 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.67 0.86 81928 0.61 0.87 2332 0.67 0.86 84260 4.6 0.85 0.92 4137 0.77 0.91 345 0.85 0.92 4482 2.9 0.81 0.89 11903 0.69 0.87 496 0.80 0.89 12399 2.3 0.75 0.87 16949 0.63 0.88 534 0.75 0.87 17483 2.0 0.68 0.85 14217 0.60 0.86 358 0.68 0.85 14575 1.7 0.59 0.79 24723 0.46 0.81 471 0.59 0.79 25194 1.6 0.46 0.67 9999 0.36 0.70 128 0.46 0.67 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.93 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.57 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.42 0.48 0.42 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 81912 2332 84244 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.54 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.78 0.29 0.78 4137 2.9 0.40 0.73 0.75 0.76 0.26 0.75 11903 2.3 0.21 0.53 0.56 0.66 0.29 0.56 16949 2.0 0.14 0.40 0.44 0.56 0.31 0.44 14217 1.7 0.06 0.21 0.24 0.42 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.27 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.46 0.48 0.52 0.32 0.48 2332 4.6 0.43 0.67 0.69 0.66 0.36 0.69 345 2.9 0.39 0.66 0.68 0.63 0.34 0.68 496 2.3 0.22 0.51 0.54 0.59 0.28 0.54 534 2.0 0.14 0.37 0.39 0.52 0.26 0.39 358 1.7 0.06 0.21 0.23 0.32 0.23 0.23 471 1.6 0.03 0.07 0.09 0.10 0.29 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.54 0.34 0.43 84260 4.6 0.48 0.74 0.77 0.77 0.29 0.77 4482 2.9 0.40 0.72 0.74 0.75 0.26 0.74 12399 2.3 0.21 0.53 0.56 0.66 0.29 0.56 17483 2.0 0.14 0.40 0.44 0.56 0.31 0.44 14575 1.7 0.06 0.21 0.24 0.42 0.36 0.24 25194 1.6 0.03 0.10 0.12 0.26 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.78 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.53 0.99 42 0.34 0.99 10.73 507 0.88 0.98 60 0.79 0.98 7.75 1058 0.91 0.96 91 0.92 0.96 5.96 1884 0.93 0.95 131 0.90 0.95 4.77 1883 0.94 0.93 100 0.91 0.93 4.17 1899 0.89 0.91 74 0.88 0.91 3.58 4133 0.93 0.88 173 0.94 0.88 3.16 4651 0.92 0.85 176 0.91 0.85 2.86 5367 0.89 0.83 187 0.86 0.83 2.62 5570 0.88 0.80 178 0.86 0.80 2.44 6624 0.85 0.78 188 0.89 0.78 2.27 4223 0.80 0.75 104 0.84 0.74 2.15 8006 0.84 0.72 205 0.88 0.72 2.03 8584 0.72 0.70 187 0.77 0.70 1.91 10719 0.65 0.66 212 0.65 0.66 1.79 9039 0.52 0.63 129 0.38 0.63 1.70 7523 0.38 0.60 95 0.17 0.60 1.61 Overall average CC: 0.74682949265495779 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.665 B-value to apply to Fc= 12.470 Overall R-factor for FC vs FP: 0.310 for 84258 reflections Writing overall R-factor of 0.310 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.67 0.86 81928 0.61 0.87 2332 0.67 0.86 84260 4.6 0.86 0.92 4137 0.76 0.91 345 0.85 0.92 4482 2.9 0.82 0.89 11903 0.69 0.87 496 0.82 0.89 12399 2.3 0.76 0.88 16949 0.64 0.89 534 0.76 0.88 17483 2.0 0.68 0.85 14217 0.62 0.85 358 0.68 0.85 14575 1.7 0.59 0.79 24723 0.46 0.81 471 0.59 0.79 25194 1.6 0.47 0.67 9999 0.31 0.67 128 0.47 0.67 10127 Minor cycle 5 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0255707 Values of m, alpha, s Centric: 0.48093369408121911 0.2585602 0.4185602 Acentric: 0.42563144663334851 0.2453789 0.3905051 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 10 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . oo oo . . . o xxxxxx . . . xx xx. . p(rho) . x oxx . . xx oxx . . o .oox . . xo . ooxxx . . x o . oooxxx . . xx o . oooxxx . . xx o . oxxxooooo . .xxxooo . xxxxxoooooooooo 0.0 xoooo...................................xxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 11 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . ooxxx . . o xxo x . . oxx oo x . . o x .oox . p(rho) . ox . o x . . oxx . o x . . o x . oo x . . ox . ox . . x . ox . . xx . ox . . xo . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxoo.....................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 0.94679796315446552 RMS in NCS unit : 2: 0.94192239230623320 Average RMS ncs in std crystal: 0.94436016678810120 Including ncs au 1 with rms of 0.94769577631073876 Including ncs au 2 with rms of 0.94286645365292365 RMS rho in NCS region: 0.94528419902727001 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.41 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4023809 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.942 and the mean uncertainty in it is 0.430 +/- 0.142 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.947 and the mean uncertainty in it is 0.430 +/- 0.142 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.39 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.44 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.64 offset is -0.58 and sigma is a random variable with rms value of 0.39 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.48 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.11 0.06 0.11 81915 2332 84247 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.42 0.43 0.48 0.33 0.43 81928 4.6 0.48 0.76 0.78 0.76 0.27 0.78 4137 2.9 0.40 0.76 0.76 0.68 0.23 0.76 11903 2.3 0.21 0.56 0.57 0.58 0.27 0.57 16949 2.0 0.14 0.43 0.44 0.48 0.30 0.44 14217 1.7 0.06 0.23 0.24 0.37 0.35 0.24 24723 1.6 0.03 0.11 0.12 0.24 0.38 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.48 0.49 0.48 0.31 0.49 2332 4.6 0.43 0.68 0.70 0.66 0.36 0.70 345 2.9 0.39 0.70 0.70 0.61 0.32 0.70 496 2.3 0.22 0.55 0.55 0.54 0.26 0.55 534 2.0 0.14 0.38 0.40 0.44 0.25 0.40 358 1.7 0.06 0.22 0.23 0.30 0.22 0.23 471 1.6 0.03 0.08 0.09 0.12 0.27 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.42 0.43 0.48 0.33 0.43 84260 4.6 0.48 0.76 0.78 0.75 0.28 0.78 4482 2.9 0.40 0.76 0.75 0.68 0.23 0.75 12399 2.3 0.21 0.56 0.57 0.58 0.27 0.57 17483 2.0 0.14 0.43 0.44 0.48 0.30 0.44 14575 1.7 0.06 0.23 0.24 0.37 0.35 0.24 25194 1.6 0.03 0.11 0.12 0.24 0.38 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.33 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.67 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.55 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.53 0.96 42 0.44 0.96 10.73 507 0.86 0.95 60 0.77 0.95 7.75 1058 0.91 0.94 91 0.92 0.94 5.96 1884 0.92 0.92 131 0.90 0.92 4.77 1883 0.93 0.90 100 0.90 0.90 4.17 1899 0.86 0.88 74 0.84 0.88 3.58 4133 0.90 0.85 173 0.91 0.85 3.16 4651 0.88 0.83 176 0.91 0.83 2.86 5367 0.85 0.80 187 0.81 0.80 2.62 5570 0.84 0.78 178 0.85 0.78 2.44 6624 0.82 0.75 188 0.86 0.75 2.27 4223 0.78 0.72 104 0.80 0.72 2.15 8006 0.81 0.70 205 0.88 0.70 2.03 8584 0.70 0.68 187 0.72 0.68 1.91 10719 0.63 0.64 212 0.65 0.64 1.79 9039 0.52 0.61 129 0.41 0.61 1.70 7523 0.38 0.58 95 0.17 0.59 1.61 Overall average CC: 0.72417595677146562 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.441 B-value to apply to Fc= 12.592 Overall R-factor for FC vs FP: 0.315 for 84258 reflections Writing overall R-factor of 0.315 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.64 0.82 81928 0.59 0.85 2332 0.63 0.82 84260 4.6 0.84 0.90 4137 0.80 0.90 345 0.84 0.90 4482 2.9 0.78 0.85 11903 0.68 0.84 496 0.77 0.85 12399 2.3 0.71 0.84 16949 0.61 0.86 534 0.71 0.84 17483 2.0 0.63 0.80 14217 0.55 0.82 358 0.63 0.80 14575 1.7 0.56 0.76 24723 0.42 0.78 471 0.55 0.76 25194 1.6 0.45 0.65 9999 0.27 0.66 128 0.45 0.65 10127 Minor cycle 6 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0253202 Values of m, alpha, s Centric: 0.49182867611768916 0.2650972 0.4250972 Acentric: 0.43219098730248368 0.2493146 0.3957528 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 12 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . oo oo . . . o xxxxxx . . . xx xxx . p(rho) . x oxx . . xx oxx . . o .ooxx . . xo . oo xx . . xoo . ooooxx . . xx o . oooxxx . . xx o . xxxxooooo . .xxxooo . xxxxooooooooooo 0.0 xoooo..................................xxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 13 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . oooxx . . o xxoxx . . o xx oo x . . x .o x . p(rho) . ox . o x . . oxx . o x . . o x . oo x . . xx . oxx . . x . ox . . xx . oxo . . x . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxo......................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 0.94255893981994332 RMS in NCS unit : 2: 0.93802325042325563 Average RMS ncs in std crystal: 0.94029110670089722 Including ncs au 1 with rms of 0.94344252061741940 Including ncs au 2 with rms of 0.93895955124073394 RMS rho in NCS region: 0.94120370499035710 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4006439 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.938 and the mean uncertainty in it is 0.428 +/- 0.141 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.943 and the mean uncertainty in it is 0.428 +/- 0.141 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.62 offset is -0.61 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.11 0.06 0.11 81912 2332 84244 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.75 0.73 0.24 0.75 11903 2.3 0.21 0.54 0.56 0.64 0.28 0.56 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.48 0.51 0.32 0.48 2332 4.6 0.43 0.67 0.69 0.66 0.36 0.69 345 2.9 0.39 0.67 0.69 0.64 0.34 0.69 496 2.3 0.22 0.53 0.54 0.55 0.27 0.54 534 2.0 0.14 0.37 0.40 0.53 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.23 0.23 471 1.6 0.03 0.07 0.09 0.19 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.74 0.73 0.25 0.74 12399 2.3 0.21 0.54 0.56 0.63 0.28 0.56 17483 2.0 0.14 0.41 0.44 0.54 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.40 0.35 0.24 25194 1.6 0.03 0.10 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.33 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.62 offset is -0.61 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.11 0.06 0.11 81912 2332 84244 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.75 0.73 0.24 0.75 11903 2.3 0.21 0.54 0.56 0.64 0.28 0.56 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.48 0.51 0.32 0.48 2332 4.6 0.43 0.67 0.69 0.66 0.36 0.69 345 2.9 0.39 0.67 0.69 0.64 0.34 0.69 496 2.3 0.22 0.53 0.54 0.55 0.27 0.54 534 2.0 0.14 0.37 0.40 0.53 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.23 0.23 471 1.6 0.03 0.07 0.09 0.19 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.74 0.73 0.25 0.74 12399 2.3 0.21 0.54 0.56 0.63 0.28 0.56 17483 2.0 0.14 0.41 0.44 0.54 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.40 0.35 0.24 25194 1.6 0.03 0.10 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.33 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.54 0.99 42 0.34 0.99 10.73 507 0.89 0.98 60 0.80 0.98 7.75 1058 0.92 0.97 91 0.93 0.97 5.96 1884 0.93 0.95 131 0.91 0.95 4.77 1883 0.95 0.93 100 0.91 0.93 4.17 1899 0.90 0.91 74 0.90 0.91 3.58 4133 0.92 0.88 173 0.94 0.88 3.16 4651 0.91 0.86 176 0.90 0.86 2.86 5367 0.89 0.83 187 0.85 0.83 2.62 5570 0.88 0.81 178 0.87 0.81 2.44 6624 0.85 0.78 188 0.90 0.78 2.27 4223 0.82 0.75 104 0.84 0.75 2.15 8006 0.84 0.73 205 0.86 0.73 2.03 8584 0.74 0.70 187 0.78 0.70 1.91 10719 0.65 0.67 212 0.63 0.67 1.79 9039 0.53 0.64 129 0.40 0.64 1.70 7523 0.39 0.61 95 0.14 0.61 1.61 Overall average CC: 0.75153741757650816 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.502 B-value to apply to Fc= 12.793 Overall R-factor for FC vs FP: 0.304 for 84258 reflections Writing overall R-factor of 0.304 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.66 0.85 81928 0.61 0.87 2332 0.66 0.85 84260 4.6 0.85 0.91 4137 0.77 0.90 345 0.84 0.91 4482 2.9 0.81 0.88 11903 0.70 0.86 496 0.81 0.88 12399 2.3 0.75 0.87 16949 0.63 0.88 534 0.75 0.87 17483 2.0 0.67 0.84 14217 0.59 0.85 358 0.67 0.84 14575 1.7 0.58 0.78 24723 0.44 0.80 471 0.57 0.78 25194 1.6 0.45 0.66 9999 0.38 0.69 128 0.45 0.66 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.62 offset is -0.61 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.48 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.03 0.02 0.03 81914 2332 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.53 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.78 0.28 0.78 4137 2.9 0.40 0.73 0.75 0.75 0.25 0.75 11903 2.3 0.21 0.53 0.56 0.66 0.29 0.56 16949 2.0 0.14 0.41 0.44 0.55 0.31 0.44 14217 1.7 0.06 0.21 0.24 0.41 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.46 0.49 0.51 0.32 0.49 2332 4.6 0.43 0.67 0.69 0.66 0.36 0.69 345 2.9 0.39 0.67 0.69 0.64 0.34 0.69 496 2.3 0.22 0.52 0.54 0.58 0.28 0.54 534 2.0 0.14 0.37 0.40 0.50 0.26 0.40 358 1.7 0.06 0.21 0.23 0.30 0.23 0.23 471 1.6 0.03 0.07 0.09 0.05 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.53 0.34 0.43 84260 4.6 0.48 0.74 0.77 0.77 0.29 0.77 4482 2.9 0.40 0.73 0.75 0.75 0.26 0.75 12399 2.3 0.21 0.53 0.56 0.65 0.29 0.56 17483 2.0 0.14 0.41 0.44 0.55 0.31 0.44 14575 1.7 0.06 0.21 0.24 0.41 0.36 0.24 25194 1.6 0.03 0.10 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.60 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.52 1.00 42 0.38 1.00 10.73 507 0.88 0.99 60 0.80 0.99 7.75 1058 0.91 0.97 91 0.92 0.97 5.96 1884 0.93 0.96 131 0.91 0.96 4.77 1883 0.95 0.94 100 0.91 0.94 4.17 1899 0.89 0.92 74 0.88 0.92 3.58 4133 0.93 0.89 173 0.94 0.89 3.16 4651 0.92 0.86 176 0.92 0.86 2.86 5367 0.90 0.84 187 0.86 0.84 2.62 5570 0.89 0.81 178 0.86 0.81 2.44 6624 0.86 0.78 188 0.91 0.78 2.27 4223 0.82 0.75 104 0.84 0.75 2.15 8006 0.85 0.73 205 0.88 0.73 2.03 8584 0.74 0.71 187 0.78 0.71 1.91 10719 0.66 0.67 212 0.66 0.67 1.79 9039 0.54 0.64 129 0.41 0.64 1.70 7523 0.40 0.61 95 0.14 0.61 1.61 Overall average CC: 0.75652919550816677 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.643 B-value to apply to Fc= 12.381 Overall R-factor for FC vs FP: 0.301 for 84258 reflections Writing overall R-factor of 0.301 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.67 0.85 81928 0.62 0.87 2332 0.66 0.85 84260 4.6 0.85 0.91 4137 0.77 0.90 345 0.84 0.91 4482 2.9 0.82 0.89 11903 0.72 0.86 496 0.81 0.89 12399 2.3 0.76 0.87 16949 0.66 0.89 534 0.75 0.87 17483 2.0 0.67 0.84 14217 0.60 0.84 358 0.67 0.84 14575 1.7 0.58 0.78 24723 0.44 0.80 471 0.58 0.78 25194 1.6 0.46 0.66 9999 0.31 0.67 128 0.46 0.66 10127 Minor cycle 7 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0254224 Values of m, alpha, s Centric: 0.48557505117019983 0.2613450 0.4213451 Acentric: 0.42841134559468014 0.2470468 0.3927291 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 14 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . oo o . . . o xxxxxx . . . xxx xx. . p(rho) . x ooxx . . xx ooxx . . o oo x . . xo . ooxxx . . x o . oooxxx . . xx o . oooxxx . . xx o . oxxxoooo . .xxxooo . xxxxxoooooooooo 0.0 xoooo...................................xxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 15 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . ooxxx . . o xoo x . . o xx oo x . . o x .oox . p(rho) . x . o xx . . oxx . o x . . o x . oo x . . ox . oxx . . x . ox . . xx . xo . . x . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxoo.....................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.96 RMS in NCS unit : 1: 0.94960819971063415 RMS in NCS unit : 2: 0.94490522546129407 Average RMS ncs in std crystal: 0.94725671410560608 Including ncs au 1 with rms of 0.95050278368854590 Including ncs au 2 with rms of 0.94583622689289115 RMS rho in NCS region: 0.94817237618026373 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4036103 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.945 and the mean uncertainty in it is 0.431 +/- 0.142 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.950 and the mean uncertainty in it is 0.431 +/- 0.142 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.39 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.95 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.64 offset is -0.58 and sigma is a random variable with rms value of 0.39 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.08 0.04 0.08 81914 2332 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.42 0.43 0.50 0.33 0.43 81928 4.6 0.48 0.76 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.75 0.76 0.70 0.24 0.76 11903 2.3 0.21 0.55 0.57 0.60 0.28 0.57 16949 2.0 0.14 0.42 0.44 0.50 0.30 0.44 14217 1.7 0.06 0.22 0.24 0.38 0.35 0.24 24723 1.6 0.03 0.11 0.12 0.24 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.48 0.49 0.48 0.31 0.49 2332 4.6 0.43 0.68 0.70 0.66 0.36 0.70 345 2.9 0.39 0.69 0.70 0.61 0.33 0.70 496 2.3 0.22 0.54 0.55 0.55 0.27 0.55 534 2.0 0.14 0.38 0.40 0.44 0.25 0.40 358 1.7 0.06 0.21 0.23 0.29 0.22 0.23 471 1.6 0.03 0.08 0.09 0.06 0.28 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.42 0.43 0.50 0.33 0.43 84260 4.6 0.48 0.75 0.78 0.76 0.28 0.78 4482 2.9 0.40 0.75 0.76 0.70 0.24 0.76 12399 2.3 0.21 0.55 0.57 0.60 0.28 0.57 17483 2.0 0.14 0.42 0.44 0.50 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.38 0.35 0.24 25194 1.6 0.03 0.11 0.12 0.24 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.33 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.67 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.82 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.54 0.98 42 0.45 0.98 10.73 507 0.87 0.97 60 0.79 0.97 7.75 1058 0.91 0.96 91 0.92 0.96 5.96 1884 0.93 0.94 131 0.91 0.94 4.77 1883 0.94 0.92 100 0.91 0.92 4.17 1899 0.88 0.90 74 0.86 0.90 3.58 4133 0.91 0.87 173 0.93 0.87 3.16 4651 0.90 0.85 176 0.92 0.85 2.86 5367 0.88 0.82 187 0.85 0.82 2.62 5570 0.86 0.80 178 0.87 0.80 2.44 6624 0.84 0.77 188 0.88 0.77 2.27 4223 0.81 0.74 104 0.83 0.74 2.15 8006 0.83 0.72 205 0.89 0.72 2.03 8584 0.73 0.69 187 0.75 0.69 1.91 10719 0.65 0.66 212 0.66 0.66 1.79 9039 0.53 0.63 129 0.41 0.63 1.70 7523 0.39 0.60 95 0.11 0.60 1.61 Overall average CC: 0.74291873718290136 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.453 B-value to apply to Fc= 12.558 Overall R-factor for FC vs FP: 0.305 for 84258 reflections Writing overall R-factor of 0.305 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.64 0.83 81928 0.60 0.85 2332 0.64 0.83 84260 4.6 0.84 0.90 4137 0.79 0.90 345 0.83 0.90 4482 2.9 0.79 0.86 11903 0.71 0.85 496 0.78 0.86 12399 2.3 0.73 0.84 16949 0.63 0.86 534 0.72 0.85 17483 2.0 0.64 0.81 14217 0.58 0.82 358 0.64 0.81 14575 1.7 0.56 0.76 24723 0.43 0.78 471 0.56 0.76 25194 1.6 0.45 0.65 9999 0.33 0.68 128 0.44 0.65 10127 Minor cycle 8 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0253315 Values of m, alpha, s Centric: 0.49148386722617243 0.2648903 0.4248903 Acentric: 0.43233861757052422 0.2494032 0.3958709 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 16 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . oooo . . . oo oo . . . o xxxxxx . . . xx xx. . p(rho) . x oxx . . xx ooxx . . o .o xx . . xo . oo xx . . x o . oooxxx . . xx o . oooxxx . . xx o . xxxxooooo . .xxxooo . xxxxooooooooooo 0.0 xoooo..................................xxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 17 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . ooooxx . . o xxo x . . o xx oo x . . o x .o x . p(rho) . x . o xx . . oxx . o x . . o x . oo x . . xx . oxx . . x . ox . . xx . xo . . x . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxo......................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.96 RMS in NCS unit : 1: 0.94718956046968805 RMS in NCS unit : 2: 0.94213652929622438 Average RMS ncs in std crystal: 0.94466304779052734 Including ncs au 1 with rms of 0.94807556483987276 Including ncs au 2 with rms of 0.94307198992373786 RMS rho in NCS region: 0.94557708697524023 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4025055 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.942 and the mean uncertainty in it is 0.430 +/- 0.142 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.947 and the mean uncertainty in it is 0.430 +/- 0.142 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.46 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.62 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.08 0.04 0.08 81914 2332 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.75 0.74 0.24 0.75 11903 2.3 0.21 0.54 0.56 0.64 0.29 0.56 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.24 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.50 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.67 0.36 0.70 345 2.9 0.39 0.68 0.69 0.64 0.33 0.69 496 2.3 0.22 0.53 0.54 0.53 0.27 0.54 534 2.0 0.14 0.37 0.40 0.52 0.26 0.40 358 1.7 0.06 0.21 0.23 0.30 0.23 0.23 471 1.6 0.03 0.07 0.09 0.15 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.75 0.73 0.25 0.75 12399 2.3 0.21 0.54 0.56 0.64 0.29 0.56 17483 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14575 1.7 0.06 0.22 0.24 0.40 0.35 0.24 25194 1.6 0.03 0.10 0.12 0.24 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.33 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.46 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.62 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.08 0.04 0.08 81914 2332 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.75 0.74 0.24 0.75 11903 2.3 0.21 0.54 0.56 0.64 0.29 0.56 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.24 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.50 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.67 0.36 0.70 345 2.9 0.39 0.68 0.69 0.64 0.33 0.69 496 2.3 0.22 0.53 0.54 0.53 0.27 0.54 534 2.0 0.14 0.37 0.40 0.52 0.26 0.40 358 1.7 0.06 0.21 0.23 0.30 0.23 0.23 471 1.6 0.03 0.07 0.09 0.15 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.75 0.73 0.25 0.75 12399 2.3 0.21 0.54 0.56 0.64 0.29 0.56 17483 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14575 1.7 0.06 0.22 0.24 0.40 0.35 0.24 25194 1.6 0.03 0.10 0.12 0.24 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.33 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.54 1.00 42 0.37 1.00 10.73 507 0.88 0.99 60 0.81 0.99 7.75 1058 0.92 0.97 91 0.92 0.98 5.96 1884 0.93 0.96 131 0.91 0.96 4.77 1883 0.95 0.94 100 0.91 0.94 4.17 1899 0.90 0.92 74 0.90 0.92 3.58 4133 0.93 0.89 173 0.94 0.89 3.16 4651 0.92 0.86 176 0.91 0.86 2.86 5367 0.89 0.84 187 0.86 0.84 2.62 5570 0.88 0.81 178 0.88 0.81 2.44 6624 0.86 0.79 188 0.90 0.79 2.27 4223 0.83 0.75 104 0.84 0.75 2.15 8006 0.85 0.73 205 0.87 0.73 2.03 8584 0.75 0.71 187 0.78 0.71 1.91 10719 0.66 0.67 212 0.63 0.67 1.79 9039 0.54 0.64 129 0.42 0.64 1.70 7523 0.40 0.61 95 0.11 0.61 1.61 Overall average CC: 0.75717679313603847 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.511 B-value to apply to Fc= 12.715 Overall R-factor for FC vs FP: 0.298 for 84258 reflections Writing overall R-factor of 0.298 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.66 0.84 81928 0.61 0.86 2332 0.66 0.84 84260 4.6 0.84 0.90 4137 0.77 0.89 345 0.84 0.90 4482 2.9 0.81 0.88 11903 0.71 0.86 496 0.81 0.88 12399 2.3 0.75 0.87 16949 0.64 0.88 534 0.75 0.87 17483 2.0 0.67 0.83 14217 0.59 0.84 358 0.66 0.83 14575 1.7 0.57 0.77 24723 0.44 0.79 471 0.57 0.77 25194 1.6 0.45 0.66 9999 0.34 0.70 128 0.45 0.66 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.46 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.62 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 81916 2332 84248 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.53 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.76 0.75 0.25 0.76 11903 2.3 0.21 0.53 0.57 0.65 0.29 0.57 16949 2.0 0.14 0.41 0.44 0.55 0.31 0.44 14217 1.7 0.06 0.21 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.52 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.68 0.36 0.70 345 2.9 0.39 0.68 0.70 0.66 0.33 0.70 496 2.3 0.22 0.52 0.55 0.57 0.27 0.55 534 2.0 0.14 0.37 0.40 0.52 0.26 0.40 358 1.7 0.06 0.21 0.23 0.30 0.23 0.23 471 1.6 0.03 0.07 0.09 0.08 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.40 0.43 0.53 0.34 0.43 84260 4.6 0.48 0.74 0.77 0.77 0.29 0.77 4482 2.9 0.40 0.73 0.76 0.75 0.25 0.76 12399 2.3 0.21 0.53 0.57 0.65 0.29 0.57 17483 2.0 0.14 0.41 0.44 0.55 0.31 0.44 14575 1.7 0.06 0.21 0.24 0.40 0.36 0.24 25194 1.6 0.03 0.10 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.50 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.52 1.00 42 0.40 1.00 10.73 507 0.88 0.99 60 0.80 0.99 7.75 1058 0.92 0.98 91 0.92 0.98 5.96 1884 0.94 0.96 131 0.91 0.96 4.77 1883 0.95 0.94 100 0.91 0.94 4.17 1899 0.90 0.92 74 0.88 0.92 3.58 4133 0.93 0.89 173 0.94 0.89 3.16 4651 0.93 0.87 176 0.92 0.87 2.86 5367 0.90 0.84 187 0.87 0.84 2.62 5570 0.89 0.81 178 0.86 0.81 2.44 6624 0.86 0.79 188 0.91 0.79 2.27 4223 0.83 0.76 104 0.84 0.76 2.15 8006 0.85 0.74 205 0.88 0.73 2.03 8584 0.75 0.71 187 0.77 0.71 1.91 10719 0.66 0.67 212 0.65 0.67 1.79 9039 0.54 0.64 129 0.43 0.64 1.70 7523 0.40 0.61 95 0.10 0.61 1.61 Overall average CC: 0.75985843716289403 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.602 B-value to apply to Fc= 12.421 Overall R-factor for FC vs FP: 0.297 for 84258 reflections Writing overall R-factor of 0.297 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.66 0.85 81928 0.63 0.86 2332 0.66 0.85 84260 4.6 0.85 0.90 4137 0.77 0.89 345 0.84 0.90 4482 2.9 0.81 0.88 11903 0.73 0.86 496 0.81 0.88 12399 2.3 0.75 0.87 16949 0.66 0.88 534 0.75 0.87 17483 2.0 0.67 0.83 14217 0.62 0.84 358 0.67 0.83 14575 1.7 0.57 0.77 24723 0.45 0.79 471 0.57 0.77 25194 1.6 0.45 0.66 9999 0.39 0.69 128 0.45 0.66 10127 Minor cycle 9 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0253979 Values of m, alpha, s Centric: 0.48838153159794245 0.2630289 0.4230289 Acentric: 0.42992970517121576 0.2479578 0.3939438 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 18 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . ooo . . . oo o . . . o xxxxx . . . xxx xx. . p(rho) . x ooxx . . xx ooxx . . o oo x . . xo . ooxxx . . x o . oooxxx . . xx o . oooxxx . . xx o . xxxoooooo . .xxxooo . xxxxxooooooooooo 0.0 xoooo..................................xxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 19 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . oooxx . . o xxoxx . . o xx oo x . . o x .o x . p(rho) . x . o xx . . oxx . o x . . o x . oo x . . xx . oxx . . x . ox . . xx . xo . . x . xoo . . xxo . xxoooo . 0.0 xxxxxxxxxo......................xxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.97 RMS in NCS unit : 1: 0.95085140389606659 RMS in NCS unit : 2: 0.94639106426126995 Average RMS ncs in std crystal: 0.94862121343612671 Including ncs au 1 with rms of 0.95174886455129248 Including ncs au 2 with rms of 0.94732025000209863 RMS rho in NCS region: 0.94953713914694060 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4041912 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.946 and the mean uncertainty in it is 0.432 +/- 0.143 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.951 and the mean uncertainty in it is 0.432 +/- 0.143 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.95 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.63 offset is -0.62 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.06 0.03 0.06 81914 2332 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.50 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.76 0.28 0.78 4137 2.9 0.40 0.75 0.76 0.71 0.24 0.76 11903 2.3 0.21 0.54 0.57 0.62 0.28 0.57 16949 2.0 0.14 0.42 0.44 0.51 0.30 0.44 14217 1.7 0.06 0.22 0.24 0.38 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.24 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.49 0.31 0.49 2332 4.6 0.43 0.67 0.70 0.68 0.36 0.70 345 2.9 0.39 0.69 0.70 0.62 0.33 0.70 496 2.3 0.22 0.54 0.55 0.55 0.27 0.55 534 2.0 0.14 0.38 0.40 0.44 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.22 0.23 471 1.6 0.03 0.07 0.09 0.12 0.29 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.50 0.34 0.43 84260 4.6 0.48 0.75 0.78 0.76 0.28 0.78 4482 2.9 0.40 0.75 0.76 0.71 0.24 0.76 12399 2.3 0.21 0.54 0.57 0.61 0.28 0.57 17483 2.0 0.14 0.42 0.44 0.51 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.38 0.35 0.24 25194 1.6 0.03 0.10 0.11 0.24 0.39 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.01 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.53 0.99 42 0.45 0.99 10.73 507 0.88 0.98 60 0.80 0.98 7.75 1058 0.92 0.97 91 0.93 0.97 5.96 1884 0.93 0.95 131 0.91 0.95 4.77 1883 0.94 0.93 100 0.91 0.93 4.17 1899 0.89 0.91 74 0.87 0.91 3.58 4133 0.92 0.88 173 0.93 0.88 3.16 4651 0.91 0.86 176 0.92 0.86 2.86 5367 0.89 0.83 187 0.87 0.83 2.62 5570 0.87 0.80 178 0.87 0.80 2.44 6624 0.85 0.78 188 0.89 0.78 2.27 4223 0.82 0.75 104 0.84 0.75 2.15 8006 0.84 0.73 205 0.89 0.73 2.03 8584 0.74 0.70 187 0.76 0.70 1.91 10719 0.65 0.66 212 0.65 0.67 1.79 9039 0.53 0.64 129 0.42 0.64 1.70 7523 0.40 0.60 95 0.07 0.60 1.61 Overall average CC: 0.75060360359487399 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.511 B-value to apply to Fc= 12.616 Overall R-factor for FC vs FP: 0.300 for 84258 reflections Writing overall R-factor of 0.300 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.65 0.83 81928 0.61 0.85 2332 0.64 0.83 84260 4.6 0.84 0.90 4137 0.77 0.89 345 0.83 0.90 4482 2.9 0.79 0.86 11903 0.72 0.85 496 0.79 0.86 12399 2.3 0.73 0.85 16949 0.64 0.86 534 0.73 0.85 17483 2.0 0.65 0.81 14217 0.56 0.82 358 0.65 0.81 14575 1.7 0.56 0.76 24723 0.43 0.78 471 0.56 0.76 25194 1.6 0.45 0.65 9999 0.36 0.70 128 0.44 0.65 10127 Minor cycle 10 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0253401 Values of m, alpha, s Centric: 0.49116047926298140 0.2646963 0.4246963 Acentric: 0.43107687378438092 0.2486461 0.3948615 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 20 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . ooo . . . oo o . . . o xxxxxx . . . xxx xx. . p(rho) . x ooxx . . xx ooxx . . o oo x . . xo . ooxxx . . x o . oooxxx . . xx o . oooxxx . . xx o . oxxxooooo . .xxxooo . xxxxxoooooooooo 0.0 xoooo...................................xxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 21 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.06.................................................. . . . . . . . oooxxx . . o xoo x . . o xx oo x . . o x .o x . p(rho) . o x . o xx . . xx . o x . . o x . oo x . . xx . oxx . . x . ox . . xx . xo . . x . xoo . . xxo . xxxooo . 0.0 xxxxxxxxxo.......................xxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.97 RMS in NCS unit : 1: 0.94912170773077431 RMS in NCS unit : 2: 0.94400274543937124 Average RMS ncs in std crystal: 0.94656223058700562 Including ncs au 1 with rms of 0.95001163845553493 Including ncs au 2 with rms of 0.94493893679647933 RMS rho in NCS region: 0.94747868247128153 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.42 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4033150 For NCS asym unit 1 the mean target rho is 0.041 +/- 0.944 and the mean uncertainty in it is 0.431 +/- 0.142 For NCS asym unit 2 the mean target rho is 0.042 +/- 0.949 and the mean uncertainty in it is 0.431 +/- 0.142 For a.u. 1 total of 420158 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420158 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420166 grid points filled in, for 420113 unique mappings and 5 attempts to write duplicates and 6 errors out of range and 420166 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.64 offset is -0.60 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.06 0.03 0.06 81915 2331 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.76 0.74 0.24 0.76 11903 2.3 0.21 0.54 0.57 0.64 0.29 0.57 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.51 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.69 0.36 0.70 345 2.9 0.39 0.68 0.70 0.65 0.33 0.70 496 2.3 0.22 0.53 0.55 0.54 0.27 0.55 534 2.0 0.14 0.38 0.40 0.51 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.23 0.23 471 1.6 0.03 0.07 0.09 0.12 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.76 0.74 0.25 0.76 12399 2.3 0.21 0.54 0.57 0.64 0.29 0.57 17483 2.0 0.14 0.41 0.44 0.54 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.39 0.35 0.24 25194 1.6 0.03 0.10 0.11 0.24 0.39 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.31 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.64 offset is -0.60 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.06 0.03 0.06 81915 2331 84246 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.76 0.74 0.24 0.76 11903 2.3 0.21 0.54 0.57 0.64 0.29 0.57 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.51 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.69 0.36 0.70 345 2.9 0.39 0.68 0.70 0.65 0.33 0.70 496 2.3 0.22 0.53 0.55 0.54 0.27 0.55 534 2.0 0.14 0.38 0.40 0.51 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.23 0.23 471 1.6 0.03 0.07 0.09 0.12 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.75 0.77 0.76 0.29 0.77 4482 2.9 0.40 0.74 0.76 0.74 0.25 0.76 12399 2.3 0.21 0.54 0.57 0.64 0.29 0.57 17483 2.0 0.14 0.41 0.44 0.54 0.30 0.44 14575 1.7 0.06 0.22 0.24 0.39 0.35 0.24 25194 1.6 0.03 0.10 0.11 0.24 0.39 0.11 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.31 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.53 1.00 42 0.39 1.00 10.73 507 0.88 0.99 60 0.81 0.99 7.75 1058 0.92 0.98 91 0.93 0.98 5.96 1884 0.94 0.96 131 0.91 0.96 4.77 1883 0.95 0.94 100 0.91 0.94 4.17 1899 0.90 0.92 74 0.89 0.92 3.58 4133 0.93 0.89 173 0.94 0.89 3.16 4651 0.92 0.87 176 0.92 0.87 2.86 5367 0.90 0.84 187 0.86 0.84 2.62 5570 0.89 0.81 178 0.88 0.81 2.44 6624 0.86 0.79 188 0.91 0.79 2.27 4223 0.83 0.76 104 0.84 0.76 2.15 8006 0.85 0.73 205 0.87 0.73 2.03 8584 0.75 0.71 187 0.77 0.71 1.91 10719 0.66 0.67 212 0.64 0.67 1.79 9039 0.54 0.64 129 0.43 0.64 1.70 7523 0.40 0.61 95 0.09 0.61 1.61 Overall average CC: 0.75928689698386731 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.488 B-value to apply to Fc= 12.663 Overall R-factor for FC vs FP: 0.296 for 84258 reflections Writing overall R-factor of 0.296 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.66 0.84 81928 0.61 0.86 2332 0.65 0.84 84260 4.6 0.84 0.90 4137 0.77 0.89 345 0.84 0.90 4482 2.9 0.81 0.88 11903 0.72 0.86 496 0.80 0.88 12399 2.3 0.75 0.86 16949 0.64 0.88 534 0.74 0.86 17483 2.0 0.66 0.82 14217 0.59 0.83 358 0.66 0.83 14575 1.7 0.57 0.77 24723 0.44 0.78 471 0.56 0.77 25194 1.6 0.45 0.66 9999 0.34 0.71 128 0.45 0.66 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.40 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 and 0.45 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.64 offset is -0.60 and sigma is a random variable with rms value of 0.40 Number of points with protein histograms included: 840324 Mean starting figure of merit this cycle Overall Centric Acentric 0.43 0.49 0.43 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 81917 2332 84249 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 81928 4.6 0.48 0.75 0.78 0.77 0.28 0.78 4137 2.9 0.40 0.74 0.76 0.75 0.25 0.76 11903 2.3 0.21 0.53 0.57 0.65 0.29 0.57 16949 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14217 1.7 0.06 0.22 0.24 0.40 0.36 0.24 24723 1.6 0.03 0.10 0.12 0.25 0.39 0.12 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.47 0.49 0.52 0.32 0.49 2332 4.6 0.43 0.67 0.70 0.67 0.36 0.70 345 2.9 0.39 0.68 0.70 0.66 0.33 0.70 496 2.3 0.22 0.53 0.55 0.57 0.27 0.55 534 2.0 0.14 0.38 0.40 0.49 0.26 0.40 358 1.7 0.06 0.21 0.23 0.31 0.23 0.23 471 1.6 0.03 0.07 0.09 0.12 0.30 0.09 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.41 0.43 0.52 0.34 0.43 84260 4.6 0.48 0.74 0.78 0.76 0.29 0.78 4482 2.9 0.40 0.74 0.76 0.74 0.25 0.76 12399 2.3 0.21 0.53 0.57 0.65 0.29 0.57 17483 2.0 0.14 0.41 0.44 0.54 0.31 0.44 14575 1.7 0.06 0.22 0.24 0.39 0.35 0.24 25194 1.6 0.03 0.10 0.12 0.25 0.39 0.12 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.43 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.34 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.66 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.40 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 256 0.53 1.00 42 0.41 1.00 10.73 507 0.88 0.99 60 0.80 0.99 7.75 1058 0.92 0.98 91 0.92 0.98 5.96 1884 0.94 0.96 131 0.91 0.96 4.77 1883 0.95 0.94 100 0.91 0.94 4.17 1899 0.90 0.92 74 0.88 0.92 3.58 4133 0.93 0.89 173 0.94 0.89 3.16 4651 0.93 0.87 176 0.93 0.87 2.86 5367 0.90 0.84 187 0.88 0.84 2.62 5570 0.89 0.81 178 0.87 0.81 2.44 6624 0.86 0.79 188 0.91 0.79 2.27 4223 0.83 0.76 104 0.84 0.76 2.15 8006 0.85 0.74 205 0.88 0.74 2.03 8584 0.75 0.71 187 0.77 0.71 1.91 10719 0.66 0.67 212 0.65 0.67 1.79 9039 0.54 0.64 129 0.43 0.64 1.70 7523 0.40 0.61 95 0.07 0.61 1.61 Overall average CC: 0.76081495510155639 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.543 B-value to apply to Fc= 12.482 Overall R-factor for FC vs FP: 0.295 for 84258 reflections Writing overall R-factor of 0.295 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.66 0.84 81928 0.62 0.86 2332 0.66 0.84 84260 4.6 0.84 0.90 4137 0.76 0.89 345 0.84 0.90 4482 2.9 0.81 0.88 11903 0.72 0.86 496 0.81 0.88 12399 2.3 0.75 0.86 16949 0.66 0.88 534 0.74 0.86 17483 2.0 0.66 0.82 14217 0.60 0.83 358 0.66 0.83 14575 1.7 0.57 0.77 24723 0.44 0.78 471 0.57 0.77 25194 1.6 0.45 0.66 9999 0.42 0.71 128 0.45 0.66 10127 Restoring phases from beginning of cycle at the end of this cycle. Mask cycle 2 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 5.82 Using histogram-based mask Assuming this cycle is unbiased (no previous density modification) Plot 22 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 .......................................xxxxxxxxxxx . + xxxx . . + xxxx . . + xx . . + xx . . + x . . +x . p(protein) . x . 0.5 . + . . xx+ . . x + . . xx + . . xxxx + . . x + . . xxx + . 0.0 .xxxxxxxxxx.............+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Saving phases and map as this is a test cycle. This is a cycle to estimate errors in NCS. NCS omitted. Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: -2.28644e-09 Values of m, alpha, s Centric: 0.23111231844139474 0.1186674 0.2348899 Acentric: 0.17329066504681193 8.9316264E-02 0.1832907 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 23 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.05.................................................. . . . . . . . xxo . . . xx xx. . . ox x . . xx .x . p(rho) . x . x . . x . ox . . x . xxx . . x . oxxx . . x . oxxx . . xo . ooxx . . x . xxxoo . . xxo . xxxooooo . 0.0 xxxxxxxo..............................xxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 24 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.08.................................................. . . . . xx . . xox . . x. x . . x . x . . x . x . p(rho) . x . x . . x . x . . x . ox . . o . ox . . ox . x . . x . ox . . ox . xo . . ox . xoo . 0.0 xxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.26 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.63 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.57 offset is -0.28 and sigma is a random variable with rms value of 0.26 Mean starting figure of merit this cycle Overall Centric Acentric 0.17 0.23 0.17 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.36 0.36 0.36 81924 2332 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.49 0.51 0.64 0.29 0.51 81928 4.6 0.48 0.86 0.88 0.78 0.17 0.88 4137 2.9 0.40 0.84 0.85 0.77 0.16 0.85 11903 2.3 0.21 0.65 0.68 0.76 0.22 0.68 16949 2.0 0.14 0.49 0.52 0.68 0.26 0.52 14217 1.7 0.06 0.27 0.30 0.56 0.32 0.30 24723 1.6 0.03 0.15 0.17 0.40 0.35 0.17 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.55 0.57 0.63 0.27 0.57 2332 4.6 0.43 0.77 0.78 0.64 0.31 0.78 345 2.9 0.39 0.79 0.80 0.67 0.28 0.80 496 2.3 0.22 0.60 0.63 0.69 0.24 0.63 534 2.0 0.14 0.45 0.47 0.57 0.22 0.47 358 1.7 0.06 0.28 0.30 0.59 0.18 0.30 471 1.6 0.03 0.17 0.19 0.52 0.15 0.19 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.49 0.51 0.64 0.29 0.51 84260 4.6 0.48 0.86 0.87 0.77 0.18 0.87 4482 2.9 0.40 0.84 0.85 0.77 0.17 0.85 12399 2.3 0.21 0.65 0.68 0.76 0.22 0.68 17483 2.0 0.14 0.49 0.52 0.68 0.26 0.52 14575 1.7 0.06 0.27 0.30 0.56 0.32 0.30 25194 1.6 0.03 0.15 0.17 0.40 0.34 0.17 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.51 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.29 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.71 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.55 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.26 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.63 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.57 offset is -0.28 and sigma is a random variable with rms value of 0.26 Mean starting figure of merit this cycle Overall Centric Acentric 0.17 0.23 0.17 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.27 0.27 0.27 81922 2332 84254 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.49 0.42 0.64 0.29 0.42 81928 4.6 0.48 0.86 0.77 0.78 0.17 0.77 4137 2.9 0.40 0.84 0.73 0.77 0.16 0.73 11903 2.3 0.21 0.65 0.56 0.76 0.22 0.56 16949 2.0 0.14 0.49 0.42 0.68 0.26 0.42 14217 1.7 0.06 0.27 0.24 0.56 0.32 0.24 24723 1.6 0.03 0.15 0.13 0.40 0.35 0.13 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.55 0.48 0.63 0.27 0.48 2332 4.6 0.43 0.77 0.69 0.64 0.31 0.69 345 2.9 0.39 0.79 0.69 0.67 0.28 0.69 496 2.3 0.22 0.60 0.52 0.69 0.24 0.52 534 2.0 0.14 0.45 0.39 0.57 0.22 0.39 358 1.7 0.06 0.28 0.24 0.59 0.18 0.24 471 1.6 0.03 0.17 0.15 0.52 0.15 0.15 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.49 0.42 0.64 0.29 0.42 84260 4.6 0.48 0.86 0.76 0.77 0.18 0.76 4482 2.9 0.40 0.84 0.73 0.77 0.17 0.73 12399 2.3 0.21 0.65 0.56 0.76 0.22 0.56 17483 2.0 0.14 0.49 0.42 0.68 0.26 0.42 14575 1.7 0.06 0.27 0.24 0.56 0.32 0.24 25194 1.6 0.03 0.15 0.13 0.40 0.34 0.13 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.42 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.29 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.71 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.55 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.36 0.70 42 -0.23 0.70 10.73 507 0.59 0.69 60 0.55 0.69 7.75 1058 0.65 0.68 91 0.76 0.68 5.96 1884 0.73 0.66 131 0.69 0.66 4.77 1883 0.76 0.64 100 0.66 0.64 4.17 1899 0.62 0.62 74 0.63 0.62 3.58 4133 0.60 0.59 173 0.58 0.59 3.16 4651 0.59 0.57 176 0.57 0.57 2.86 5367 0.57 0.54 187 0.61 0.54 2.62 5570 0.58 0.52 178 0.50 0.52 2.44 6624 0.56 0.49 188 0.49 0.49 2.27 4223 0.39 0.46 104 0.46 0.46 2.15 8006 0.52 0.44 205 0.66 0.44 2.03 8584 0.37 0.42 187 0.34 0.42 1.91 10719 0.39 0.39 212 0.48 0.39 1.79 9039 0.33 0.36 129 0.42 0.36 1.70 7523 0.22 0.34 95 0.45 0.34 1.61 Overall average CC: 0.46597719558119177 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 4.055 B-value to apply to Fc= 15.607 Overall R-factor for FC vs FP: 0.414 for 84260 reflections Writing overall R-factor of 0.414 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.74 0.87 81928 0.69 0.85 2332 0.74 0.87 84260 4.6 0.84 0.88 4137 0.70 0.84 345 0.83 0.88 4482 2.9 0.82 0.88 11903 0.71 0.83 496 0.82 0.87 12399 2.3 0.82 0.89 16949 0.73 0.88 534 0.81 0.89 17483 2.0 0.76 0.87 14217 0.67 0.88 358 0.76 0.87 14575 1.7 0.69 0.84 24723 0.65 0.88 471 0.69 0.84 25194 1.6 0.58 0.73 9999 0.59 0.88 128 0.58 0.74 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.26 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.63 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.57 offset is -0.28 and sigma is a random variable with rms value of 0.26 Mean starting figure of merit this cycle Overall Centric Acentric 0.42 0.48 0.42 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.18 0.15 0.17 81927 2332 84259 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.55 0.67 0.24 0.55 81928 4.6 0.48 0.87 0.85 0.80 0.16 0.85 4137 2.9 0.40 0.85 0.82 0.78 0.15 0.82 11903 2.3 0.21 0.72 0.68 0.75 0.18 0.68 16949 2.0 0.14 0.61 0.57 0.68 0.20 0.57 14217 1.7 0.06 0.42 0.38 0.60 0.24 0.38 24723 1.6 0.03 0.27 0.24 0.48 0.27 0.24 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.59 0.62 0.25 0.59 2332 4.6 0.43 0.78 0.76 0.65 0.31 0.76 345 2.9 0.39 0.78 0.75 0.69 0.28 0.75 496 2.3 0.22 0.67 0.63 0.63 0.22 0.63 534 2.0 0.14 0.55 0.51 0.60 0.18 0.51 358 1.7 0.06 0.41 0.37 0.54 0.13 0.37 471 1.6 0.03 0.29 0.26 0.66 0.09 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.55 0.66 0.24 0.55 84260 4.6 0.48 0.86 0.84 0.79 0.17 0.84 4482 2.9 0.40 0.85 0.82 0.78 0.15 0.82 12399 2.3 0.21 0.72 0.68 0.75 0.18 0.68 17483 2.0 0.14 0.61 0.57 0.68 0.20 0.57 14575 1.7 0.06 0.42 0.38 0.59 0.24 0.38 25194 1.6 0.03 0.27 0.24 0.49 0.27 0.24 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.55 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.54 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.60 0.90 42 0.19 0.90 10.73 507 0.80 0.89 60 0.79 0.89 7.75 1058 0.81 0.87 91 0.83 0.87 5.96 1884 0.86 0.85 131 0.83 0.85 4.77 1883 0.88 0.83 100 0.82 0.83 4.17 1899 0.81 0.81 74 0.79 0.82 3.58 4133 0.82 0.78 173 0.83 0.78 3.16 4651 0.80 0.76 176 0.80 0.76 2.86 5367 0.77 0.73 187 0.74 0.73 2.62 5570 0.77 0.70 178 0.76 0.70 2.44 6624 0.74 0.68 188 0.76 0.68 2.27 4223 0.62 0.65 104 0.67 0.64 2.15 8006 0.72 0.62 205 0.81 0.62 2.03 8584 0.55 0.60 187 0.54 0.60 1.91 10719 0.55 0.56 212 0.59 0.56 1.79 9039 0.49 0.53 129 0.51 0.53 1.70 7523 0.40 0.50 95 0.56 0.50 1.61 Overall average CC: 0.64831678281515415 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 2.864 B-value to apply to Fc= 10.000 Overall R-factor for FC vs FP: 0.346 for 84260 reflections Writing overall R-factor of 0.346 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.73 0.85 81928 0.67 0.84 2332 0.73 0.85 84260 4.6 0.84 0.88 4137 0.69 0.82 345 0.83 0.87 4482 2.9 0.82 0.87 11903 0.73 0.84 496 0.82 0.87 12399 2.3 0.80 0.87 16949 0.70 0.85 534 0.79 0.87 17483 2.0 0.74 0.84 14217 0.63 0.84 358 0.74 0.84 14575 1.7 0.68 0.81 24723 0.59 0.85 471 0.68 0.81 25194 1.6 0.60 0.76 9999 0.69 0.90 128 0.60 0.76 10127 Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0201999 Values of m, alpha, s Centric: 0.58594830919539531 0.3215690 0.4743793 Acentric: 0.54765888845684274 0.3381271 0.4590636 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 25 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.04.................................................. . . . . . . . xxxxx . . . xx xx . . . x xo. . . x xx . p(rho) . x .x . . o . xx . . xo . xxx . . xx . ooxxxx . . o . oooxxxx . . xx . oooooxxx . . xo . oooxxxoooo . .xxxo . xxxxxooooooo 0.0 xoo........................................xxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 26 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . ooo . . .o . . o. o . . o xxo . p(rho) . xx. x . . x . x . . x . x . . xo . x . . o . o x . . xo . o x . . xxo . oxx . . xxoo . oxxx . 0.0 xxxxxxxxxxxoo..............ooxxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.29 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.02 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.78 offset is -0.43 and sigma is a random variable with rms value of 0.29 Mean starting figure of merit this cycle Overall Centric Acentric 0.55 0.59 0.55 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.08 0.06 0.08 81923 2332 84255 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.57 0.57 0.66 0.24 0.57 81928 4.6 0.48 0.85 0.86 0.77 0.18 0.86 4137 2.9 0.40 0.85 0.85 0.77 0.15 0.85 11903 2.3 0.21 0.70 0.71 0.75 0.19 0.71 16949 2.0 0.14 0.60 0.60 0.67 0.20 0.60 14217 1.7 0.06 0.40 0.41 0.58 0.25 0.41 24723 1.6 0.03 0.25 0.26 0.47 0.28 0.26 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.60 0.61 0.62 0.25 0.61 2332 4.6 0.43 0.76 0.77 0.63 0.31 0.77 345 2.9 0.39 0.78 0.78 0.70 0.28 0.78 496 2.3 0.22 0.65 0.65 0.64 0.22 0.65 534 2.0 0.14 0.53 0.54 0.60 0.19 0.54 358 1.7 0.06 0.39 0.40 0.52 0.13 0.40 471 1.6 0.03 0.28 0.29 0.63 0.10 0.29 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.57 0.57 0.65 0.24 0.57 84260 4.6 0.48 0.85 0.85 0.76 0.19 0.85 4482 2.9 0.40 0.85 0.84 0.77 0.16 0.84 12399 2.3 0.21 0.70 0.71 0.74 0.19 0.71 17483 2.0 0.14 0.60 0.60 0.67 0.20 0.60 14575 1.7 0.06 0.40 0.41 0.58 0.25 0.41 25194 1.6 0.03 0.25 0.26 0.47 0.28 0.26 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.57 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.61 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.64 0.90 42 0.13 0.90 10.73 507 0.80 0.89 60 0.79 0.89 7.75 1058 0.83 0.88 91 0.86 0.88 5.96 1884 0.88 0.87 131 0.86 0.87 4.77 1883 0.89 0.85 100 0.85 0.85 4.17 1899 0.82 0.84 74 0.78 0.84 3.58 4133 0.84 0.82 173 0.82 0.82 3.16 4651 0.84 0.79 176 0.83 0.80 2.86 5367 0.82 0.77 187 0.80 0.77 2.62 5570 0.82 0.75 178 0.83 0.75 2.44 6624 0.79 0.73 188 0.81 0.73 2.27 4223 0.70 0.71 104 0.75 0.71 2.15 8006 0.78 0.69 205 0.84 0.69 2.03 8584 0.64 0.67 187 0.63 0.67 1.91 10719 0.62 0.64 212 0.69 0.64 1.79 9039 0.58 0.62 129 0.61 0.62 1.70 7523 0.47 0.59 95 0.60 0.59 1.61 Overall average CC: 0.70949138592377770 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.803 B-value to apply to Fc= 8.491 Overall R-factor for FC vs FP: 0.312 for 84260 reflections Writing overall R-factor of 0.312 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.72 0.84 81928 0.66 0.83 2332 0.72 0.84 84260 4.6 0.82 0.86 4137 0.66 0.78 345 0.81 0.85 4482 2.9 0.81 0.85 11903 0.72 0.83 496 0.80 0.85 12399 2.3 0.79 0.87 16949 0.69 0.84 534 0.79 0.86 17483 2.0 0.73 0.83 14217 0.64 0.84 358 0.72 0.83 14575 1.7 0.67 0.81 24723 0.58 0.84 471 0.66 0.81 25194 1.6 0.60 0.76 9999 0.69 0.92 128 0.60 0.76 10127 Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0150901 Values of m, alpha, s Centric: 0.60639635512324797 0.3351171 0.4825585 Acentric: 0.57115324200384576 0.3611532 0.4684613 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 27 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xooxxx . . . x xo . . . xx xxo . . x xo . p(rho) . x .xo . . x . xx . . xx . xxx . . x . ooxxx . . xx . oo xxxx . . xx . oooooxxxx . . xo . oooxxxxooo . xxxo . xxxxxxoooo 0.0 oo............................................xxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 28 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . oxxxo . . xx. xo . . xx . x . . o . xx . . xo . o x . . xo . oxx . . xxoo . oxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo.............ooxxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.30 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.06 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.85 offset is -0.39 and sigma is a random variable with rms value of 0.30 Mean starting figure of merit this cycle Overall Centric Acentric 0.57 0.61 0.57 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.57 0.58 0.65 0.24 0.58 81928 4.6 0.48 0.85 0.86 0.76 0.18 0.86 4137 2.9 0.40 0.85 0.85 0.76 0.15 0.85 11903 2.3 0.21 0.71 0.72 0.74 0.18 0.72 16949 2.0 0.14 0.61 0.62 0.66 0.20 0.62 14217 1.7 0.06 0.41 0.42 0.58 0.24 0.42 24723 1.6 0.03 0.27 0.27 0.47 0.27 0.27 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.61 0.62 0.62 0.25 0.62 2332 4.6 0.43 0.76 0.77 0.62 0.32 0.77 345 2.9 0.39 0.78 0.78 0.70 0.28 0.78 496 2.3 0.22 0.66 0.66 0.65 0.22 0.66 534 2.0 0.14 0.54 0.55 0.57 0.18 0.55 358 1.7 0.06 0.41 0.41 0.53 0.13 0.41 471 1.6 0.03 0.30 0.30 0.65 0.09 0.30 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.58 0.65 0.24 0.58 84260 4.6 0.48 0.84 0.85 0.75 0.19 0.85 4482 2.9 0.40 0.85 0.85 0.76 0.16 0.85 12399 2.3 0.21 0.71 0.72 0.73 0.18 0.72 17483 2.0 0.14 0.61 0.62 0.66 0.20 0.62 14575 1.7 0.06 0.41 0.42 0.58 0.24 0.42 25194 1.6 0.03 0.27 0.27 0.47 0.27 0.27 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.58 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.46 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.68 0.91 42 0.24 0.91 10.73 507 0.82 0.90 60 0.79 0.90 7.75 1058 0.84 0.89 91 0.87 0.89 5.96 1884 0.89 0.88 131 0.87 0.88 4.77 1883 0.90 0.87 100 0.86 0.87 4.17 1899 0.83 0.86 74 0.79 0.86 3.58 4133 0.86 0.84 173 0.85 0.84 3.16 4651 0.85 0.82 176 0.85 0.82 2.86 5367 0.84 0.80 187 0.82 0.80 2.62 5570 0.84 0.78 178 0.83 0.78 2.44 6624 0.81 0.77 188 0.84 0.77 2.27 4223 0.74 0.74 104 0.76 0.74 2.15 8006 0.81 0.73 205 0.85 0.73 2.03 8584 0.69 0.71 187 0.66 0.71 1.91 10719 0.66 0.68 212 0.73 0.68 1.79 9039 0.63 0.66 129 0.63 0.66 1.70 7523 0.54 0.64 95 0.63 0.64 1.61 Overall average CC: 0.74423085717210680 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.646 B-value to apply to Fc= 7.581 Overall R-factor for FC vs FP: 0.293 for 84260 reflections Writing overall R-factor of 0.293 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.71 0.83 81928 0.65 0.82 2332 0.71 0.83 84260 4.6 0.81 0.85 4137 0.67 0.77 345 0.80 0.84 4482 2.9 0.80 0.84 11903 0.72 0.83 496 0.79 0.84 12399 2.3 0.78 0.85 16949 0.68 0.84 534 0.77 0.85 17483 2.0 0.72 0.82 14217 0.61 0.83 358 0.71 0.82 14575 1.7 0.66 0.80 24723 0.57 0.83 471 0.65 0.80 25194 1.6 0.59 0.75 9999 0.70 0.92 128 0.59 0.75 10127 Minor cycle 4 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0149556 Values of m, alpha, s Centric: 0.61668541270652799 0.3433483 0.4866742 Acentric: 0.58386970349048839 0.3738697 0.4735479 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 29 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . x xxo. . . xx xo . . x xo . p(rho) . x .xx . . x . xx . . x . xxx . . xx . ooxxxx . . x . oooxxxxx . . xo . oooooxxxx . . xo . ooooxxxxooo . xxxo . xxxxxoooo 0.0 o.............................................xxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 30 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o xxo . . xx. xo . . xx . x . . o . xx . . xo . o x . . xo . oxx . . xxoo . oxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo.............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.30 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.07 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.87 offset is -0.39 and sigma is a random variable with rms value of 0.30 Mean starting figure of merit this cycle Overall Centric Acentric 0.58 0.62 0.58 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.03 0.02 0.03 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.59 0.65 0.24 0.59 81928 4.6 0.48 0.85 0.86 0.75 0.18 0.86 4137 2.9 0.40 0.85 0.86 0.76 0.15 0.86 11903 2.3 0.21 0.71 0.72 0.73 0.18 0.72 16949 2.0 0.14 0.61 0.62 0.66 0.20 0.62 14217 1.7 0.06 0.41 0.43 0.58 0.24 0.43 24723 1.6 0.03 0.27 0.28 0.47 0.27 0.28 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.61 0.62 0.61 0.25 0.62 2332 4.6 0.43 0.76 0.77 0.61 0.31 0.77 345 2.9 0.39 0.78 0.79 0.69 0.28 0.79 496 2.3 0.22 0.66 0.67 0.63 0.22 0.67 534 2.0 0.14 0.55 0.56 0.57 0.18 0.56 358 1.7 0.06 0.41 0.42 0.52 0.12 0.42 471 1.6 0.03 0.30 0.31 0.69 0.09 0.31 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.59 0.64 0.24 0.59 84260 4.6 0.48 0.85 0.86 0.74 0.19 0.86 4482 2.9 0.40 0.85 0.86 0.75 0.15 0.86 12399 2.3 0.21 0.71 0.72 0.73 0.18 0.72 17483 2.0 0.14 0.61 0.62 0.66 0.20 0.62 14575 1.7 0.06 0.41 0.43 0.58 0.24 0.43 25194 1.6 0.03 0.27 0.28 0.48 0.27 0.28 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.59 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.39 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.70 0.91 42 0.29 0.91 10.73 507 0.82 0.91 60 0.80 0.91 7.75 1058 0.85 0.90 91 0.87 0.90 5.96 1884 0.89 0.89 131 0.87 0.89 4.77 1883 0.90 0.87 100 0.86 0.88 4.17 1899 0.84 0.86 74 0.79 0.86 3.58 4133 0.86 0.84 173 0.85 0.84 3.16 4651 0.86 0.83 176 0.85 0.83 2.86 5367 0.85 0.81 187 0.84 0.81 2.62 5570 0.85 0.79 178 0.84 0.79 2.44 6624 0.82 0.78 188 0.85 0.78 2.27 4223 0.76 0.76 104 0.77 0.76 2.15 8006 0.82 0.74 205 0.86 0.74 2.03 8584 0.71 0.72 187 0.69 0.72 1.91 10719 0.68 0.70 212 0.74 0.70 1.79 9039 0.65 0.68 129 0.64 0.68 1.70 7523 0.56 0.66 95 0.64 0.66 1.61 Overall average CC: 0.75742566351960738 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.628 B-value to apply to Fc= 7.092 Overall R-factor for FC vs FP: 0.284 for 84260 reflections Writing overall R-factor of 0.284 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.82 81928 0.65 0.82 2332 0.70 0.82 84260 4.6 0.80 0.84 4137 0.65 0.76 345 0.79 0.83 4482 2.9 0.79 0.83 11903 0.72 0.83 496 0.79 0.83 12399 2.3 0.77 0.85 16949 0.66 0.83 534 0.77 0.85 17483 2.0 0.71 0.81 14217 0.60 0.83 358 0.71 0.81 14575 1.7 0.65 0.79 24723 0.57 0.82 471 0.65 0.79 25194 1.6 0.58 0.75 9999 0.73 0.92 128 0.59 0.75 10127 Minor cycle 5 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0141275 Values of m, alpha, s Centric: 0.62307155836004857 0.3484573 0.4892286 Acentric: 0.58956383358821374 0.3795638 0.4758255 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 31 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . ox xxo. . . xx xo . . x xo . p(rho) . xx .xo . . x . xx . . x . xxxx . . x . oxxxx . . x . oooxxxxx . . x . oooooxxxxx . . xo . oooxxxxooo . xxxo . xxxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 32 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o x o . . xxxxx . . xx . x . . o . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo.............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.89 offset is -0.38 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.62 0.59 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.02 0.02 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.59 0.64 0.24 0.59 81928 4.6 0.48 0.85 0.86 0.75 0.18 0.86 4137 2.9 0.40 0.85 0.86 0.75 0.15 0.86 11903 2.3 0.21 0.71 0.72 0.73 0.18 0.72 16949 2.0 0.14 0.61 0.63 0.65 0.20 0.63 14217 1.7 0.06 0.42 0.43 0.57 0.24 0.43 24723 1.6 0.03 0.27 0.29 0.47 0.27 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.61 0.25 0.63 2332 4.6 0.43 0.77 0.77 0.59 0.31 0.77 345 2.9 0.39 0.79 0.80 0.70 0.28 0.80 496 2.3 0.22 0.66 0.67 0.64 0.22 0.67 534 2.0 0.14 0.55 0.56 0.56 0.18 0.56 358 1.7 0.06 0.41 0.42 0.52 0.12 0.42 471 1.6 0.03 0.30 0.32 0.67 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.59 0.64 0.24 0.59 84260 4.6 0.48 0.85 0.86 0.74 0.19 0.86 4482 2.9 0.40 0.85 0.86 0.75 0.15 0.86 12399 2.3 0.21 0.71 0.72 0.72 0.18 0.72 17483 2.0 0.14 0.61 0.63 0.65 0.20 0.63 14575 1.7 0.06 0.42 0.43 0.57 0.24 0.43 25194 1.6 0.03 0.27 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.59 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.32 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.71 0.91 42 0.32 0.91 10.73 507 0.83 0.90 60 0.80 0.90 7.75 1058 0.86 0.90 91 0.88 0.90 5.96 1884 0.90 0.89 131 0.87 0.89 4.77 1883 0.90 0.88 100 0.87 0.88 4.17 1899 0.84 0.86 74 0.79 0.87 3.58 4133 0.87 0.85 173 0.86 0.85 3.16 4651 0.86 0.83 176 0.86 0.83 2.86 5367 0.85 0.82 187 0.84 0.82 2.62 5570 0.86 0.80 178 0.84 0.80 2.44 6624 0.83 0.79 188 0.86 0.79 2.27 4223 0.77 0.77 104 0.77 0.77 2.15 8006 0.82 0.75 205 0.86 0.75 2.03 8584 0.72 0.74 187 0.70 0.74 1.91 10719 0.69 0.71 212 0.75 0.71 1.79 9039 0.66 0.69 129 0.65 0.69 1.70 7523 0.57 0.67 95 0.65 0.67 1.61 Overall average CC: 0.76571237394157787 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.610 B-value to apply to Fc= 6.823 Overall R-factor for FC vs FP: 0.279 for 84260 reflections Writing overall R-factor of 0.279 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.81 81928 0.64 0.81 2332 0.70 0.81 84260 4.6 0.79 0.84 4137 0.63 0.75 345 0.78 0.83 4482 2.9 0.78 0.82 11903 0.71 0.82 496 0.78 0.82 12399 2.3 0.76 0.84 16949 0.67 0.83 534 0.76 0.84 17483 2.0 0.70 0.81 14217 0.58 0.82 358 0.70 0.81 14575 1.7 0.64 0.79 24723 0.57 0.82 471 0.64 0.79 25194 1.6 0.58 0.75 9999 0.73 0.92 128 0.58 0.75 10127 Minor cycle 6 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0140085 Values of m, alpha, s Centric: 0.62617763817586591 0.3509421 0.4904710 Acentric: 0.59258157133021749 0.3825815 0.4770326 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 33 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . ox xxo. . . xx xo . . x xo . p(rho) . xx .xo . . x . xx . . x . xxxx . . x . oxxxx . . x . ooo xxxx . . x . oooooxxxxx . . xx . oooxxxooo . xxxo . xxxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 34 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o . o . . xxxxx . . x . x . . x . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo.............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.28 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.89 offset is -0.38 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.63 0.59 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.59 0.64 0.24 0.59 81928 4.6 0.48 0.85 0.86 0.74 0.18 0.86 4137 2.9 0.40 0.86 0.86 0.75 0.14 0.86 11903 2.3 0.21 0.71 0.73 0.72 0.18 0.73 16949 2.0 0.14 0.62 0.63 0.65 0.20 0.63 14217 1.7 0.06 0.42 0.43 0.57 0.24 0.43 24723 1.6 0.03 0.28 0.29 0.47 0.27 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.61 0.25 0.63 2332 4.6 0.43 0.77 0.78 0.60 0.31 0.78 345 2.9 0.39 0.79 0.80 0.69 0.28 0.80 496 2.3 0.22 0.66 0.67 0.63 0.22 0.67 534 2.0 0.14 0.56 0.56 0.58 0.18 0.56 358 1.7 0.06 0.41 0.42 0.51 0.12 0.42 471 1.6 0.03 0.31 0.32 0.67 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.64 0.24 0.60 84260 4.6 0.48 0.85 0.86 0.73 0.19 0.86 4482 2.9 0.40 0.85 0.86 0.74 0.15 0.86 12399 2.3 0.21 0.71 0.72 0.72 0.18 0.72 17483 2.0 0.14 0.61 0.63 0.65 0.20 0.63 14575 1.7 0.06 0.42 0.43 0.57 0.24 0.43 25194 1.6 0.03 0.28 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.60 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.27 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.72 0.92 42 0.33 0.92 10.73 507 0.83 0.91 60 0.81 0.91 7.75 1058 0.86 0.90 91 0.87 0.90 5.96 1884 0.90 0.89 131 0.88 0.89 4.77 1883 0.90 0.88 100 0.88 0.88 4.17 1899 0.85 0.87 74 0.80 0.87 3.58 4133 0.87 0.85 173 0.86 0.85 3.16 4651 0.87 0.84 176 0.86 0.84 2.86 5367 0.86 0.82 187 0.85 0.82 2.62 5570 0.86 0.81 178 0.84 0.81 2.44 6624 0.83 0.79 188 0.86 0.79 2.27 4223 0.78 0.77 104 0.77 0.77 2.15 8006 0.83 0.76 205 0.86 0.76 2.03 8584 0.73 0.74 187 0.70 0.74 1.91 10719 0.69 0.72 212 0.76 0.72 1.79 9039 0.67 0.70 129 0.65 0.70 1.70 7523 0.58 0.68 95 0.65 0.68 1.61 Overall average CC: 0.77081453450609494 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.607 B-value to apply to Fc= 6.685 Overall R-factor for FC vs FP: 0.275 for 84260 reflections Writing overall R-factor of 0.275 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.69 0.81 81928 0.64 0.81 2332 0.69 0.81 84260 4.6 0.79 0.83 4137 0.62 0.74 345 0.77 0.82 4482 2.9 0.78 0.82 11903 0.72 0.82 496 0.78 0.82 12399 2.3 0.76 0.84 16949 0.66 0.82 534 0.76 0.84 17483 2.0 0.70 0.80 14217 0.58 0.81 358 0.70 0.80 14575 1.7 0.64 0.78 24723 0.56 0.81 471 0.64 0.78 25194 1.6 0.58 0.74 9999 0.70 0.91 128 0.58 0.75 10127 Minor cycle 7 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.013776 Values of m, alpha, s Centric: 0.62844053912713316 0.3527525 0.4913762 Acentric: 0.59440193908607186 0.3844019 0.4777608 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 35 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . xx xo. . . x xo . . x xo . p(rho) . x .xo . . ox . xx . . x . xxxx . . xx . oxxxx . . o . ooo xxxx . . x . ooooooxxxx . . xx . oooxxxxooo . xxxo . xxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 36 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o . o . . oxxxx . . x . x . . x . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo.............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.28 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.90 offset is -0.37 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.59 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.63 0.24 0.60 81928 4.6 0.48 0.85 0.86 0.74 0.18 0.86 4137 2.9 0.40 0.86 0.86 0.74 0.14 0.86 11903 2.3 0.21 0.71 0.73 0.72 0.18 0.73 16949 2.0 0.14 0.62 0.63 0.65 0.19 0.63 14217 1.7 0.06 0.42 0.44 0.57 0.24 0.44 24723 1.6 0.03 0.28 0.29 0.47 0.26 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.60 0.24 0.63 2332 4.6 0.43 0.77 0.78 0.59 0.31 0.78 345 2.9 0.39 0.80 0.80 0.69 0.27 0.80 496 2.3 0.22 0.66 0.67 0.64 0.22 0.67 534 2.0 0.14 0.56 0.57 0.56 0.18 0.57 358 1.7 0.06 0.41 0.43 0.50 0.12 0.43 471 1.6 0.03 0.31 0.32 0.66 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.63 0.24 0.60 84260 4.6 0.48 0.85 0.86 0.73 0.19 0.86 4482 2.9 0.40 0.85 0.86 0.74 0.15 0.86 12399 2.3 0.21 0.71 0.73 0.71 0.18 0.73 17483 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14575 1.7 0.06 0.42 0.44 0.57 0.24 0.44 25194 1.6 0.03 0.28 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.60 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.24 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.76 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.22 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.72 0.92 42 0.35 0.92 10.73 507 0.84 0.91 60 0.81 0.91 7.75 1058 0.86 0.91 91 0.88 0.91 5.96 1884 0.90 0.90 131 0.88 0.90 4.77 1883 0.90 0.88 100 0.88 0.88 4.17 1899 0.85 0.87 74 0.80 0.87 3.58 4133 0.87 0.86 173 0.86 0.86 3.16 4651 0.87 0.84 176 0.87 0.84 2.86 5367 0.86 0.82 187 0.85 0.82 2.62 5570 0.86 0.81 178 0.84 0.81 2.44 6624 0.83 0.79 188 0.86 0.79 2.27 4223 0.79 0.77 104 0.77 0.77 2.15 8006 0.83 0.76 205 0.86 0.76 2.03 8584 0.73 0.74 187 0.72 0.74 1.91 10719 0.70 0.72 212 0.75 0.72 1.79 9039 0.68 0.70 129 0.66 0.70 1.70 7523 0.59 0.68 95 0.65 0.68 1.61 Overall average CC: 0.77411095248586115 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.598 B-value to apply to Fc= 6.599 Overall R-factor for FC vs FP: 0.273 for 84260 reflections Writing overall R-factor of 0.273 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.69 0.80 81928 0.63 0.80 2332 0.69 0.80 84260 4.6 0.78 0.83 4137 0.62 0.74 345 0.77 0.82 4482 2.9 0.77 0.81 11903 0.71 0.81 496 0.77 0.81 12399 2.3 0.76 0.83 16949 0.67 0.82 534 0.75 0.83 17483 2.0 0.69 0.80 14217 0.58 0.81 358 0.69 0.80 14575 1.7 0.64 0.78 24723 0.56 0.82 471 0.63 0.78 25194 1.6 0.57 0.74 9999 0.67 0.91 128 0.58 0.74 10127 Minor cycle 8 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0137345 Values of m, alpha, s Centric: 0.63032253061076815 0.3542580 0.4921290 Acentric: 0.59560170670237134 0.3856016 0.4782406 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 37 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . xx xxo. . . x xo . . x xo . p(rho) . x .xo . . xx . xx . . x . xxxx . . xx . oxxxx . . o . ooo xxxx . . x . ooooooxxxx . . xx . oooxxxxooo . xxxo . xxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 38 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o . o . . xxxx . . x . xx . . x . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo............ooooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.28 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.91 offset is -0.37 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.60 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.63 0.23 0.60 81928 4.6 0.48 0.85 0.86 0.73 0.18 0.86 4137 2.9 0.40 0.86 0.86 0.74 0.14 0.86 11903 2.3 0.21 0.71 0.73 0.71 0.18 0.73 16949 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14217 1.7 0.06 0.42 0.44 0.57 0.24 0.44 24723 1.6 0.03 0.28 0.29 0.47 0.26 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.60 0.24 0.63 2332 4.6 0.43 0.77 0.78 0.58 0.31 0.78 345 2.9 0.39 0.80 0.80 0.70 0.27 0.80 496 2.3 0.22 0.66 0.67 0.63 0.22 0.67 534 2.0 0.14 0.56 0.57 0.56 0.18 0.57 358 1.7 0.06 0.41 0.43 0.51 0.12 0.43 471 1.6 0.03 0.31 0.32 0.65 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.63 0.23 0.60 84260 4.6 0.48 0.85 0.86 0.72 0.19 0.86 4482 2.9 0.40 0.86 0.86 0.74 0.15 0.86 12399 2.3 0.21 0.71 0.73 0.71 0.18 0.73 17483 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14575 1.7 0.06 0.42 0.44 0.56 0.24 0.44 25194 1.6 0.03 0.28 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.60 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.23 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.77 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.19 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.72 0.92 42 0.35 0.92 10.73 507 0.84 0.92 60 0.81 0.92 7.75 1058 0.86 0.91 91 0.88 0.91 5.96 1884 0.90 0.90 131 0.88 0.90 4.77 1883 0.90 0.89 100 0.88 0.89 4.17 1899 0.85 0.88 74 0.81 0.88 3.58 4133 0.87 0.86 173 0.87 0.86 3.16 4651 0.87 0.84 176 0.87 0.84 2.86 5367 0.86 0.83 187 0.85 0.83 2.62 5570 0.86 0.81 178 0.85 0.81 2.44 6624 0.84 0.80 188 0.86 0.80 2.27 4223 0.79 0.78 104 0.78 0.78 2.15 8006 0.83 0.76 205 0.86 0.76 2.03 8584 0.74 0.74 187 0.70 0.75 1.91 10719 0.70 0.72 212 0.76 0.72 1.79 9039 0.68 0.70 129 0.66 0.70 1.70 7523 0.59 0.68 95 0.65 0.68 1.61 Overall average CC: 0.77661070191616854 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.593 B-value to apply to Fc= 6.548 Overall R-factor for FC vs FP: 0.271 for 84260 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.69 0.80 81928 0.63 0.80 2332 0.69 0.80 84260 4.6 0.78 0.82 4137 0.62 0.74 345 0.77 0.82 4482 2.9 0.77 0.81 11903 0.71 0.81 496 0.77 0.81 12399 2.3 0.75 0.83 16949 0.66 0.82 534 0.75 0.83 17483 2.0 0.69 0.79 14217 0.58 0.80 358 0.69 0.80 14575 1.7 0.63 0.78 24723 0.55 0.81 471 0.63 0.78 25194 1.6 0.57 0.74 9999 0.67 0.91 128 0.57 0.74 10127 Minor cycle 9 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0136712 Values of m, alpha, s Centric: 0.63148101655801669 0.3551848 0.4925924 Acentric: 0.59648000121984335 0.3864800 0.4785920 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 39 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . xx xxo. . . x xo . . x xo . p(rho) . x .xo . . xx . xx . . x . xxxx . . xx . oxxxx . . o . ooo xxxx . . x . ooooooxxxx . . xx . oooxxxxoo . xxxo . xxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 40 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o . o . . xxxx . . x . xx . . x . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo............ooooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.28 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.91 offset is -0.37 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.60 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81921 2332 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.58 0.60 0.63 0.23 0.60 81928 4.6 0.48 0.85 0.86 0.73 0.18 0.86 4137 2.9 0.40 0.86 0.87 0.74 0.14 0.87 11903 2.3 0.21 0.72 0.73 0.71 0.18 0.73 16949 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14217 1.7 0.06 0.42 0.44 0.56 0.24 0.44 24723 1.6 0.03 0.28 0.29 0.47 0.26 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.61 0.24 0.63 2332 4.6 0.43 0.77 0.78 0.58 0.31 0.78 345 2.9 0.39 0.80 0.81 0.70 0.27 0.81 496 2.3 0.22 0.66 0.67 0.64 0.22 0.67 534 2.0 0.14 0.56 0.57 0.56 0.18 0.57 358 1.7 0.06 0.41 0.43 0.51 0.12 0.43 471 1.6 0.03 0.31 0.32 0.65 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.59 0.60 0.63 0.23 0.60 84260 4.6 0.48 0.85 0.86 0.72 0.19 0.86 4482 2.9 0.40 0.86 0.86 0.73 0.15 0.86 12399 2.3 0.21 0.71 0.73 0.71 0.18 0.73 17483 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14575 1.7 0.06 0.42 0.44 0.56 0.24 0.44 25194 1.6 0.03 0.28 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.60 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.23 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.77 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.15 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.73 0.92 42 0.36 0.92 10.73 507 0.84 0.92 60 0.82 0.92 7.75 1058 0.86 0.91 91 0.88 0.91 5.96 1884 0.90 0.90 131 0.88 0.90 4.77 1883 0.90 0.89 100 0.88 0.89 4.17 1899 0.85 0.88 74 0.81 0.88 3.58 4133 0.87 0.86 173 0.87 0.86 3.16 4651 0.87 0.84 176 0.87 0.84 2.86 5367 0.86 0.83 187 0.86 0.83 2.62 5570 0.87 0.81 178 0.84 0.81 2.44 6624 0.84 0.80 188 0.86 0.80 2.27 4223 0.79 0.78 104 0.78 0.78 2.15 8006 0.83 0.76 205 0.86 0.76 2.03 8584 0.74 0.75 187 0.73 0.75 1.91 10719 0.70 0.72 212 0.76 0.72 1.79 9039 0.68 0.70 129 0.66 0.70 1.70 7523 0.59 0.68 95 0.65 0.68 1.61 Overall average CC: 0.77835601589302250 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.588 B-value to apply to Fc= 6.516 Overall R-factor for FC vs FP: 0.269 for 84260 reflections Writing overall R-factor of 0.269 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.80 81928 0.64 0.80 2332 0.68 0.80 84260 4.6 0.78 0.82 4137 0.62 0.73 345 0.77 0.81 4482 2.9 0.77 0.80 11903 0.71 0.81 496 0.76 0.80 12399 2.3 0.75 0.83 16949 0.67 0.82 534 0.75 0.83 17483 2.0 0.69 0.79 14217 0.58 0.80 358 0.69 0.79 14575 1.7 0.63 0.78 24723 0.56 0.81 471 0.63 0.78 25194 1.6 0.57 0.74 9999 0.67 0.91 128 0.57 0.74 10127 Minor cycle 10 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0136515 Values of m, alpha, s Centric: 0.63297155453690912 0.3563772 0.4931886 Acentric: 0.59713494845928938 0.3871350 0.4788540 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 41 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . xx xxo. . . x xo . . x xo . p(rho) . x .xo . . xx . xx . . x . xxxx . . xx . oxxxx . . x . ooo xxxx . . x . ooooooxxxx . . xo . oooxxxxooo . xxxo . xxxxxooo 0.0 o..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 42 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.11.................................................. . . . . . . . oo . . o.o . . o. o . . . . p(rho) . o . o . . xxxx . . x . xx . . x . x . . xo . xx . . xo . o xx . . xx o . ooxx . . xxooo . ooxxx . 0.0 xxxxxxxxxxxooo............ooooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.09 and 0.27 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.91 offset is -0.37 and sigma is a random variable with rms value of 0.31 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.60 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81922 2331 84253 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.59 0.60 0.63 0.23 0.60 81928 4.6 0.48 0.85 0.86 0.73 0.18 0.86 4137 2.9 0.40 0.86 0.87 0.73 0.14 0.87 11903 2.3 0.21 0.72 0.73 0.71 0.18 0.73 16949 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14217 1.7 0.06 0.42 0.44 0.56 0.24 0.44 24723 1.6 0.03 0.28 0.29 0.46 0.26 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.62 0.63 0.60 0.24 0.63 2332 4.6 0.43 0.78 0.79 0.58 0.31 0.79 345 2.9 0.39 0.80 0.81 0.69 0.27 0.81 496 2.3 0.22 0.66 0.67 0.63 0.22 0.67 534 2.0 0.14 0.56 0.57 0.55 0.18 0.57 358 1.7 0.06 0.42 0.43 0.52 0.12 0.43 471 1.6 0.03 0.31 0.32 0.66 0.09 0.32 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.59 0.60 0.63 0.23 0.60 84260 4.6 0.48 0.85 0.86 0.72 0.19 0.86 4482 2.9 0.40 0.86 0.86 0.73 0.15 0.86 12399 2.3 0.21 0.71 0.73 0.71 0.18 0.73 17483 2.0 0.14 0.62 0.63 0.64 0.19 0.63 14575 1.7 0.06 0.42 0.44 0.56 0.24 0.44 25194 1.6 0.03 0.28 0.29 0.47 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.60 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.23 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.77 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.13 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.73 0.92 42 0.39 0.93 10.73 507 0.84 0.92 60 0.82 0.92 7.75 1058 0.86 0.91 91 0.88 0.91 5.96 1884 0.90 0.90 131 0.88 0.90 4.77 1883 0.90 0.89 100 0.88 0.89 4.17 1899 0.85 0.88 74 0.81 0.88 3.58 4133 0.88 0.86 173 0.87 0.86 3.16 4651 0.88 0.85 176 0.87 0.85 2.86 5367 0.87 0.83 187 0.86 0.83 2.62 5570 0.87 0.81 178 0.85 0.81 2.44 6624 0.84 0.80 188 0.86 0.80 2.27 4223 0.80 0.78 104 0.78 0.78 2.15 8006 0.83 0.77 205 0.85 0.77 2.03 8584 0.74 0.75 187 0.73 0.75 1.91 10719 0.70 0.72 212 0.76 0.72 1.79 9039 0.68 0.70 129 0.66 0.70 1.70 7523 0.60 0.68 95 0.65 0.68 1.61 Overall average CC: 0.77976476445337839 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.581 B-value to apply to Fc= 6.491 Overall R-factor for FC vs FP: 0.268 for 84260 reflections Writing overall R-factor of 0.268 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.80 81928 0.63 0.80 2332 0.68 0.80 84260 4.6 0.77 0.82 4137 0.62 0.73 345 0.76 0.81 4482 2.9 0.76 0.80 11903 0.72 0.80 496 0.76 0.80 12399 2.3 0.75 0.82 16949 0.65 0.81 534 0.74 0.82 17483 2.0 0.69 0.79 14217 0.58 0.79 358 0.68 0.79 14575 1.7 0.63 0.77 24723 0.57 0.81 471 0.63 0.77 25194 1.6 0.57 0.74 9999 0.69 0.91 128 0.57 0.74 10127 Restoring phases from beginning of cycle at the end of this cycle. Mask cycle 3 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 5.82 Using histogram-based mask Assuming this cycle is unbiased (no previous density modification) Plot 43 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 .......................................xxxxxxxxxxx . + xxxx . . + xxxx . . + xx . . + xx . . + x . . +x . p(protein) . x . 0.5 . + . . xx+ . . x + . . xx + . . xxxx + . . x + . . xxx + . 0.0 .xxxxxxxxxx.............+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0045 Y + 0.0022 Z + 82.4558 New Y-prime= 0.0045 X + -1.0000 Y + 0.0037 Z + 50.4985 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2898 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.10 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0045 Y + 0.0022 Z + 82.2274 New Y-prime= -0.0045 X + -1.0000 Y + 0.0037 Z + 50.8735 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0757 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0045 0.0022 rota_matrix -0.0045 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2274 50.8735 -0.0757 center_orth 88.1038 7.8844 65.6165 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.15047 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 3.91 95090 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.11 63677 17.3 2.90 231387 25.4 1.17 514760 33.4 1.01 805030 41.5 1.52 908023 49.2 1.40 524858 56.6 1.71 123538 63.3 2.68 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.41 which is very good. The fall-off of the overlap has a characteristic length of 7348.9 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 51.9% of asymmetric unit used in NCS with 25.9% within molecule 1 and 25.9% in NCS-related molecules. Cutoff in used in identifying NCS = 0.99 Asymmetric unit of NCS contains 420159 points (plus the 95297 border points) which can be represented by 18222 continuous rows along x with mean length of 28.3 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.89 Final overall correlation of NCS is: 0.89 Refined NCS operators: Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0045 Y + 0.0022 Z + 82.4560 New Y-prime= 0.0045 X + -1.0000 Y + 0.0037 Z + 50.4986 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2898 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.10 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0045 Y + 0.0022 Z + 82.2273 New Y-prime= -0.0045 X + -1.0000 Y + 0.0037 Z + 50.8738 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0757 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0045 0.0022 rota_matrix -0.0045 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2273 50.8738 -0.0757 center_orth 88.1038 7.8844 65.6165 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.15047 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 3.91 95090 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.11 63677 17.3 2.90 231387 25.4 1.17 514760 33.4 1.01 805030 41.5 1.52 908023 49.2 1.40 524858 56.6 1.71 123538 63.3 2.68 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.41 which is very good. The fall-off of the overlap has a characteristic length of 7348.9 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 51.9% of asymmetric unit used in NCS with 25.9% within molecule 1 and 25.9% in NCS-related molecules. Cutoff in used in identifying NCS = 0.99 Asymmetric unit of NCS contains 420162 points (plus the 95244 border points) which can be represented by 18211 continuous rows along x with mean length of 28.3 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: -1.78513e-09 Values of m, alpha, s Centric: 0.23111231844139474 0.1186674 0.2348899 Acentric: 0.17329066504681193 8.9316264E-02 0.1832907 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 44 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.05.................................................. . . . . . . . xxo . . . xx xx. . . ox x . . xx .x . p(rho) . x . x . . x . ox . . x . xxx . . x . oxxx . . x . oxxx . . xo . ooxx . . x . xxxoo . . xxo . xxxooooo . 0.0 xxxxxxxo..............................xxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 45 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.08.................................................. . . . . xx . . xox . . x. x . . x . x . . x . x . p(rho) . x . x . . x . x . . x . ox . . o . ox . . ox . x . . x . ox . . ox . xo . . ox . xoo . 0.0 xxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.89 RMS in NCS unit : 1: 0.63132695076282874 RMS in NCS unit : 2: 0.63108245502824589 Average RMS ncs in std crystal: 0.63120472431182861 Including ncs au 1 with rms of 0.63199984895867301 Including ncs au 2 with rms of 0.63185415291390878 RMS rho in NCS region: 0.63192700513522082 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.41 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.2689868 For NCS asym unit 1 the mean target rho is 0.029 +/- 0.631 and the mean uncertainty in it is 0.287 +/- 0.095 For NCS asym unit 2 the mean target rho is 0.031 +/- 0.631 and the mean uncertainty in it is 0.287 +/- 0.095 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.26 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.63 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.57 offset is -0.28 and sigma is a random variable with rms value of 0.26 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.17 0.23 0.17 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.39 0.39 0.39 81922 2332 84254 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.52 0.54 0.64 0.27 0.54 81928 4.6 0.48 0.89 0.90 0.81 0.14 0.90 4137 2.9 0.40 0.88 0.88 0.80 0.13 0.88 11903 2.3 0.21 0.71 0.73 0.76 0.18 0.73 16949 2.0 0.14 0.54 0.57 0.68 0.23 0.57 14217 1.7 0.06 0.29 0.31 0.55 0.31 0.31 24723 1.6 0.03 0.14 0.16 0.35 0.35 0.16 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.59 0.60 0.61 0.26 0.60 2332 4.6 0.43 0.81 0.82 0.67 0.29 0.82 345 2.9 0.39 0.82 0.82 0.68 0.26 0.82 496 2.3 0.22 0.67 0.69 0.65 0.21 0.69 534 2.0 0.14 0.49 0.51 0.61 0.20 0.51 358 1.7 0.06 0.29 0.31 0.51 0.17 0.31 471 1.6 0.03 0.14 0.16 0.43 0.18 0.16 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.52 0.54 0.64 0.27 0.54 84260 4.6 0.48 0.88 0.89 0.80 0.15 0.89 4482 2.9 0.40 0.87 0.88 0.79 0.13 0.88 12399 2.3 0.21 0.71 0.72 0.76 0.18 0.72 17483 2.0 0.14 0.54 0.56 0.68 0.23 0.56 14575 1.7 0.06 0.29 0.31 0.55 0.31 0.31 25194 1.6 0.03 0.14 0.16 0.35 0.35 0.16 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.54 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.27 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.73 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 7.05 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.46 0.87 42 -0.05 0.87 10.73 507 0.74 0.85 60 0.67 0.85 7.75 1058 0.80 0.84 91 0.87 0.84 5.96 1884 0.84 0.81 131 0.83 0.81 4.77 1883 0.86 0.79 100 0.82 0.79 4.17 1899 0.72 0.77 74 0.73 0.77 3.58 4133 0.77 0.73 173 0.76 0.73 3.16 4651 0.74 0.70 176 0.74 0.70 2.86 5367 0.71 0.67 187 0.73 0.67 2.62 5570 0.71 0.64 178 0.64 0.63 2.44 6624 0.69 0.61 188 0.71 0.61 2.27 4223 0.52 0.57 104 0.59 0.57 2.15 8006 0.68 0.55 205 0.80 0.55 2.03 8584 0.46 0.52 187 0.40 0.52 1.91 10719 0.49 0.48 212 0.48 0.48 1.79 9039 0.38 0.45 129 0.41 0.45 1.70 7523 0.23 0.41 95 0.27 0.41 1.61 Overall average CC: 0.57477289014892707 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.559 B-value to apply to Fc= 23.733 Overall R-factor for FC vs FP: 0.383 for 84260 reflections Writing overall R-factor of 0.383 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.71 0.84 81928 0.65 0.82 2332 0.71 0.84 84260 4.6 0.83 0.86 4137 0.73 0.81 345 0.83 0.86 4482 2.9 0.82 0.85 11903 0.70 0.81 496 0.81 0.85 12399 2.3 0.80 0.86 16949 0.68 0.83 534 0.79 0.86 17483 2.0 0.74 0.84 14217 0.64 0.86 358 0.73 0.84 14575 1.7 0.65 0.81 24723 0.58 0.84 471 0.65 0.81 25194 1.6 0.49 0.67 9999 0.50 0.74 128 0.49 0.67 10127 Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0188298 Values of m, alpha, s Centric: 0.60309438253149905 0.3324755 0.4812377 Acentric: 0.53566433069476749 0.3285315 0.4542657 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 46 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . . . . xxxxo . . . xxo xxo. . . o xo . . xo xo . p(rho) . x .xx . . x . xx . . x . xxx . . xo . oxxx . . xx . oooxxxxx . . x . ooooxxxxx . . x . oooooxxxxoo . oxxx . xxxxxooo 0.0 x..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 47 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.07.................................................. . . . . . . . oxo . . xxxx . . x . x . . x . x . p(rho) . x . x . . x . xx . . x . ox . . xx . x . . o . ox . . x . xx . . x . oxx . . xxx . oxx . 0.0 xxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.94 RMS in NCS unit : 1: 1.0346907041270945 RMS in NCS unit : 2: 1.0327992411548657 Average RMS ncs in std crystal: 1.0337449908256531 Including ncs au 1 with rms of 1.0350594383841836 Including ncs au 2 with rms of 1.0332323836046091 RMS rho in NCS region: 1.0341463144829757 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.38 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4401960 For NCS asym unit 1 the mean target rho is 0.028 +/- 1.033 and the mean uncertainty in it is 0.470 +/- 0.155 For NCS asym unit 2 the mean target rho is 0.030 +/- 1.035 and the mean uncertainty in it is 0.470 +/- 0.155 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.29 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.04 and 0.35 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.90 offset is -0.29 and sigma is a random variable with rms value of 0.29 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.54 0.60 0.54 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.19 0.14 0.19 81925 2332 84257 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.60 0.61 0.68 0.23 0.61 81928 4.6 0.48 0.88 0.89 0.79 0.15 0.89 4137 2.9 0.40 0.88 0.88 0.80 0.12 0.88 11903 2.3 0.21 0.76 0.77 0.78 0.15 0.77 16949 2.0 0.14 0.65 0.67 0.71 0.18 0.67 14217 1.7 0.06 0.42 0.44 0.60 0.24 0.44 24723 1.6 0.03 0.23 0.24 0.43 0.29 0.24 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.64 0.65 0.61 0.24 0.65 2332 4.6 0.43 0.80 0.81 0.62 0.29 0.81 345 2.9 0.39 0.81 0.81 0.67 0.27 0.81 496 2.3 0.22 0.69 0.70 0.65 0.21 0.70 534 2.0 0.14 0.60 0.61 0.66 0.16 0.61 358 1.7 0.06 0.42 0.43 0.47 0.12 0.43 471 1.6 0.03 0.21 0.23 0.46 0.13 0.23 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.60 0.61 0.67 0.23 0.61 84260 4.6 0.48 0.87 0.88 0.78 0.16 0.88 4482 2.9 0.40 0.87 0.88 0.80 0.13 0.88 12399 2.3 0.21 0.75 0.77 0.78 0.15 0.77 17483 2.0 0.14 0.65 0.66 0.71 0.18 0.66 14575 1.7 0.06 0.42 0.44 0.60 0.24 0.44 25194 1.6 0.03 0.23 0.24 0.43 0.29 0.24 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.61 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.23 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.77 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.46 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.07 0.92 10.73 507 0.81 0.91 60 0.77 0.91 7.75 1058 0.86 0.90 91 0.88 0.90 5.96 1883 0.90 0.88 131 0.88 0.88 4.77 1878 0.90 0.86 100 0.89 0.86 4.17 1899 0.80 0.85 74 0.80 0.85 3.58 4133 0.85 0.82 173 0.85 0.82 3.16 4651 0.85 0.80 176 0.85 0.80 2.86 5367 0.83 0.78 187 0.84 0.78 2.62 5570 0.84 0.76 178 0.83 0.76 2.44 6624 0.82 0.73 188 0.86 0.73 2.27 4223 0.67 0.71 104 0.78 0.71 2.15 8006 0.80 0.69 205 0.86 0.69 2.03 8584 0.62 0.67 187 0.58 0.67 1.91 10719 0.65 0.63 212 0.62 0.63 1.79 9039 0.55 0.61 129 0.50 0.61 1.70 7523 0.40 0.58 95 0.39 0.58 1.61 Overall average CC: 0.70742084206029243 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 0.837 B-value to apply to Fc= 13.579 Overall R-factor for FC vs FP: 0.340 for 84254 reflections Writing overall R-factor of 0.340 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.73 0.84 81928 0.63 0.82 2332 0.72 0.84 84260 4.6 0.82 0.86 4137 0.64 0.77 345 0.81 0.85 4482 2.9 0.82 0.86 11903 0.69 0.82 496 0.82 0.86 12399 2.3 0.81 0.87 16949 0.67 0.86 534 0.80 0.87 17483 2.0 0.75 0.84 14217 0.66 0.83 358 0.75 0.84 14575 1.7 0.67 0.82 24723 0.52 0.82 471 0.67 0.82 25194 1.6 0.54 0.72 9999 0.48 0.82 128 0.54 0.72 10127 Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0181635 Values of m, alpha, s Centric: 0.64556519162847537 0.3664522 0.4982261 Acentric: 0.61003000250079809 0.4000300 0.4820060 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 48 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xx . . . xxoxxoo . . . xo xxo. . . xo xo . . x xx . p(rho) . x .xo . . xo . xx . . xx . oxxx . . x . oxxxx . . xx . ooo xxxx . . xx . ooooxxxxx . . xx . oooooxxxoo . xxxx . xxxxxxooo 0.0 x..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 49 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . ooo . . o. o . . . . . oxxxo . p(rho) . x . xx . . xx . x . . x . xx . . x . o x . . xo . ox . . xo . ox . . xoo . oox . . xxo . ooxx . 0.0 xxxxxxxxxxxo................ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.94 RMS in NCS unit : 1: 1.0794304540874142 RMS in NCS unit : 2: 1.0753386445852715 Average RMS ncs in std crystal: 1.0773845314979553 Including ncs au 1 with rms of 1.0797710360168764 Including ncs au 2 with rms of 1.0757001502492090 RMS rho in NCS region: 1.0777375152297357 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4587511 For NCS asym unit 1 the mean target rho is 0.027 +/- 1.075 and the mean uncertainty in it is 0.490 +/- 0.162 For NCS asym unit 2 the mean target rho is 0.028 +/- 1.079 and the mean uncertainty in it is 0.490 +/- 0.162 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.08 and 0.32 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.89 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.61 0.65 0.61 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.10 0.07 0.10 81924 2332 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.61 0.62 0.67 0.22 0.62 81928 4.6 0.48 0.88 0.89 0.79 0.15 0.89 4137 2.9 0.40 0.88 0.89 0.79 0.12 0.89 11903 2.3 0.21 0.76 0.77 0.77 0.15 0.77 16949 2.0 0.14 0.66 0.68 0.70 0.17 0.68 14217 1.7 0.06 0.45 0.47 0.61 0.22 0.47 24723 1.6 0.03 0.26 0.27 0.45 0.27 0.27 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.64 0.65 0.60 0.24 0.65 2332 4.6 0.43 0.81 0.81 0.61 0.29 0.81 345 2.9 0.39 0.81 0.82 0.68 0.27 0.82 496 2.3 0.22 0.69 0.70 0.62 0.20 0.70 534 2.0 0.14 0.61 0.62 0.65 0.16 0.62 358 1.7 0.06 0.43 0.44 0.48 0.12 0.44 471 1.6 0.03 0.24 0.26 0.52 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.61 0.63 0.67 0.22 0.63 84260 4.6 0.48 0.88 0.88 0.77 0.16 0.88 4482 2.9 0.40 0.88 0.89 0.78 0.13 0.89 12399 2.3 0.21 0.76 0.77 0.76 0.15 0.77 17483 2.0 0.14 0.66 0.67 0.70 0.17 0.67 14575 1.7 0.06 0.45 0.47 0.61 0.22 0.47 25194 1.6 0.03 0.26 0.27 0.45 0.27 0.27 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.63 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.22 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.78 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.28 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.17 0.92 10.73 507 0.81 0.91 60 0.77 0.91 7.75 1058 0.88 0.91 91 0.90 0.91 5.96 1884 0.91 0.89 131 0.90 0.89 4.77 1882 0.91 0.88 100 0.90 0.88 4.17 1899 0.80 0.87 74 0.75 0.87 3.58 4133 0.86 0.85 173 0.86 0.85 3.16 4651 0.87 0.83 176 0.87 0.83 2.86 5367 0.86 0.81 187 0.86 0.81 2.62 5570 0.87 0.79 178 0.88 0.79 2.44 6624 0.84 0.77 188 0.88 0.77 2.27 4223 0.71 0.75 104 0.80 0.75 2.15 8006 0.84 0.74 205 0.86 0.74 2.03 8584 0.69 0.72 187 0.62 0.72 1.91 10719 0.72 0.69 212 0.67 0.69 1.79 9039 0.63 0.67 129 0.56 0.67 1.70 7523 0.47 0.65 95 0.36 0.65 1.61 Overall average CC: 0.75385849870220811 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.026 B-value to apply to Fc= 9.570 Overall R-factor for FC vs FP: 0.303 for 84259 reflections Writing overall R-factor of 0.303 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.72 0.83 81928 0.63 0.81 2332 0.72 0.83 84260 4.6 0.81 0.85 4137 0.63 0.76 345 0.80 0.84 4482 2.9 0.81 0.84 11903 0.70 0.80 496 0.80 0.84 12399 2.3 0.80 0.86 16949 0.64 0.82 534 0.79 0.86 17483 2.0 0.74 0.83 14217 0.66 0.83 358 0.74 0.83 14575 1.7 0.68 0.81 24723 0.52 0.82 471 0.67 0.81 25194 1.6 0.56 0.74 9999 0.56 0.82 128 0.56 0.74 10127 Minor cycle 4 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0169866 Values of m, alpha, s Centric: 0.65181014207997490 0.3714481 0.5003620 Acentric: 0.62478162286835504 0.4147816 0.4849563 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 50 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxooxxo . . . oo xxo. . . xo xo . . x xo . p(rho) . x .xo . . x . xx . . x . oxxx . . xx . oxxxx . . x . ooo xxxx . . x . ooooxxxxx . . xx . oooooxxxxoo o xxx . xxxxxooo 0.0 x..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 51 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . ooo . . o. o . . . o . . oxxxx . p(rho) . x . xx . . xx . x . . x . xx . . x . x . . xo . ox . . xo . ox . . xoo . oxx . . xxo . ooxxx . 0.0 xxxxxxxxxxxo................ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0885756204506469 RMS in NCS unit : 2: 1.0837869856203302 Average RMS ncs in std crystal: 1.0861812829971313 Including ncs au 1 with rms of 1.0888712866631336 Including ncs au 2 with rms of 1.0840957198682664 RMS rho in NCS region: 1.0864861270987594 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4624750 For NCS asym unit 1 the mean target rho is 0.025 +/- 1.084 and the mean uncertainty in it is 0.494 +/- 0.163 For NCS asym unit 2 the mean target rho is 0.026 +/- 1.089 and the mean uncertainty in it is 0.494 +/- 0.163 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.09 and 0.32 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.90 offset is -0.35 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.63 0.65 0.62 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.06 0.04 0.06 81926 2332 84258 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.62 0.63 0.67 0.21 0.63 81928 4.6 0.48 0.88 0.89 0.77 0.15 0.89 4137 2.9 0.40 0.88 0.89 0.78 0.12 0.89 11903 2.3 0.21 0.76 0.77 0.76 0.15 0.77 16949 2.0 0.14 0.67 0.68 0.70 0.17 0.68 14217 1.7 0.06 0.47 0.48 0.61 0.22 0.48 24723 1.6 0.03 0.28 0.29 0.45 0.26 0.29 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.65 0.66 0.60 0.23 0.66 2332 4.6 0.43 0.81 0.81 0.60 0.29 0.81 345 2.9 0.39 0.82 0.82 0.68 0.26 0.82 496 2.3 0.22 0.70 0.70 0.63 0.20 0.70 534 2.0 0.14 0.62 0.62 0.63 0.16 0.62 358 1.7 0.06 0.44 0.45 0.48 0.12 0.45 471 1.6 0.03 0.25 0.27 0.52 0.11 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.62 0.63 0.67 0.21 0.63 84260 4.6 0.48 0.87 0.88 0.76 0.16 0.88 4482 2.9 0.40 0.88 0.89 0.78 0.12 0.89 12399 2.3 0.21 0.76 0.77 0.76 0.15 0.77 17483 2.0 0.14 0.67 0.68 0.70 0.17 0.68 14575 1.7 0.06 0.47 0.48 0.61 0.21 0.48 25194 1.6 0.03 0.28 0.29 0.45 0.26 0.29 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.63 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.17 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.91 42 0.20 0.91 10.73 507 0.82 0.91 60 0.77 0.91 7.75 1058 0.88 0.90 91 0.90 0.90 5.96 1883 0.91 0.89 131 0.90 0.89 4.77 1882 0.91 0.88 100 0.90 0.88 4.17 1899 0.81 0.87 74 0.77 0.87 3.58 4133 0.87 0.85 173 0.87 0.85 3.16 4651 0.87 0.84 176 0.88 0.84 2.86 5367 0.87 0.82 187 0.86 0.82 2.62 5570 0.87 0.80 178 0.88 0.80 2.44 6624 0.85 0.79 188 0.88 0.79 2.27 4223 0.73 0.77 104 0.80 0.77 2.15 8006 0.85 0.76 205 0.87 0.76 2.03 8584 0.71 0.74 187 0.66 0.74 1.91 10719 0.75 0.72 212 0.67 0.72 1.79 9039 0.66 0.70 129 0.57 0.70 1.70 7523 0.50 0.67 95 0.38 0.67 1.61 Overall average CC: 0.76893540441639030 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.087 B-value to apply to Fc= 8.371 Overall R-factor for FC vs FP: 0.290 for 84258 reflections Writing overall R-factor of 0.290 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.72 0.83 81928 0.62 0.80 2332 0.72 0.83 84260 4.6 0.80 0.84 4137 0.62 0.74 345 0.79 0.83 4482 2.9 0.80 0.84 11903 0.69 0.79 496 0.80 0.83 12399 2.3 0.79 0.85 16949 0.64 0.83 534 0.79 0.85 17483 2.0 0.73 0.82 14217 0.64 0.82 358 0.73 0.82 14575 1.7 0.67 0.81 24723 0.52 0.81 471 0.67 0.81 25194 1.6 0.56 0.74 9999 0.53 0.81 128 0.56 0.74 10127 Minor cycle 5 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0165928 Values of m, alpha, s Centric: 0.65783581143363112 0.3762687 0.5015672 Acentric: 0.63260259976336841 0.4226026 0.4865205 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 52 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . o xxo. . . x xo . . x xo . p(rho) . x .xo . . x . xx . . x . oxxx . . xx . oxxxx . . x . ooooxxxx . . x . oooooxxxx . . xx . ooooxxxxoo o xxx . xxxxxooo 0.0 x..............................................xxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 53 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o.o . . o. o . . o xxo . p(rho) . xx. xo . . ox . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . oox . . xxoo . ooxx . 0.0 xxxxxxxxxxxo................ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0935606177820381 RMS in NCS unit : 2: 1.0889500339453628 Average RMS ncs in std crystal: 1.0912553071975708 Including ncs au 1 with rms of 1.0938450051487680 Including ncs au 2 with rms of 1.0892398837112436 RMS rho in NCS region: 1.0915448730025239 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4646283 For NCS asym unit 1 the mean target rho is 0.025 +/- 1.089 and the mean uncertainty in it is 0.497 +/- 0.164 For NCS asym unit 2 the mean target rho is 0.025 +/- 1.094 and the mean uncertainty in it is 0.497 +/- 0.164 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.09 and 0.31 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.90 offset is -0.35 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.63 0.66 0.63 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 81927 2332 84259 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.66 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.77 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.77 0.12 0.89 11903 2.3 0.21 0.76 0.77 0.76 0.15 0.77 16949 2.0 0.14 0.67 0.69 0.69 0.16 0.69 14217 1.7 0.06 0.47 0.49 0.60 0.21 0.49 24723 1.6 0.03 0.28 0.30 0.45 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.65 0.66 0.59 0.23 0.66 2332 4.6 0.43 0.81 0.82 0.59 0.29 0.82 345 2.9 0.39 0.82 0.83 0.69 0.26 0.83 496 2.3 0.22 0.70 0.71 0.60 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.44 0.46 0.46 0.11 0.46 471 1.6 0.03 0.26 0.27 0.48 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.66 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.75 0.16 0.88 4482 2.9 0.40 0.88 0.89 0.77 0.12 0.89 12399 2.3 0.21 0.76 0.77 0.75 0.15 0.77 17483 2.0 0.14 0.67 0.68 0.69 0.16 0.68 14575 1.7 0.06 0.47 0.49 0.60 0.21 0.49 25194 1.6 0.03 0.28 0.30 0.45 0.26 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.06 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.92 42 0.27 0.92 10.73 507 0.82 0.91 60 0.78 0.91 7.75 1058 0.88 0.91 91 0.90 0.91 5.96 1884 0.91 0.90 131 0.90 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.87 74 0.76 0.88 3.58 4133 0.87 0.86 173 0.87 0.86 3.16 4651 0.88 0.84 176 0.88 0.84 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.81 178 0.90 0.81 2.44 6624 0.85 0.79 188 0.88 0.79 2.27 4223 0.74 0.77 104 0.80 0.77 2.15 8006 0.85 0.76 205 0.87 0.76 2.03 8584 0.72 0.74 187 0.66 0.74 1.91 10719 0.75 0.72 212 0.68 0.72 1.79 9039 0.67 0.70 129 0.57 0.70 1.70 7523 0.52 0.68 95 0.38 0.68 1.61 Overall average CC: 0.77541783505725503 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.110 B-value to apply to Fc= 7.887 Overall R-factor for FC vs FP: 0.283 for 84259 reflections Writing overall R-factor of 0.283 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.71 0.82 81928 0.61 0.79 2332 0.71 0.82 84260 4.6 0.80 0.83 4137 0.62 0.72 345 0.78 0.82 4482 2.9 0.79 0.83 11903 0.69 0.79 496 0.79 0.83 12399 2.3 0.78 0.85 16949 0.62 0.81 534 0.78 0.84 17483 2.0 0.73 0.81 14217 0.64 0.82 358 0.72 0.81 14575 1.7 0.67 0.80 24723 0.52 0.82 471 0.66 0.80 25194 1.6 0.55 0.73 9999 0.55 0.81 128 0.55 0.73 10127 Minor cycle 6 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0161244 Values of m, alpha, s Centric: 0.66251824980861851 0.3800146 0.5025036 Acentric: 0.63609425339549386 0.4260943 0.4872189 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 54 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . o xxo. . . xxo xo . . x xo . p(rho) . xx .xo . . o . xx . . x . oxxx . . x . oxxxx . . x . ooooxxxx . . x . oooooxxxx . . xx . ooooxxxxoo o xxx . xxxxxxoo 0.0 x...............................................xx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 55 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o.o . . o. o . . o xxo . p(rho) . xx. xo . . ox . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . oox . . xxoo . ooxxx . 0.0 xxxxxxxxxxxo................ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0960519725291569 RMS in NCS unit : 2: 1.0907562097770809 Average RMS ncs in std crystal: 1.0934040546417236 Including ncs au 1 with rms of 1.0963213518377339 Including ncs au 2 with rms of 1.0910291027928349 RMS rho in NCS region: 1.0936784284322916 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4655365 For NCS asym unit 1 the mean target rho is 0.024 +/- 1.091 and the mean uncertainty in it is 0.498 +/- 0.164 For NCS asym unit 2 the mean target rho is 0.024 +/- 1.096 and the mean uncertainty in it is 0.498 +/- 0.164 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.31 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.91 offset is -0.35 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.66 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.03 0.02 0.03 81927 2332 84259 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.66 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.76 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.77 0.12 0.89 11903 2.3 0.21 0.77 0.77 0.75 0.15 0.77 16949 2.0 0.14 0.68 0.69 0.69 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.60 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.45 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.66 0.59 0.23 0.66 2332 4.6 0.43 0.81 0.82 0.58 0.29 0.82 345 2.9 0.39 0.82 0.83 0.68 0.26 0.83 496 2.3 0.22 0.71 0.71 0.61 0.20 0.71 534 2.0 0.14 0.62 0.63 0.63 0.16 0.63 358 1.7 0.06 0.45 0.46 0.46 0.11 0.46 471 1.6 0.03 0.26 0.27 0.49 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.66 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.75 0.16 0.88 4482 2.9 0.40 0.88 0.89 0.77 0.12 0.89 12399 2.3 0.21 0.76 0.77 0.75 0.15 0.77 17483 2.0 0.14 0.67 0.69 0.69 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.60 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.45 0.26 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.01 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.92 42 0.26 0.92 10.73 507 0.82 0.92 60 0.78 0.92 7.75 1058 0.89 0.91 91 0.91 0.91 5.96 1884 0.91 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.77 0.88 3.58 4133 0.87 0.86 173 0.87 0.86 3.16 4651 0.88 0.84 176 0.88 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.81 178 0.89 0.81 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.74 0.78 104 0.80 0.78 2.15 8006 0.85 0.76 205 0.88 0.76 2.03 8584 0.73 0.75 187 0.66 0.75 1.91 10719 0.76 0.72 212 0.68 0.72 1.79 9039 0.68 0.70 129 0.59 0.70 1.70 7523 0.52 0.68 95 0.38 0.68 1.61 Overall average CC: 0.77931002148142048 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.114 B-value to apply to Fc= 7.695 Overall R-factor for FC vs FP: 0.279 for 84259 reflections Writing overall R-factor of 0.279 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.71 0.81 81928 0.61 0.79 2332 0.71 0.81 84260 4.6 0.79 0.83 4137 0.60 0.71 345 0.78 0.82 4482 2.9 0.79 0.82 11903 0.69 0.78 496 0.79 0.82 12399 2.3 0.78 0.84 16949 0.63 0.81 534 0.77 0.84 17483 2.0 0.72 0.81 14217 0.65 0.82 358 0.72 0.81 14575 1.7 0.66 0.80 24723 0.51 0.81 471 0.66 0.80 25194 1.6 0.55 0.73 9999 0.53 0.80 128 0.55 0.73 10127 Minor cycle 7 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0159792 Values of m, alpha, s Centric: 0.66392725495846505 0.3811418 0.5027854 Acentric: 0.63786999788334753 0.4278700 0.4875740 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 56 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . x xxo. . . xx xo . . x xo . p(rho) . xx .xx . . x . x . . x . oxxx . . x . oxxxx . . x . ooooxxxx . . x . oooooxxxxx . . xx . oooxxxxoo o xxx . xxxxxxoo 0.0 x...............................................xx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 57 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o.o . . o. o . . o xxo . p(rho) . xx.xxo . . x . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . oox . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo...............ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0976379109895129 RMS in NCS unit : 2: 1.0925702225570904 Average RMS ncs in std crystal: 1.0951040387153625 Including ncs au 1 with rms of 1.0979033511292335 Including ncs au 2 with rms of 1.0928392715887494 RMS rho in NCS region: 1.0953742378628935 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4662583 For NCS asym unit 1 the mean target rho is 0.024 +/- 1.093 and the mean uncertainty in it is 0.498 +/- 0.165 For NCS asym unit 2 the mean target rho is 0.024 +/- 1.098 and the mean uncertainty in it is 0.498 +/- 0.165 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.31 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.66 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.03 0.02 0.03 81926 2332 84258 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.66 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.76 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.76 0.12 0.89 11903 2.3 0.21 0.77 0.78 0.75 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.60 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.59 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.59 0.29 0.82 345 2.9 0.39 0.83 0.84 0.69 0.26 0.84 496 2.3 0.22 0.71 0.71 0.60 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.45 0.46 0.47 0.11 0.46 471 1.6 0.03 0.26 0.27 0.49 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.74 0.16 0.88 4482 2.9 0.40 0.88 0.89 0.76 0.12 0.89 12399 2.3 0.21 0.76 0.77 0.74 0.15 0.77 17483 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.45 0.26 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.96 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.93 42 0.29 0.93 10.73 507 0.82 0.92 60 0.79 0.92 7.75 1058 0.89 0.91 91 0.91 0.91 5.96 1884 0.91 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.76 0.88 3.58 4133 0.87 0.86 173 0.88 0.86 3.16 4651 0.88 0.85 176 0.88 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.82 178 0.90 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.75 0.78 104 0.80 0.78 2.15 8006 0.86 0.77 205 0.88 0.77 2.03 8584 0.73 0.75 187 0.67 0.75 1.91 10719 0.76 0.73 212 0.68 0.73 1.79 9039 0.68 0.71 129 0.58 0.71 1.70 7523 0.52 0.68 95 0.37 0.68 1.61 Overall average CC: 0.78149047108084413 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.114 B-value to apply to Fc= 7.600 Overall R-factor for FC vs FP: 0.277 for 84259 reflections Writing overall R-factor of 0.277 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.81 81928 0.61 0.78 2332 0.70 0.81 84260 4.6 0.79 0.82 4137 0.60 0.71 345 0.77 0.81 4482 2.9 0.78 0.82 11903 0.69 0.78 496 0.78 0.82 12399 2.3 0.77 0.84 16949 0.62 0.80 534 0.77 0.84 17483 2.0 0.72 0.80 14217 0.65 0.81 358 0.71 0.80 14575 1.7 0.66 0.79 24723 0.52 0.81 471 0.66 0.79 25194 1.6 0.55 0.73 9999 0.53 0.80 128 0.55 0.73 10127 Minor cycle 8 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0157604 Values of m, alpha, s Centric: 0.66596603765976703 0.3827728 0.5031932 Acentric: 0.63900979143777648 0.4290098 0.4878020 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 58 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . o xxo. . . xx xo . . x xo . p(rho) . xx .xo . . x . xx . . x . oxxx . . x . oxxxx . . x . ooooxxxx . . x . oooooxxxxx . . xx . oooxxxxoo o xxx . xxxxxxoo 0.0 x...............................................xx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 59 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o. . . o. o . . o xxo . p(rho) . xx.xxo . . x . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . oox . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo...............ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0987616478030209 RMS in NCS unit : 2: 1.0932224528931260 Average RMS ncs in std crystal: 1.0959920883178711 Including ncs au 1 with rms of 1.0990211398028804 Including ncs au 2 with rms of 1.0934832013991269 RMS rho in NCS region: 1.0962556675966848 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4666335 For NCS asym unit 1 the mean target rho is 0.024 +/- 1.093 and the mean uncertainty in it is 0.499 +/- 0.165 For NCS asym unit 2 the mean target rho is 0.024 +/- 1.099 and the mean uncertainty in it is 0.499 +/- 0.165 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.31 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.02 0.02 81927 2331 84258 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.75 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.76 0.12 0.89 11903 2.3 0.21 0.77 0.78 0.74 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.59 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.59 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.59 0.29 0.82 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.71 0.71 0.62 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.45 0.46 0.46 0.11 0.46 471 1.6 0.03 0.26 0.27 0.46 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.74 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.76 0.12 0.89 12399 2.3 0.21 0.77 0.77 0.74 0.15 0.77 17483 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.44 0.26 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.93 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.92 42 0.28 0.92 10.73 507 0.82 0.91 60 0.80 0.91 7.75 1058 0.89 0.91 91 0.91 0.91 5.96 1884 0.91 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.76 0.88 3.58 4133 0.87 0.86 173 0.88 0.86 3.16 4651 0.88 0.85 176 0.89 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.82 178 0.90 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.75 0.78 104 0.80 0.78 2.15 8006 0.86 0.77 205 0.88 0.77 2.03 8584 0.73 0.75 187 0.66 0.75 1.91 10719 0.76 0.73 212 0.68 0.73 1.79 9039 0.68 0.71 129 0.60 0.71 1.70 7523 0.52 0.69 95 0.37 0.69 1.61 Overall average CC: 0.78303148193934857 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.113 B-value to apply to Fc= 7.552 Overall R-factor for FC vs FP: 0.275 for 84259 reflections Writing overall R-factor of 0.275 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.81 81928 0.61 0.78 2332 0.70 0.81 84260 4.6 0.78 0.82 4137 0.60 0.70 345 0.77 0.81 4482 2.9 0.78 0.81 11903 0.69 0.78 496 0.78 0.81 12399 2.3 0.77 0.84 16949 0.63 0.81 534 0.77 0.83 17483 2.0 0.71 0.80 14217 0.64 0.81 358 0.71 0.80 14575 1.7 0.66 0.79 24723 0.52 0.80 471 0.65 0.79 25194 1.6 0.55 0.73 9999 0.52 0.79 128 0.55 0.73 10127 Minor cycle 9 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0156411 Values of m, alpha, s Centric: 0.66633527603787501 0.3830682 0.5032670 Acentric: 0.63970070823058589 0.4297007 0.4879401 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 60 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxx . . . x xo. . . xx xo . . x xo . p(rho) . xx .xx . . x . x . . x . oxxx . . ox . oxxxx . . x . ooooxxxx . . x . oooooxxxxx . . xx . ooooxxxxoo o xxx . xxxxxxoo 0.0 x...............................................xx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 61 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o.o . . o. o . . o x o . p(rho) . oxxxxo . . x . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo...............ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.0995813955784313 RMS in NCS unit : 2: 1.0941587968741300 Average RMS ncs in std crystal: 1.0968700647354126 Including ncs au 1 with rms of 1.0998358952801102 Including ncs au 2 with rms of 1.0944182965389559 RMS rho in NCS region: 1.0971304399080886 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4670059 For NCS asym unit 1 the mean target rho is 0.024 +/- 1.094 and the mean uncertainty in it is 0.499 +/- 0.165 For NCS asym unit 2 the mean target rho is 0.024 +/- 1.100 and the mean uncertainty in it is 0.499 +/- 0.165 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.02 0.02 81926 2332 84258 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.75 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.76 0.11 0.89 11903 2.3 0.21 0.77 0.78 0.74 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.59 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.58 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.59 0.29 0.82 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.71 0.71 0.60 0.20 0.71 534 2.0 0.14 0.62 0.63 0.60 0.16 0.63 358 1.7 0.06 0.45 0.46 0.47 0.11 0.46 471 1.6 0.03 0.26 0.27 0.43 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.74 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.75 0.12 0.89 12399 2.3 0.21 0.77 0.77 0.74 0.15 0.77 17483 2.0 0.14 0.68 0.69 0.68 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.44 0.25 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.89 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.92 42 0.30 0.92 10.73 507 0.82 0.91 60 0.80 0.91 7.75 1058 0.89 0.91 91 0.92 0.91 5.96 1884 0.91 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.76 0.88 3.58 4133 0.87 0.86 173 0.88 0.86 3.16 4651 0.89 0.85 176 0.88 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.82 178 0.91 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.75 0.78 104 0.80 0.78 2.15 8006 0.86 0.77 205 0.88 0.77 2.03 8584 0.73 0.76 187 0.67 0.76 1.91 10719 0.76 0.73 212 0.68 0.73 1.79 9039 0.68 0.71 129 0.59 0.71 1.70 7523 0.53 0.69 95 0.37 0.69 1.61 Overall average CC: 0.78406031484396421 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.113 B-value to apply to Fc= 7.528 Overall R-factor for FC vs FP: 0.274 for 84259 reflections Writing overall R-factor of 0.274 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.80 81928 0.61 0.78 2332 0.70 0.80 84260 4.6 0.78 0.82 4137 0.60 0.70 345 0.77 0.81 4482 2.9 0.78 0.81 11903 0.69 0.78 496 0.77 0.81 12399 2.3 0.77 0.83 16949 0.61 0.79 534 0.76 0.83 17483 2.0 0.71 0.80 14217 0.64 0.81 358 0.71 0.80 14575 1.7 0.65 0.79 24723 0.52 0.81 471 0.65 0.79 25194 1.6 0.55 0.73 9999 0.50 0.80 128 0.55 0.73 10127 Minor cycle 10 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0154923 Values of m, alpha, s Centric: 0.66681637923996451 0.3834531 0.5033633 Acentric: 0.64023292793637565 0.4302329 0.4880466 Using all points for histograms Fraction protein = 0.533 863336 Fraction solvent= 0.467 756664 Plot 62 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxo . . . o xxo. . . xx xo . . x xo . p(rho) . xx .xo . . x . xx . . x . oxxx . . ox . oxxxx . . x . ooooxxxx . . x . oooooxxxxx . . xx . oooxxxxoo o xxx . xxxxxxoo 0.0 x...............................................xx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 63 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.09.................................................. . . . . . . . oo . . o.o . . o. o . . o xxo . p(rho) . oxxxxo . . x . x . . x . x . . xo . oxx . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo...............ooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1002085695507522 RMS in NCS unit : 2: 1.0944924347474592 Average RMS ncs in std crystal: 1.0973504781723022 Including ncs au 1 with rms of 1.1004593728440315 Including ncs au 2 with rms of 1.0947455599798444 RMS rho in NCS region: 1.0976061844705189 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4672084 For NCS asym unit 1 the mean target rho is 0.023 +/- 1.094 and the mean uncertainty in it is 0.499 +/- 0.165 For NCS asym unit 2 the mean target rho is 0.024 +/- 1.100 and the mean uncertainty in it is 0.499 +/- 0.165 For a.u. 1 total of 420162 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 420162 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 420174 grid points filled in, for 420115 unique mappings and 10 attempts to write duplicates and 6 errors out of range and 420174 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 81925 2332 84257 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.75 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.75 0.11 0.89 11903 2.3 0.21 0.77 0.78 0.74 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.59 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.59 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.59 0.29 0.82 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.71 0.71 0.61 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.45 0.46 0.47 0.11 0.46 471 1.6 0.03 0.26 0.27 0.46 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.74 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.75 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.73 0.15 0.78 17483 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.44 0.25 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.88 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Trying 2 small cycles with damping factor 0.75f Small cycle 1 of 2 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81925 2332 84257 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.75 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.75 0.11 0.89 11903 2.3 0.21 0.77 0.78 0.74 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.59 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.59 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.59 0.29 0.82 345 2.9 0.39 0.83 0.83 0.68 0.26 0.83 496 2.3 0.22 0.71 0.71 0.61 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.45 0.46 0.47 0.11 0.46 471 1.6 0.03 0.26 0.27 0.46 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.74 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.75 0.12 0.89 12399 2.3 0.21 0.77 0.77 0.73 0.15 0.77 17483 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.44 0.25 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.88 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.62 0.92 42 0.29 0.92 10.73 507 0.82 0.91 60 0.80 0.91 7.75 1058 0.89 0.91 91 0.92 0.91 5.96 1884 0.91 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.77 0.88 3.58 4133 0.88 0.86 173 0.88 0.86 3.16 4651 0.89 0.85 176 0.89 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.82 178 0.90 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.75 0.78 104 0.80 0.78 2.15 8006 0.86 0.77 205 0.88 0.77 2.03 8584 0.74 0.76 187 0.66 0.76 1.91 10719 0.76 0.73 212 0.68 0.73 1.79 9039 0.68 0.72 129 0.60 0.72 1.70 7523 0.53 0.70 95 0.37 0.70 1.61 Overall average CC: 0.78477074870670316 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.111 B-value to apply to Fc= 7.514 Overall R-factor for FC vs FP: 0.274 for 84259 reflections Writing overall R-factor of 0.274 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.80 81928 0.61 0.78 2332 0.69 0.80 84260 4.6 0.78 0.81 4137 0.60 0.70 345 0.76 0.81 4482 2.9 0.78 0.81 11903 0.69 0.78 496 0.77 0.81 12399 2.3 0.77 0.83 16949 0.63 0.81 534 0.76 0.83 17483 2.0 0.71 0.80 14217 0.64 0.81 358 0.71 0.80 14575 1.7 0.65 0.79 24723 0.54 0.81 471 0.65 0.79 25194 1.6 0.55 0.73 9999 0.48 0.79 128 0.54 0.73 10127 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.92 offset is -0.34 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 840336 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 81925 2332 84257 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 81928 4.6 0.48 0.88 0.89 0.75 0.15 0.89 4137 2.9 0.40 0.89 0.89 0.75 0.11 0.89 11903 2.3 0.21 0.77 0.78 0.74 0.15 0.78 16949 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14217 1.7 0.06 0.48 0.49 0.59 0.21 0.49 24723 1.6 0.03 0.29 0.30 0.44 0.26 0.30 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.58 0.23 0.67 2332 4.6 0.43 0.82 0.82 0.58 0.29 0.82 345 2.9 0.39 0.83 0.83 0.68 0.26 0.83 496 2.3 0.22 0.70 0.71 0.60 0.20 0.71 534 2.0 0.14 0.62 0.63 0.62 0.16 0.63 358 1.7 0.06 0.45 0.46 0.48 0.11 0.46 471 1.6 0.03 0.26 0.27 0.45 0.10 0.27 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.63 0.64 0.65 0.21 0.64 84260 4.6 0.48 0.88 0.88 0.73 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.75 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.73 0.15 0.78 17483 2.0 0.14 0.68 0.69 0.67 0.16 0.69 14575 1.7 0.06 0.48 0.49 0.59 0.21 0.49 25194 1.6 0.03 0.29 0.30 0.44 0.25 0.30 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.64 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.87 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.63 0.92 42 0.30 0.92 10.73 507 0.82 0.91 60 0.80 0.91 7.75 1058 0.89 0.91 91 0.92 0.91 5.96 1884 0.92 0.90 131 0.91 0.90 4.77 1882 0.91 0.89 100 0.90 0.89 4.17 1899 0.81 0.88 74 0.76 0.88 3.58 4133 0.88 0.86 173 0.88 0.86 3.16 4651 0.89 0.85 176 0.89 0.85 2.86 5367 0.88 0.83 187 0.87 0.83 2.62 5570 0.88 0.82 178 0.89 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.75 0.79 104 0.80 0.78 2.15 8006 0.86 0.77 205 0.88 0.77 2.03 8584 0.74 0.76 187 0.67 0.76 1.91 10719 0.76 0.73 212 0.68 0.73 1.79 9039 0.68 0.72 129 0.60 0.72 1.70 7523 0.53 0.70 95 0.37 0.70 1.61 Overall average CC: 0.78498054211854351 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.110 B-value to apply to Fc= 7.513 Overall R-factor for FC vs FP: 0.273 for 84259 reflections Writing overall R-factor of 0.273 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.70 0.80 81928 0.61 0.78 2332 0.69 0.80 84260 4.6 0.78 0.81 4137 0.60 0.70 345 0.76 0.80 4482 2.9 0.77 0.81 11903 0.69 0.78 496 0.77 0.80 12399 2.3 0.77 0.83 16949 0.64 0.81 534 0.76 0.83 17483 2.0 0.71 0.80 14217 0.64 0.81 358 0.71 0.80 14575 1.7 0.65 0.79 24723 0.54 0.81 471 0.65 0.79 25194 1.6 0.54 0.72 9999 0.47 0.79 128 0.54 0.73 10127 Mask cycle 4 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Using histogram-based mask Assuming this cycle is biased (previous density modification) -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 422749 points (plus the 90138 border points) which can be represented by 17196 continuous rows along x with mean length of 29.8 Refining NCS operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 423015 points (plus the 92215 border points) which can be represented by 17685 continuous rows along x with mean length of 29.1 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: -2.11076e-09 Values of m, alpha, s Centric: 0.66565956525733927 0.3825276 0.5031319 Acentric: 0.64062653334617214 0.4306265 0.4881253 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0978945915397482 RMS in NCS unit : 2: 1.0926616977484380 Average RMS ncs in std crystal: 1.0952781438827515 Including ncs au 1 with rms of 1.0983910476152143 Including ncs au 2 with rms of 1.0931603488126140 RMS rho in NCS region: 1.0957788193101206 Average SD of NCS targets: 0.4660177 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 81924 2332 84256 Writing overall R-factor of 0.276 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0234831 Values of m, alpha, s Centric: 0.66651144557942066 0.3832092 0.5033023 Acentric: 0.64314310615690296 0.4331431 0.4886286 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0989494989093189 RMS in NCS unit : 2: 1.0939271063986056 Average RMS ncs in std crystal: 1.0964383482933044 Including ncs au 1 with rms of 1.0994381336236208 Including ncs au 2 with rms of 1.0944208211151727 RMS rho in NCS region: 1.0969323459895326 Average SD of NCS targets: 0.4665082 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.02 0.02 81925 2332 84257 Writing overall R-factor of 0.275 to resolve.rfactor Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0230433 Values of m, alpha, s Centric: 0.66666695865669789 0.3833336 0.5033334 Acentric: 0.64343566985814471 0.4334357 0.4886871 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0994133866917239 RMS in NCS unit : 2: 1.0940565822411026 Average RMS ncs in std crystal: 1.0967350006103516 Including ncs au 1 with rms of 1.0998832549316617 Including ncs au 2 with rms of 1.0945343940203134 RMS rho in NCS region: 1.0972120839136985 Average SD of NCS targets: 0.4666272 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.30 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.274 to resolve.rfactor Minor cycle 4 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0229057 Values of m, alpha, s Centric: 0.66722368184187753 0.3837790 0.5034447 Acentric: 0.64384494606451070 0.4338450 0.4887690 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0994863314455798 RMS in NCS unit : 2: 1.0942288704759353 Average RMS ncs in std crystal: 1.0968576073646545 Including ncs au 1 with rms of 1.0999513120700630 Including ncs au 2 with rms of 1.0947019446529951 RMS rho in NCS region: 1.0973297673333440 Average SD of NCS targets: 0.4666772 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.273 to resolve.rfactor Minor cycle 5 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0227321 Values of m, alpha, s Centric: 0.66719094380383581 0.3837528 0.5034382 Acentric: 0.64404707666594185 0.4340471 0.4888094 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0997627562753161 RMS in NCS unit : 2: 1.0942663836002382 Average RMS ncs in std crystal: 1.0970146059989929 Including ncs au 1 with rms of 1.1002205770842313 Including ncs au 2 with rms of 1.0947353387067391 RMS rho in NCS region: 1.0974813848200153 Average SD of NCS targets: 0.4667417 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.10 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.273 to resolve.rfactor Minor cycle 6 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0226539 Values of m, alpha, s Centric: 0.66722950189181740 0.3837836 0.5034459 Acentric: 0.64422163652195097 0.4342217 0.4888443 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0997622366253179 RMS in NCS unit : 2: 1.0944311505576623 Average RMS ncs in std crystal: 1.0970966815948486 Including ncs au 1 with rms of 1.1002168480810173 Including ncs au 2 with rms of 1.0948976836371178 RMS rho in NCS region: 1.0975604881816889 Average SD of NCS targets: 0.4667754 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.273 to resolve.rfactor Minor cycle 7 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0225009 Values of m, alpha, s Centric: 0.66742055852874549 0.3839365 0.5034841 Acentric: 0.64433519827854968 0.4343352 0.4888670 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1000004510726269 RMS in NCS unit : 2: 1.0944187108468946 Average RMS ncs in std crystal: 1.0972096323966980 Including ncs au 1 with rms of 1.1004496325586453 Including ncs au 2 with rms of 1.0948802865012885 RMS rho in NCS region: 1.0976684917514032 Average SD of NCS targets: 0.4668213 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.33 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.64 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 8 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.022384 Values of m, alpha, s Centric: 0.66735720100722162 0.3838858 0.5034714 Acentric: 0.64442453265600297 0.4344245 0.4888849 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.0999999346018936 RMS in NCS unit : 2: 1.0945501815517824 Average RMS ncs in std crystal: 1.0972750186920166 Including ncs au 1 with rms of 1.1004430598794621 Including ncs au 2 with rms of 1.0950085402570719 RMS rho in NCS region: 1.0977291631529147 Average SD of NCS targets: 0.4668471 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 9 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0222915 Values of m, alpha, s Centric: 0.66738305929507091 0.3839065 0.5034766 Acentric: 0.64449813003307066 0.4344981 0.4888996 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1001685833773742 RMS in NCS unit : 2: 1.0945429360675341 Average RMS ncs in std crystal: 1.0973557829856873 Including ncs au 1 with rms of 1.1006100342944118 Including ncs au 2 with rms of 1.0949956379086552 RMS rho in NCS region: 1.0978064252473041 Average SD of NCS targets: 0.4668800 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 10 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0221715 Values of m, alpha, s Centric: 0.66718740747710958 0.3837499 0.5034375 Acentric: 0.64454903551691067 0.4345490 0.4889098 Using all points for histograms Fraction protein = 0.532 861090 Fraction solvent= 0.468 757975 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1001644676756996 RMS in NCS unit : 2: 1.0946469334026325 Average RMS ncs in std crystal: 1.0974056720733643 Including ncs au 1 with rms of 1.1005970850109208 Including ncs au 2 with rms of 1.0950983503832150 RMS rho in NCS region: 1.0978511603461043 Average SD of NCS targets: 0.4668990 For a.u. 1 total of 423015 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423015 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423037 grid points filled in, for 422997 unique mappings and 5 attempts to write duplicates and 5 errors out of range and 423036 newly-filled in points and 1 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.93 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846051 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81923 2332 84255 Writing overall R-factor of 0.272 to resolve.rfactor Mask cycle 5 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Using histogram-based mask Assuming this cycle is biased (previous density modification) -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 423378 points (plus the 92842 border points) which can be represented by 17975 continuous rows along x with mean length of 28.7 Refining NCS operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 423384 points (plus the 92892 border points) which can be represented by 17983 continuous rows along x with mean length of 28.7 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: 1.7322e-09 Values of m, alpha, s Centric: 0.66731138321045691 0.3838491 0.5034623 Acentric: 0.64461363710820763 0.4346136 0.4889227 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1001532885255694 RMS in NCS unit : 2: 1.0945932682682267 Average RMS ncs in std crystal: 1.0973733067512512 Including ncs au 1 with rms of 1.1006674927065900 Including ncs au 2 with rms of 1.0951096853536098 RMS rho in NCS region: 1.0978921059139402 Average SD of NCS targets: 0.4668792 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0242514 Values of m, alpha, s Centric: 0.66731844191326828 0.3838547 0.5034637 Acentric: 0.64477561715834530 0.4347756 0.4889551 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1002151563967650 RMS in NCS unit : 2: 1.0947584238785966 Average RMS ncs in std crystal: 1.0974867939949036 Including ncs au 1 with rms of 1.1007306891565982 Including ncs au 2 with rms of 1.0952865388360871 RMS rho in NCS region: 1.0980119881419088 Average SD of NCS targets: 0.4669302 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81922 2332 84254 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0242506 Values of m, alpha, s Centric: 0.66742207421577493 0.3839377 0.5034844 Acentric: 0.64486024866559766 0.4348603 0.4889721 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1003754550736187 RMS in NCS unit : 2: 1.0947357899078618 Average RMS ncs in std crystal: 1.0975555777549744 Including ncs au 1 with rms of 1.1008982144455461 Including ncs au 2 with rms of 1.0952580001896082 RMS rho in NCS region: 1.0980817286406170 Average SD of NCS targets: 0.4669599 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 4 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0242344 Values of m, alpha, s Centric: 0.66737644862765799 0.3839012 0.5034753 Acentric: 0.64493296312872062 0.4349330 0.4889866 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1003983755232709 RMS in NCS unit : 2: 1.0947969170913150 Average RMS ncs in std crystal: 1.0975976586341858 Including ncs au 1 with rms of 1.1009161092155084 Including ncs au 2 with rms of 1.0953247340958019 RMS rho in NCS region: 1.0981239803984457 Average SD of NCS targets: 0.4669778 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 5 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0242407 Values of m, alpha, s Centric: 0.66739093068147748 0.3839127 0.5034782 Acentric: 0.64499535528807916 0.4349953 0.4889991 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1005171268074132 RMS in NCS unit : 2: 1.0947749874127619 Average RMS ncs in std crystal: 1.0976460576057434 Including ncs au 1 with rms of 1.1010414097367747 Including ncs au 2 with rms of 1.0952986950045718 RMS rho in NCS region: 1.0981738061968749 Average SD of NCS targets: 0.4669990 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.64 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.272 to resolve.rfactor Minor cycle 6 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0242204 Values of m, alpha, s Centric: 0.66717916219170503 0.3837433 0.5034359 Acentric: 0.64504147705741932 0.4350415 0.4890083 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1005359751177690 RMS in NCS unit : 2: 1.0948187023511788 Average RMS ncs in std crystal: 1.0976773500442505 Including ncs au 1 with rms of 1.1010556985647604 Including ncs au 2 with rms of 1.0953464867424116 RMS rho in NCS region: 1.0982048027032292 Average SD of NCS targets: 0.4670122 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81924 2332 84256 Writing overall R-factor of 0.271 to resolve.rfactor Minor cycle 7 of 10 Resolution = 1.61 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0242084 Values of m, alpha, s Centric: 0.66708627549819988 0.3836690 0.5034173 Acentric: 0.64508448147856012 0.4350845 0.4890169 Using all points for histograms Fraction protein = 0.530 858280 Fraction solvent= 0.470 760758 Plot 64 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxxo . . . o xo. . . xx xo . . x xoo . p(rho) . xx .xx . . x . x . . x . oxxx . . xx . ooxxxx . . x . oooxxxxx . . x . oooooxxxx . . xo . oooxxxxoo o xxx . xxxxxxo 0.0 o................................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 65 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . oo . . o. o . . o. . . o . o . p(rho) . xxxxo . . x . xx . . x . x . . xo . ox . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo..............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1006342611759883 RMS in NCS unit : 2: 1.0948065960387900 Average RMS ncs in std crystal: 1.0977203845977783 Including ncs au 1 with rms of 1.1011568662322280 Including ncs au 2 with rms of 1.0953316512323072 RMS rho in NCS region: 1.0982481209275237 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4670306 For NCS asym unit 1 the mean target rho is 0.034 +/- 1.095 and the mean uncertainty in it is 0.508 +/- 0.183 For NCS asym unit 2 the mean target rho is 0.034 +/- 1.101 and the mean uncertainty in it is 0.508 +/- 0.183 For a.u. 1 total of 423384 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423384 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423407 grid points filled in, for 423371 unique mappings and 7 attempts to write duplicates and 1 errors out of range and 423407 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 846791 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81924 2332 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.20 0.65 81928 4.6 0.48 0.88 0.89 0.73 0.15 0.89 4137 2.9 0.40 0.89 0.90 0.73 0.11 0.90 11903 2.3 0.21 0.77 0.78 0.72 0.14 0.78 16949 2.0 0.14 0.69 0.70 0.66 0.16 0.70 14217 1.7 0.06 0.48 0.50 0.57 0.21 0.50 24723 1.6 0.03 0.30 0.31 0.42 0.25 0.31 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.61 0.23 0.67 2332 4.6 0.43 0.80 0.81 0.62 0.30 0.81 345 2.9 0.39 0.83 0.84 0.67 0.26 0.84 496 2.3 0.22 0.71 0.72 0.63 0.20 0.72 534 2.0 0.14 0.61 0.62 0.63 0.16 0.62 358 1.7 0.06 0.46 0.47 0.52 0.11 0.47 471 1.6 0.03 0.25 0.26 0.48 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.21 0.65 84260 4.6 0.48 0.88 0.88 0.72 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.73 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.72 0.14 0.78 17483 2.0 0.14 0.69 0.69 0.66 0.16 0.69 14575 1.7 0.06 0.48 0.50 0.57 0.21 0.50 25194 1.6 0.03 0.30 0.31 0.43 0.25 0.31 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.65 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.68 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.33 0.92 10.73 507 0.81 0.92 60 0.80 0.92 7.75 1058 0.89 0.91 91 0.90 0.91 5.96 1884 0.92 0.90 131 0.90 0.90 4.77 1881 0.92 0.89 100 0.89 0.89 4.17 1899 0.82 0.88 74 0.80 0.88 3.58 4133 0.88 0.86 173 0.89 0.86 3.16 4651 0.89 0.85 176 0.89 0.85 2.86 5367 0.89 0.84 187 0.87 0.83 2.62 5570 0.89 0.82 178 0.91 0.82 2.44 6624 0.86 0.81 188 0.87 0.81 2.27 4223 0.76 0.79 104 0.81 0.79 2.15 8006 0.86 0.77 205 0.87 0.77 2.03 8584 0.75 0.76 187 0.70 0.76 1.91 10719 0.76 0.74 212 0.68 0.74 1.79 9039 0.68 0.72 129 0.62 0.72 1.70 7523 0.52 0.70 95 0.36 0.70 1.61 Overall average CC: 0.78749869034798170 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.054 B-value to apply to Fc= 7.626 Overall R-factor for FC vs FP: 0.271 for 84258 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.78 81928 0.63 0.78 2332 0.68 0.78 84260 4.6 0.76 0.80 4137 0.66 0.74 345 0.76 0.80 4482 2.9 0.75 0.78 11903 0.68 0.77 496 0.75 0.78 12399 2.3 0.75 0.81 16949 0.65 0.79 534 0.75 0.81 17483 2.0 0.69 0.78 14217 0.66 0.82 358 0.69 0.78 14575 1.7 0.64 0.77 24723 0.55 0.80 471 0.64 0.77 25194 1.6 0.53 0.71 9999 0.50 0.79 128 0.53 0.71 10127 *** Ending these minor cycles as nothing much is happening *** Mask cycle 6 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Using histogram-based mask Assuming this cycle is biased (previous density modification) -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 423518 points (plus the 92885 border points) which can be represented by 17976 continuous rows along x with mean length of 28.7 Refining NCS operators Defining NCS regions automatically Creating NCS mask... Number of NCS operators in std crystal to use: 2 Asymmetric unit of NCS contains 423519 points (plus the 92652 border points) which can be represented by 17958 continuous rows along x with mean length of 28.7 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: -1.26894e-09 Values of m, alpha, s Centric: 0.66695690639244898 0.3835655 0.5033914 Acentric: 0.64510516973914611 0.4351052 0.4890210 Using all points for histograms Fraction protein = 0.530 858323 Fraction solvent= 0.470 760707 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1006335566529770 RMS in NCS unit : 2: 1.0949748141770064 Average RMS ncs in std crystal: 1.0978041291236877 Including ncs au 1 with rms of 1.1011919496014675 Including ncs au 2 with rms of 1.0955317206301463 RMS rho in NCS region: 1.0983654812433632 Average SD of NCS targets: 0.4670165 For a.u. 1 total of 423519 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423519 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423547 grid points filled in, for 423510 unique mappings and 2 attempts to write duplicates and 2 errors out of range and 423547 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847066 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.271 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0251242 Values of m, alpha, s Centric: 0.66686011887072028 0.3834881 0.5033720 Acentric: 0.64517884985325147 0.4351788 0.4890358 Using all points for histograms Fraction protein = 0.530 858323 Fraction solvent= 0.470 760707 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1007849555377995 RMS in NCS unit : 2: 1.0949431670620466 Average RMS ncs in std crystal: 1.0978640317916870 Including ncs au 1 with rms of 1.1013484189637242 Including ncs au 2 with rms of 1.0955015010107625 RMS rho in NCS region: 1.0984288503746451 Average SD of NCS targets: 0.4670435 For a.u. 1 total of 423519 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423519 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423547 grid points filled in, for 423510 unique mappings and 2 attempts to write duplicates and 2 errors out of range and 423547 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.32 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847066 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81924 2332 84256 Writing overall R-factor of 0.271 to resolve.rfactor Minor cycle 3 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.0251058 Values of m, alpha, s Centric: 0.66684395041512234 0.3834752 0.5033688 Acentric: 0.64521479842537122 0.4352148 0.4890430 Using all points for histograms Fraction protein = 0.530 858323 Fraction solvent= 0.470 760707 Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators RMS in NCS unit : 1: 1.1007967999684225 RMS in NCS unit : 2: 1.0949843672495980 Average RMS ncs in std crystal: 1.0978906154632568 Including ncs au 1 with rms of 1.1013586306353282 Including ncs au 2 with rms of 1.0955419705532068 RMS rho in NCS region: 1.0984541507315015 Average SD of NCS targets: 0.4670542 For a.u. 1 total of 423519 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423519 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423547 grid points filled in, for 423510 unique mappings and 2 attempts to write duplicates and 2 errors out of range and 423547 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847066 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81924 2332 84256 Writing overall R-factor of 0.271 to resolve.rfactor Minor cycle 4 of 10 Resolution = 1.61 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0251235 Values of m, alpha, s Centric: 0.66665247554267204 0.3833220 0.5033305 Acentric: 0.64525541326203573 0.4352554 0.4890511 Using all points for histograms Fraction protein = 0.530 858323 Fraction solvent= 0.470 760707 Plot 66 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxxo . . . o xo. . . xx xo . . x xo . p(rho) . xx .xx . . x . x . . x . oxxx . . ox . ooxxxx . . x . oooxxxxx . . x . oooooxxxx . . xx . oooxxxxoo o xxx . xxxxxxo 0.0 o................................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 67 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . oo . . o. o . . o. . . o . o . p(rho) . xxxxo . . x . xx . . x . x . . xo . ox . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo..............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1009084115677492 RMS in NCS unit : 2: 1.0949566996698958 Average RMS ncs in std crystal: 1.0979325771331787 Including ncs au 1 with rms of 1.1014716591937304 Including ncs au 2 with rms of 1.0955148342723933 RMS rho in NCS region: 1.0984972845023011 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4670726 For NCS asym unit 1 the mean target rho is 0.035 +/- 1.095 and the mean uncertainty in it is 0.508 +/- 0.183 For NCS asym unit 2 the mean target rho is 0.035 +/- 1.101 and the mean uncertainty in it is 0.508 +/- 0.183 For a.u. 1 total of 423519 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423519 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423547 grid points filled in, for 423510 unique mappings and 2 attempts to write duplicates and 2 errors out of range and 423547 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847066 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81924 2332 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.20 0.65 81928 4.6 0.48 0.88 0.89 0.73 0.14 0.89 4137 2.9 0.40 0.89 0.90 0.73 0.11 0.90 11903 2.3 0.21 0.77 0.78 0.72 0.14 0.78 16949 2.0 0.14 0.69 0.70 0.65 0.16 0.70 14217 1.7 0.06 0.49 0.50 0.57 0.21 0.50 24723 1.6 0.03 0.30 0.31 0.42 0.25 0.31 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.60 0.23 0.67 2332 4.6 0.43 0.80 0.81 0.61 0.30 0.81 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.72 0.72 0.61 0.20 0.72 534 2.0 0.14 0.61 0.62 0.62 0.16 0.62 358 1.7 0.06 0.46 0.47 0.52 0.11 0.47 471 1.6 0.03 0.25 0.26 0.44 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.21 0.65 84260 4.6 0.48 0.88 0.88 0.72 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.73 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.72 0.14 0.78 17483 2.0 0.14 0.69 0.69 0.65 0.16 0.69 14575 1.7 0.06 0.48 0.50 0.57 0.21 0.50 25194 1.6 0.03 0.30 0.31 0.42 0.25 0.31 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.65 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.66 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.33 0.92 10.73 507 0.81 0.92 60 0.80 0.92 7.75 1058 0.89 0.91 91 0.90 0.91 5.96 1884 0.92 0.90 131 0.90 0.90 4.77 1881 0.92 0.89 100 0.89 0.89 4.17 1899 0.82 0.88 74 0.80 0.88 3.58 4133 0.88 0.86 173 0.89 0.86 3.16 4651 0.89 0.85 176 0.90 0.85 2.86 5367 0.89 0.84 187 0.87 0.84 2.62 5570 0.89 0.82 178 0.91 0.82 2.44 6624 0.86 0.81 188 0.87 0.81 2.27 4223 0.76 0.79 104 0.81 0.79 2.15 8006 0.86 0.77 205 0.87 0.77 2.03 8584 0.75 0.76 187 0.69 0.76 1.91 10719 0.76 0.74 212 0.68 0.74 1.79 9039 0.68 0.72 129 0.61 0.72 1.70 7523 0.52 0.70 95 0.36 0.70 1.61 Overall average CC: 0.78751103480182982 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.053 B-value to apply to Fc= 7.629 Overall R-factor for FC vs FP: 0.271 for 84258 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.78 81928 0.63 0.78 2332 0.68 0.78 84260 4.6 0.76 0.80 4137 0.66 0.74 345 0.75 0.79 4482 2.9 0.75 0.78 11903 0.69 0.77 496 0.75 0.78 12399 2.3 0.75 0.81 16949 0.64 0.79 534 0.74 0.81 17483 2.0 0.69 0.77 14217 0.63 0.82 358 0.69 0.77 14575 1.7 0.64 0.77 24723 0.55 0.80 471 0.63 0.77 25194 1.6 0.53 0.71 9999 0.52 0.80 128 0.53 0.71 10127 *** Ending these minor cycles as nothing much is happening *** Mask cycle 7 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Using histogram-based mask Assuming this cycle is biased (previous density modification) Plot 68 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 ....................................xxxxxxxxxxxxxx . + xxx . . + xx . . + xx . . + x . . + xx . . +x . p(protein) . x . 0.5 . x+ . . x + . . x + . . xx + . . x + . . xx + . . xxx + . 0.0 .xxxxxxxxxxxx...........+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0038 Y + 0.0023 Z + 82.4154 New Y-prime= 0.0038 X + -1.0000 Y + 0.0031 Z + 50.5345 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.2631 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.10 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0038 Y + 0.0023 Z + 82.2262 New Y-prime= -0.0038 X + -1.0000 Y + 0.0031 Z + 50.8453 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.0802 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0038 0.0023 rota_matrix -0.0038 -1.0000 0.0031 rota_matrix 0.0023 0.0030 1.0000 tran_orth 82.2262 50.8453 -0.0802 center_orth 88.1034 7.8844 65.6164 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.15068 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 4.62 95091 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.82 63677 17.3 3.45 231387 25.4 1.43 514760 33.4 1.23 805030 41.5 1.75 908023 49.2 1.64 524858 56.6 1.91 123538 63.3 2.74 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.67 which is very good. The fall-off of the overlap has a characteristic length of 276.0 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 52.3% of asymmetric unit used in NCS with 26.1% within molecule 1 and 26.1% in NCS-related molecules. Cutoff in used in identifying NCS = 1.27 Asymmetric unit of NCS contains 423524 points (plus the 92016 border points) which can be represented by 17683 continuous rows along x with mean length of 29.2 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.95 Final overall correlation of NCS is: 0.95 Refined NCS operators: Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0038 Y + 0.0023 Z + 82.4154 New Y-prime= 0.0038 X + -1.0000 Y + 0.0031 Z + 50.5345 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.2631 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.10 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0038 Y + 0.0023 Z + 82.2262 New Y-prime= -0.0038 X + -1.0000 Y + 0.0031 Z + 50.8453 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.0802 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0038 0.0023 rota_matrix -0.0038 -1.0000 0.0031 rota_matrix 0.0023 0.0030 1.0000 tran_orth 82.2262 50.8453 -0.0802 center_orth 88.1035 7.8845 65.6164 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 43.15068 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 4.62 95091 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.82 63677 17.3 3.45 231387 25.4 1.43 514760 33.4 1.23 805030 41.5 1.75 908023 49.2 1.64 524858 56.6 1.91 123538 63.3 2.74 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.67 which is very good. The fall-off of the overlap has a characteristic length of 276.0 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2650000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 52.3% of asymmetric unit used in NCS with 26.1% within molecule 1 and 26.1% in NCS-related molecules. Cutoff in used in identifying NCS = 1.27 Asymmetric unit of NCS contains 423522 points (plus the 92007 border points) which can be represented by 17683 continuous rows along x with mean length of 29.2 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Using NCS or image this mask cycle Minor cycle 1 of 10 Resolution = 1.61 Offset for s_rho_cur: 1.54762e-10 Values of m, alpha, s Centric: 0.66670101368463464 0.3833608 0.5033402 Acentric: 0.64528722501747793 0.4352872 0.4890575 Using all points for histograms Fraction protein = 0.530 858416 Fraction solvent= 0.470 760647 Plot 69 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxoo . . . o xxo. . . xxo xo . . x xo . p(rho) . xx .xx . . x . x . . x . oxxx . . ox . ooxxxx . . x . oooxxxxx . . x . oooooxxxx . . xx . oooxxxxoo o xxx . xxxxxxo 0.0 o................................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 70 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . oo . . o. o . . o. . . o . o . p(rho) . xxxxo . . x . xx . . x . x . . xo . ox . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo..............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1010315041946011 RMS in NCS unit : 2: 1.0951847659951519 Average RMS ncs in std crystal: 1.0981081724166870 Including ncs au 1 with rms of 1.1016157439583281 Including ncs au 2 with rms of 1.0957583188160478 RMS rho in NCS region: 1.0986909348382357 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4669139 For NCS asym unit 1 the mean target rho is 0.036 +/- 1.095 and the mean uncertainty in it is 0.508 +/- 0.183 For NCS asym unit 2 the mean target rho is 0.035 +/- 1.101 and the mean uncertainty in it is 0.508 +/- 0.183 For a.u. 1 total of 423522 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423522 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423549 grid points filled in, for 423510 unique mappings and 5 attempts to write duplicates and 2 errors out of range and 423549 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847071 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 81925 2332 84257 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.20 0.65 81928 4.6 0.48 0.88 0.89 0.73 0.14 0.89 4137 2.9 0.40 0.89 0.90 0.73 0.11 0.90 11903 2.3 0.21 0.77 0.78 0.72 0.14 0.78 16949 2.0 0.14 0.69 0.70 0.65 0.16 0.70 14217 1.7 0.06 0.49 0.50 0.57 0.21 0.50 24723 1.6 0.03 0.30 0.31 0.42 0.25 0.31 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.60 0.23 0.67 2332 4.6 0.43 0.80 0.80 0.61 0.30 0.80 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.72 0.72 0.63 0.20 0.72 534 2.0 0.14 0.61 0.62 0.62 0.16 0.62 358 1.7 0.06 0.46 0.47 0.51 0.11 0.47 471 1.6 0.03 0.25 0.26 0.45 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.21 0.65 84260 4.6 0.48 0.88 0.88 0.72 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.72 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.72 0.14 0.78 17483 2.0 0.14 0.69 0.69 0.65 0.16 0.69 14575 1.7 0.06 0.48 0.50 0.57 0.21 0.50 25194 1.6 0.03 0.30 0.31 0.42 0.25 0.31 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.65 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.66 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.32 0.92 10.73 507 0.81 0.92 60 0.80 0.92 7.75 1058 0.89 0.91 91 0.90 0.91 5.96 1884 0.92 0.90 131 0.90 0.90 4.77 1881 0.92 0.89 100 0.89 0.89 4.17 1899 0.82 0.88 74 0.80 0.88 3.58 4133 0.88 0.86 173 0.89 0.86 3.16 4651 0.89 0.85 176 0.90 0.85 2.86 5367 0.89 0.84 187 0.87 0.83 2.62 5570 0.89 0.82 178 0.90 0.82 2.44 6624 0.86 0.81 188 0.88 0.81 2.27 4223 0.76 0.79 104 0.81 0.79 2.15 8006 0.86 0.77 205 0.87 0.77 2.03 8584 0.75 0.76 187 0.69 0.76 1.91 10719 0.76 0.74 212 0.68 0.74 1.79 9039 0.68 0.72 129 0.61 0.72 1.70 7523 0.52 0.70 95 0.36 0.70 1.61 Overall average CC: 0.78749412697002852 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.052 B-value to apply to Fc= 7.630 Overall R-factor for FC vs FP: 0.271 for 84258 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.78 81928 0.63 0.78 2332 0.68 0.78 84260 4.6 0.76 0.80 4137 0.68 0.74 345 0.75 0.79 4482 2.9 0.75 0.78 11903 0.69 0.77 496 0.75 0.78 12399 2.3 0.75 0.81 16949 0.65 0.80 534 0.74 0.81 17483 2.0 0.69 0.77 14217 0.63 0.82 358 0.69 0.77 14575 1.7 0.63 0.77 24723 0.56 0.80 471 0.63 0.77 25194 1.6 0.53 0.71 9999 0.52 0.80 128 0.53 0.71 10127 Minor cycle 2 of 10 Resolution = 1.61 Offset for s_rho_cur: -0.025496 Values of m, alpha, s Centric: 0.66639874142563282 0.3831190 0.5032797 Acentric: 0.64534326437404854 0.4353433 0.4890687 Using all points for histograms Fraction protein = 0.530 858416 Fraction solvent= 0.470 760647 Plot 71 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxxo . . . o xo. . . xxo xo . . x xo . p(rho) . xx .xx . . x . x . . x . oxxx . . ox . ooxxxx . . x . oooxxxxx . . x . oooooxxxx . . xx . oooxxxxoo o xxx . xxxxxxo 0.0 o................................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 72 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . oo . . o. o . . o. . . o . o . p(rho) . xxxxo . . x . xx . . x . x . . xo . ox . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo..............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1011616985264032 RMS in NCS unit : 2: 1.0951667773982485 Average RMS ncs in std crystal: 1.0981642603874207 Including ncs au 1 with rms of 1.1017481186368749 Including ncs au 2 with rms of 1.0957426483932027 RMS rho in NCS region: 1.0987494865590708 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4669388 For NCS asym unit 1 the mean target rho is 0.036 +/- 1.095 and the mean uncertainty in it is 0.508 +/- 0.183 For NCS asym unit 2 the mean target rho is 0.036 +/- 1.101 and the mean uncertainty in it is 0.508 +/- 0.183 For a.u. 1 total of 423522 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423522 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423549 grid points filled in, for 423510 unique mappings and 5 attempts to write duplicates and 2 errors out of range and 423549 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847071 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81924 2332 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.20 0.65 81928 4.6 0.48 0.88 0.89 0.73 0.14 0.89 4137 2.9 0.40 0.89 0.90 0.73 0.11 0.90 11903 2.3 0.21 0.77 0.78 0.72 0.14 0.78 16949 2.0 0.14 0.69 0.70 0.65 0.16 0.70 14217 1.7 0.06 0.49 0.50 0.57 0.21 0.50 24723 1.6 0.03 0.30 0.31 0.42 0.25 0.31 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.60 0.23 0.67 2332 4.6 0.43 0.80 0.81 0.62 0.30 0.81 345 2.9 0.39 0.83 0.84 0.68 0.26 0.84 496 2.3 0.22 0.72 0.72 0.61 0.20 0.72 534 2.0 0.14 0.61 0.62 0.63 0.16 0.62 358 1.7 0.06 0.46 0.47 0.51 0.11 0.47 471 1.6 0.03 0.24 0.26 0.46 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.21 0.65 84260 4.6 0.48 0.88 0.88 0.72 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.72 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.72 0.14 0.78 17483 2.0 0.14 0.69 0.69 0.65 0.16 0.69 14575 1.7 0.06 0.48 0.50 0.57 0.21 0.50 25194 1.6 0.03 0.30 0.31 0.42 0.25 0.31 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.65 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.66 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.33 0.92 10.73 507 0.81 0.92 60 0.80 0.92 7.75 1058 0.89 0.91 91 0.90 0.91 5.96 1884 0.92 0.90 131 0.90 0.90 4.77 1881 0.92 0.89 100 0.89 0.89 4.17 1899 0.82 0.88 74 0.80 0.88 3.58 4133 0.88 0.86 173 0.89 0.86 3.16 4651 0.89 0.85 176 0.90 0.85 2.86 5367 0.89 0.84 187 0.87 0.84 2.62 5570 0.89 0.82 178 0.91 0.82 2.44 6624 0.86 0.81 188 0.88 0.81 2.27 4223 0.77 0.79 104 0.81 0.79 2.15 8006 0.86 0.77 205 0.87 0.77 2.03 8584 0.75 0.76 187 0.70 0.76 1.91 10719 0.76 0.74 212 0.68 0.74 1.79 9039 0.68 0.72 129 0.61 0.72 1.70 7523 0.52 0.70 95 0.36 0.70 1.61 Overall average CC: 0.78747846842032843 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.052 B-value to apply to Fc= 7.631 Overall R-factor for FC vs FP: 0.271 for 84258 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.78 81928 0.63 0.78 2332 0.67 0.78 84260 4.6 0.76 0.80 4137 0.66 0.74 345 0.75 0.79 4482 2.9 0.75 0.78 11903 0.69 0.77 496 0.74 0.78 12399 2.3 0.75 0.81 16949 0.64 0.79 534 0.74 0.81 17483 2.0 0.69 0.77 14217 0.62 0.82 358 0.69 0.77 14575 1.7 0.63 0.77 24723 0.55 0.80 471 0.63 0.77 25194 1.6 0.53 0.71 9999 0.53 0.80 128 0.53 0.71 10127 Minor cycle 3 of 10 Resolution = 1.61 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0254811 Values of m, alpha, s Centric: 0.66651752667227482 0.3832140 0.5033035 Acentric: 0.64537472268152407 0.4353747 0.4890749 Using all points for histograms Fraction protein = 0.530 858416 Fraction solvent= 0.470 760647 Plot 73 Plot of Observed (o) and model (x) electron density distributions for protein region, where the model distribution is given by, p_model(beta*(rho+offset)) = p_ideal(rho) and then convoluted with a gaussian with width of sigma where sigma, offset and beta are given below under "Error estimate." 0.03.................................................. . . . . xxx . . . xxoooxxo . . . o xo. . . xx xo . . x xo . p(rho) . xx .xxo . . x . x . . x . oxxx . . ox . ooxxxx . . x . oooxxxxx . . x . oooooxxxx . . x . oooxxxxoo o xxx . xxxxxxo 0.0 o................................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 74 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.10.................................................. . . . . . . . oo . . o. o . . o. . . o . o . p(rho) . xxxxo . . x . xx . . x . x . . xo . ox . . xo . ox . . xxo . ox . . x o . o x . . xxoo . ooxxx . 0.0 xxxxxxxxxxxoo..............oooxxxxxxxxxxxxxxxxxxxx -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Setting up NCS information for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Correlations of NCS regions : Correlation of NCS molecules 1 and 2 = 0.95 RMS in NCS unit : 1: 1.1011680832461703 RMS in NCS unit : 2: 1.0951987996703416 Average RMS ncs in std crystal: 1.0981833934783936 Including ncs au 1 with rms of 1.1017533653567748 Including ncs au 2 with rms of 1.0957733205657609 RMS rho in NCS region: 1.0987674112701680 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.89 Normalized rms error est from solvent/protein= 0.37 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.4669464 For NCS asym unit 1 the mean target rho is 0.036 +/- 1.095 and the mean uncertainty in it is 0.508 +/- 0.183 For NCS asym unit 2 the mean target rho is 0.035 +/- 1.101 and the mean uncertainty in it is 0.508 +/- 0.183 For a.u. 1 total of 423522 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 423522 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 423549 grid points filled in, for 423510 unique mappings and 5 attempts to write duplicates and 2 errors out of range and 423549 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 Error estimate for map on this cycle The estimated error in this map is 0.31 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.11 and 0.29 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 0.94 offset is -0.31 and sigma is a random variable with rms value of 0.31 Number of points with protein histograms included: 847071 Mean starting figure of merit this cycle Overall Centric Acentric 0.65 0.67 0.65 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.01 0.00 81925 2331 84256 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.20 0.65 81928 4.6 0.48 0.88 0.89 0.73 0.14 0.89 4137 2.9 0.40 0.89 0.90 0.73 0.11 0.90 11903 2.3 0.21 0.77 0.78 0.72 0.14 0.78 16949 2.0 0.14 0.69 0.70 0.65 0.16 0.70 14217 1.7 0.06 0.49 0.50 0.57 0.21 0.50 24723 1.6 0.03 0.30 0.31 0.42 0.25 0.31 9999 WGT: 1.00 1.00 Centric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.23 0.66 0.67 0.60 0.23 0.67 2332 4.6 0.43 0.80 0.81 0.62 0.29 0.81 345 2.9 0.39 0.83 0.84 0.67 0.26 0.84 496 2.3 0.22 0.72 0.72 0.63 0.20 0.72 534 2.0 0.14 0.61 0.62 0.63 0.16 0.62 358 1.7 0.06 0.46 0.47 0.51 0.11 0.47 471 1.6 0.03 0.24 0.26 0.45 0.11 0.26 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.17 0.64 0.65 0.63 0.21 0.65 84260 4.6 0.48 0.88 0.88 0.72 0.16 0.88 4482 2.9 0.40 0.89 0.89 0.72 0.12 0.89 12399 2.3 0.21 0.77 0.78 0.72 0.14 0.78 17483 2.0 0.14 0.69 0.70 0.65 0.16 0.70 14575 1.7 0.06 0.48 0.50 0.57 0.21 0.50 25194 1.6 0.03 0.30 0.31 0.42 0.25 0.31 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.65 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.21 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.79 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 5.65 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 258 0.61 0.92 42 0.32 0.92 10.73 507 0.81 0.92 60 0.79 0.92 7.75 1058 0.89 0.91 91 0.90 0.91 5.96 1884 0.92 0.90 131 0.90 0.90 4.77 1881 0.92 0.89 100 0.89 0.89 4.17 1899 0.82 0.88 74 0.80 0.88 3.58 4133 0.88 0.86 173 0.89 0.86 3.16 4651 0.89 0.85 176 0.90 0.85 2.86 5367 0.89 0.84 187 0.87 0.84 2.62 5570 0.89 0.82 178 0.90 0.82 2.44 6624 0.86 0.81 188 0.88 0.81 2.27 4223 0.77 0.79 104 0.81 0.79 2.15 8006 0.86 0.77 205 0.87 0.77 2.03 8584 0.75 0.76 187 0.69 0.76 1.91 10719 0.76 0.74 212 0.68 0.74 1.79 9039 0.68 0.72 129 0.61 0.72 1.70 7523 0.52 0.70 95 0.36 0.70 1.61 Overall average CC: 0.78750984195908358 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.051 B-value to apply to Fc= 7.631 Overall R-factor for FC vs FP: 0.271 for 84258 reflections Writing overall R-factor of 0.271 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.68 0.78 81928 0.63 0.78 2332 0.67 0.78 84260 4.6 0.76 0.80 4137 0.66 0.74 345 0.75 0.79 4482 2.9 0.75 0.78 11903 0.68 0.77 496 0.74 0.78 12399 2.3 0.75 0.81 16949 0.65 0.80 534 0.74 0.81 17483 2.0 0.69 0.77 14217 0.63 0.82 358 0.68 0.77 14575 1.7 0.63 0.77 24723 0.55 0.80 471 0.63 0.77 25194 1.6 0.53 0.71 9999 0.52 0.80 128 0.53 0.71 10127 *** Ending these minor cycles as nothing much is happening *** Writing out 13 columns of data CC of prob map with current map: 0.8243568 -------------------------------------- Getting Final NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators Final refined NCS operators: Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0038 Y + 0.0023 Z + 82.4154 New Y-prime= 0.0038 X + -1.0000 Y + 0.0031 Z + 50.5345 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.2631 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.10 7.88 65.62 and as input by user is, 88.10 7.88 65.62 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + -0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -1.0000 X + 0.0038 Y + 0.0023 Z + 82.2262 New Y-prime= -0.0038 X + -1.0000 Y + 0.0031 Z + 50.8453 New Z-prime= 0.0023 X + 0.0030 Y + 1.0000 Z + -0.0802 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 -0.0000 -0.0000 center_orth -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0038 0.0023 rota_matrix -0.0038 -1.0000 0.0031 rota_matrix 0.0023 0.0030 1.0000 tran_orth 82.2262 50.8453 -0.0802 center_orth 88.1035 7.8845 65.6164 Analysis of NC symmetry using cutoff of 0.80 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 41.205 25.358 65.691 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/aaa_resolve_main.cpp source_line: 1670 status: 0 EndOfResolve