------------------------ 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 exptl_phases_and_amplitudes_for_density_modification_aniso.mtz Data to be read from mtz file: exptl_phases_and_amplitudes_for_density_modification_aniso.mtz >labin FP=FP SIGFP=SIGFP Current value of "LABIN" is: labin FP=FP SIGFP=SIGFP >hklout resolve_work.mtz Data to be written to mtz file: resolve_work.mtz >solvent_content 0.47 Fraction of unit cell assumed to be solvent is: 0.4700000 >no_build Model will not be built >mask_cycles 0 Number of mask/image cycles: 0 >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 >seq_file seq_from_file.dat Sequence file: seq_from_file.dat Expecting 1-letter aa sequence of chains, chains separated by lines starting with ">" >image Image reconstruction will be used >composite_all All files in composite used equally >scale_refl 0.2 Overall scale on map is 0.2000000 * 2 * nrefl * n_used/n_asym_unit >composite_pdb refine.pdb_ PDB file template for creating composite map: refine.pdb_ >composite_pdb_first 1 First PDB file to consider in composite: 1 >composite_pdb_last 1 Number of last PDB file in composite: 1 >pdb_in refine.pdb_1 Name of input PDB file (to be used to initiate model-building): refine.pdb_1 If "no_reuse_model" is not set then this model will also be used as starting point for model-building >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 >hklstart image_only_dm.mtz Starting phases (but not probabilities) read from mtz file: image_only_dm.mtz >labstart FP=FWT PHIB=PHWT Current value of "LABSTART" is: labin FP=FWT PHIB=PHWT >n_xyz 120 150 180 Grid units x y z: 120 150 180 >database 5 Entry in database of histograms to use: 5 >use_any_side Best-fitting side chains used if no sequence alignment >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 Setting up PDB files for composite map Range of file numbers: 1 to 1 File 1 is refine.pdb_1 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 exptl_phases_and_amplitudes_for_density_modification_aniso.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 exptl_phases_and_amplitudes_for_density_modification_aniso.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 DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD 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 Note: not using either PHIB or PHIC 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 Reading (image_only_dm.mtz ) to get limits of reflection indices Opened mtz file image_only_dm.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 Cell dimensions for this dataset vs original: 1 : 59.554 :: 59.554 2 : 79.206 :: 79.206 3 : 87.43 :: 87.43 4 : 90 :: 90 5 : 92.26 :: 92.26 6 : 90 :: 90 Column assignments: PROGRAM INPUT_MTZ DATA# 1 H DATA# 2 K DATA# 3 L DATA# 4 FP : FWT DATA# 5 PHIB : PHWT DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP : SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 12 PHIB taken from column 13 Total of 84260 reflections read from file 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: 0.00 Copy to group 1 2 Opened mtz file image_only_dm.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 Cell dimensions for this dataset vs original: 1 : 59.554 :: 59.554 2 : 79.206 :: 79.206 3 : 87.43 :: 87.43 4 : 90 :: 90 5 : 92.26 :: 92.26 6 : 90 :: 90 Column assignments: PROGRAM INPUT_MTZ DATA# 1 H DATA# 2 K DATA# 3 L DATA# 4 FP : FWT DATA# 5 PHIB : PHWT DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP : SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 12 PHIB taken from column 13 Total of 84260 reflections read from file Adding F000 term (0.0) to this list Closed mtz file Getting phases and fom from mtz file image_only_dm.mtz Total of 84253 reflns taken from this file Scaling refl_struct_0.refl to match refl_orig: 1.000000 0.000000 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 13.80 1.00 1.00 300 8.79 1.00 1.00 567 6.66 1.00 1.00 1149 5.26 1.00 1.00 2015 4.44 1.00 1.00 1983 3.90 1.00 1.00 1973 3.35 1.00 1.00 4306 3.00 1.00 1.00 4827 2.73 1.00 1.00 5554 2.53 1.00 1.00 5748 2.36 1.00 1.00 6812 2.19 1.00 1.00 4327 2.08 1.00 1.00 8211 1.97 1.00 1.00 8771 1.84 1.00 1.00 10931 1.74 1.00 1.00 9164 1.66 1.00 1.00 7615 Mean fom of this map was: 1.00 Starting phases assumed to be density-modified (To override, use "phases_from_solve") Setting starting smoothing radius to 4.000000 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" Composite map to be derived from 1 pdb files Opening refine.pdb_1 and reading coordinates Center of molecule read in with 6157 atoms is 41.766254 24.949341 65.116585 Read 6157 atoms from PDB file for use in model-based phasing:refine.pdb_1 NOTE: Skipping reordering of residue 631 as it is does not have a complete main chain NOTE: Skipping reordering of residue 430 as it is does not have a complete main chain NOTE: Skipping reordering of residue 632 as it is does not have a complete main chain NOTE: Skipping reordering of residue 430 as it is does not have a complete main chain Getting FCALC from model Overall average CC: 0.66465789467138769 Using average of all 1 useable maps; overall CC estimate: 0.6646579 Correlation of input PDB models used in composite map Weight Map 1 1 0.66 1.00 0.66 Getting FCALC from model Adding solvent model to FCALC Mean of prot, solv in FC map: 0.2177363 2.7791245E-06 Mean of prot, solv in solv map: 2.2198368E-02 0.1579320 Multiplying solvent * 0.6646579 to get solvent density = 0.1049707 CC of composite map with input: 0.7432241 CC in recovered region is 0.7925375 n= 954668 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 ----------------------------------------------------------------- ----------------------------------------------------------------- -------------------------------------- Opening refine.pdb_1 and reading coordinates Center of molecule read in with 6045 atoms is 41.974667 24.792036 65.129456 Read 6045 atoms from PDB file for use in model-building refine.pdb_1 Adding extra mask cycle at end to include model information Solvent content will be 0.47 Using database entry 5 for histograms (" 3 A dehalogenase model ") Total mask cycles: 1 Total density modification mask cycles: 1 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 NO YES NO YES YES NO 3 Mask cycle 1 Weighting this cycle: 0.2000000 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 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 ....................................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 + -0.0042 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 4.46 95066 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.66 63677 17.3 3.33 231387 25.4 1.38 514760 33.4 1.17 805030 41.5 1.66 908023 49.2 1.54 524858 56.6 1.78 123538 63.3 2.54 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.62 which is very good. The fall-off of the overlap has a characteristic length of 159.7 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 52.2% 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 = 0.94 Asymmetric unit of NCS contains 422581 points (plus the 99554 border points) which can be represented by 19327 continuous rows along x with mean length of 27.0 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.93 Final overall correlation of NCS is: 0.93 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 + -0.0034 Y + 0.0024 Z + 82.3966 New Y-prime= 0.0034 X + -1.0000 Y + 0.0026 Z + 50.5647 New Z-prime= 0.0024 X + 0.0025 Y + 1.0000 Z + -0.2419 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 + 0.0034 Y + 0.0024 Z + 82.2255 New Y-prime= -0.0034 X + -1.0000 Y + 0.0026 Z + 50.8459 New Z-prime= 0.0024 X + 0.0025 Y + 1.0000 Z + -0.0810 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 0.0034 0.0024 rota_matrix -0.0034 -1.0000 0.0026 rota_matrix 0.0024 0.0025 1.0000 tran_orth 82.2255 50.8459 -0.0810 center_orth 88.1034 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 0.001 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: 43.15074 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 4.46 95093 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.66 63677 17.3 3.33 231387 25.4 1.38 514760 33.4 1.19 805030 41.5 1.69 908023 49.2 1.58 524858 56.6 1.83 123538 63.3 2.68 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.61 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 52.2% 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 = 0.94 Asymmetric unit of NCS contains 422621 points (plus the 101916 border points) which can be represented by 19980 continuous rows along x with mean length of 26.3 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 3 Resolution = 1.61 Offset for s_rho_cur: -1.66747e-09 Values of m, alpha, s Centric: 1.0000000000000000 0.9439998 7.0000269E-02 Acentric: 0.99991455912508542 0.9799999 6.0000230E-02 Using all points for histograms Fraction protein = 0.529 854714 Fraction solvent= 0.471 760059 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." 0.03.................................................. . . . . xx . . . xxooxxoo . . . xo xooo . . x xxoo . . ox xxoo . p(rho) . x .xoo . . x . xo . . oxx . xxx . . x . xxxx . . xx . ooxxxxxxxx . . ox . oooooo xxxxxx o .oxx . oooooooxxxxx . xx . oooxo 0.0 x................................................x -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 0.09.................................................. . . . . . . . xx . . x. x . . xo. x . . o . x . p(rho) . x . x . . x . o . . x . x . . x . x . . x . x . . x . x . . xx . x . . ox . xx . 0.0 xxxxxxxxxxxxx...............oxxxxxxxxxxxxxxxxxxxxx -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: 1.1928104516677254 RMS in NCS unit : 2: 1.1859154910952889 Average RMS ncs in std crystal: 1.1893629431724548 Including ncs au 1 with rms of 1.1935121218168070 Including ncs au 2 with rms of 1.1865513046679395 RMS rho in NCS region: 1.1900368026941111 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.93 Normalized rms error est from solvent/protein= 0.17 Normalized rms error est of NCS= 0.19 Average SD of NCS targets: 0.4175789 For NCS asym unit 1 the mean target rho is 0.041 +/- 1.186 and the mean uncertainty in it is 0.505 +/- 0.243 For NCS asym unit 2 the mean target rho is 0.039 +/- 1.193 and the mean uncertainty in it is 0.505 +/- 0.243 For a.u. 1 total of 422621 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 422621 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 422643 grid points filled in, for 422609 unique mappings and 3 attempts to write duplicates and 3 errors out of range and 422643 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 RMS CALC, OBS: 0.4097544 1.123846 954509 Scale on recov to minimize (recov-obs)**2: 1.844514 Actual scale on recov used: 1.844514 Resulting scale * rms obs (recov)= 0.7557976 Comparison of image and map: RMS map= 1.12 RMSD between image and map is: 0.83 CC of image and map= 0.79 Overall CC of model FC and obs FO, corrected for fraction of non-solvent region covered by model: 0.6646579 Overall RMSD estimated from rms of current map * *std::sqrt(1.-cc_overall_est**2) Resulting estimate of RMSD taken from from CC of Fo Fc: 0.8396789 Final RMSD used for image target: 0.839679 Image information used in phasing: Number of points with... image based on model: 190069 image + NCS 764440 image only: 0 no information: 665491 total in au: 1620000 MAP RMS and SIG: 0.517 0.840 190069 Error estimate for map on this cycle The estimated error in this map is 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.20 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 = 1.16 offset is -0.19 and sigma is a random variable with rms value of 0.20 Number of points with protein histograms included: 1035333 Mean starting figure of merit this cycle Overall Centric Acentric 1.00 1.00 1.00 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.55 0.50 0.55 81920 2331 84251 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: 0.00 0.46 0.46 0.00 0.00 0.46 81928 4.6 0.00 0.74 0.74 0.00 0.00 0.74 4137 2.9 0.00 0.75 0.75 0.00 0.00 0.75 11903 2.3 0.00 0.58 0.58 0.00 0.00 0.58 16949 2.0 0.00 0.48 0.48 0.00 0.00 0.48 14217 1.7 0.00 0.30 0.30 0.00 0.00 0.30 24723 1.6 0.00 0.18 0.18 0.00 0.00 0.18 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: 0.00 0.50 0.50 0.00 0.00 0.50 2332 4.6 0.00 0.66 0.66 0.00 0.00 0.66 345 2.9 0.00 0.69 0.69 0.00 0.00 0.69 496 2.3 0.00 0.55 0.55 0.00 0.00 0.55 534 2.0 0.00 0.43 0.43 0.00 0.00 0.43 358 1.7 0.00 0.28 0.28 0.00 0.00 0.28 471 1.6 0.00 0.14 0.14 0.00 0.01 0.14 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.00 0.46 0.46 0.00 0.00 0.46 84260 4.6 0.00 0.74 0.74 0.00 0.00 0.74 4482 2.9 0.00 0.75 0.75 0.00 0.00 0.75 12399 2.3 0.00 0.57 0.57 0.00 0.00 0.57 17483 2.0 0.00 0.47 0.47 0.00 0.00 0.47 14575 1.7 0.00 0.30 0.30 0.00 0.00 0.30 25194 1.6 0.00 0.18 0.18 0.00 0.00 0.18 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.46 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.00 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 1.00 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 0.00 * * * * 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 0.94 42 0.40 0.94 10.73 507 0.84 0.93 59 0.80 0.94 7.75 1058 0.90 0.93 91 0.90 0.93 5.96 1882 0.92 0.92 131 0.91 0.92 4.77 1878 0.92 0.91 100 0.90 0.91 4.17 1898 0.84 0.90 74 0.82 0.90 3.58 4132 0.89 0.88 173 0.90 0.88 3.16 4651 0.90 0.87 176 0.90 0.87 2.86 5367 0.90 0.85 187 0.88 0.85 2.62 5570 0.90 0.84 178 0.92 0.84 2.44 6624 0.87 0.82 188 0.89 0.82 2.27 4223 0.79 0.80 104 0.84 0.80 2.15 8006 0.87 0.79 205 0.87 0.79 2.03 8584 0.78 0.77 187 0.74 0.77 1.91 10719 0.78 0.75 212 0.71 0.75 1.79 9039 0.71 0.73 129 0.65 0.73 1.70 7523 0.54 0.71 95 0.38 0.71 1.61 Overall average CC: 0.80427336243988856 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.217 B-value to apply to Fc= 2.798 Overall R-factor for FC vs FP: 0.246 for 84250 reflections Writing overall R-factor of 0.246 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 -0.00 -0.00 81928 0.02 -0.01 2332 -0.00 -0.00 84260 4.6 -0.01 -0.01 4137 -0.02 -0.10 345 -0.01 -0.02 4482 2.9 -0.00 0.00 11903 -0.01 0.01 496 -0.00 0.00 12399 2.3 0.01 0.00 16949 0.07 0.02 534 0.01 0.00 17483 2.0 -0.00 -0.01 14217 -0.01 -0.00 358 -0.00 -0.01 14575 1.7 -0.00 -0.01 24723 0.02 0.01 471 -0.00 -0.01 25194 1.6 -0.01 -0.01 9999 0.08 0.13 128 -0.01 -0.01 10127 End of first cycle ____________________________________________________________ Minor cycle 2 of 3 Resolution = 1.61 Offset for s_rho_cur: -0.0260688 Values of m, alpha, s Centric: 0.50107852274607112 0.2706471 0.4306471 Acentric: 0.46087576574882166 0.2687006 0.4165255 Using all points for histograms Fraction protein = 0.529 854714 Fraction solvent= 0.471 760059 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." 0.03.................................................. . . . . xx . . . xooxxo . . . xxo xo. . . o xo . . x xo . p(rho) . x .xx . . x . x . . x . xxx . . xx . oxxxx . . ox . ooxxxxx . . xx . ooooxxxxx . . xx . ooxxxxoo . .xxxx . xxxxxxoo 0.0 xx..............................................xx -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 0.09.................................................. . . . . . . . oo . . o. o . . xxxo . . ox. x . p(rho) . x . x . . x . x . . o . x . . xo . ox . . o . ox . . xo . ox . . xxo . oxx . . xxoo . oxxx . 0.0 xxxxxxxxxxxo................oxxxxxxxxxxxxxxxxxxxxx -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: 0.99229193738294708 RMS in NCS unit : 2: 0.98783949577640695 Average RMS ncs in std crystal: 0.99006572365760803 Including ncs au 1 with rms of 0.99306150797028803 Including ncs au 2 with rms of 0.98853319809665119 RMS rho in NCS region: 0.99079994003618488 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.93 Normalized rms error est from solvent/protein= 0.27 Normalized rms error est of NCS= 0.00 Average SD of NCS targets: 0.3476676 For NCS asym unit 1 the mean target rho is 0.039 +/- 0.988 and the mean uncertainty in it is 0.420 +/- 0.203 For NCS asym unit 2 the mean target rho is 0.037 +/- 0.992 and the mean uncertainty in it is 0.420 +/- 0.203 For a.u. 1 total of 422621 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 422621 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 422643 grid points filled in, for 422609 unique mappings and 3 attempts to write duplicates and 3 errors out of range and 422643 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 RMS CALC, OBS: 1.015824 0.9355742 954509 Scale on recov to minimize (recov-obs)**2: 0.8366082 Actual scale on recov used: 0.8366082 Resulting scale * rms obs (recov)= 0.8498465 Comparison of image and map: RMS map= 0.94 RMSD between image and map is: 0.39 CC of image and map= 0.92 Overall CC of model FC and obs FO, corrected for fraction of non-solvent region covered by model: 0.6646579 Overall RMSD estimated from rms of current map * *std::sqrt(1.-cc_overall_est**2) Resulting estimate of RMSD taken from from CC of Fo Fc: 0.6990122 Final RMSD used for image target: 0.699012 Image information used in phasing: Number of points with... image based on model: 190069 image + NCS 764440 image only: 0 no information: 665491 total in au: 1620000 MAP RMS and SIG: 0.433 0.699 190069 Error estimate for map on this cycle The estimated error in this map is 0.27 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 1.00 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 = 0.92 offset is -0.25 and sigma is a random variable with rms value of 0.27 Number of points with protein histograms included: 1035333 Mean starting figure of merit this cycle Overall Centric Acentric 0.46 0.50 0.46 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.10 0.07 0.10 81909 2332 84241 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: 0.00 0.38 0.38 0.00 0.00 0.38 81928 4.6 0.00 0.70 0.70 0.00 0.00 0.70 4137 2.9 0.00 0.71 0.71 0.00 0.00 0.71 11903 2.3 0.00 0.50 0.50 0.00 0.00 0.50 16949 2.0 0.00 0.38 0.38 0.00 0.00 0.38 14217 1.7 0.00 0.19 0.19 0.00 0.00 0.19 24723 1.6 0.00 0.08 0.08 0.00 0.00 0.08 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: 0.00 0.44 0.44 0.00 0.00 0.44 2332 4.6 0.00 0.62 0.62 0.00 0.00 0.62 345 2.9 0.00 0.65 0.65 0.00 0.00 0.65 496 2.3 0.00 0.50 0.50 0.00 0.00 0.50 534 2.0 0.00 0.36 0.36 0.00 0.00 0.36 358 1.7 0.00 0.19 0.19 0.00 0.01 0.19 471 1.6 0.00 0.06 0.06 0.00 0.02 0.06 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.00 0.38 0.38 0.00 0.00 0.38 84260 4.6 0.00 0.69 0.69 0.00 0.00 0.69 4482 2.9 0.00 0.71 0.71 0.00 0.00 0.71 12399 2.3 0.00 0.50 0.50 0.00 0.00 0.50 17483 2.0 0.00 0.38 0.38 0.00 0.00 0.38 14575 1.7 0.00 0.19 0.19 0.00 0.00 0.19 25194 1.6 0.00 0.08 0.08 0.00 0.00 0.08 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.38 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.00 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 1.00 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 0.00 * * * * 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 0.94 42 0.45 0.94 10.73 507 0.82 0.93 60 0.80 0.94 7.75 1058 0.90 0.93 91 0.91 0.93 5.96 1884 0.92 0.92 131 0.91 0.92 4.77 1881 0.92 0.90 100 0.90 0.90 4.17 1899 0.83 0.89 74 0.81 0.89 3.58 4133 0.89 0.87 173 0.89 0.87 3.16 4651 0.90 0.85 176 0.91 0.85 2.86 5367 0.89 0.84 187 0.87 0.84 2.62 5570 0.89 0.82 178 0.88 0.82 2.44 6624 0.86 0.80 188 0.88 0.80 2.27 4223 0.76 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 0.68 0.75 1.91 10719 0.75 0.72 212 0.64 0.72 1.79 9039 0.67 0.70 129 0.57 0.70 1.70 7523 0.50 0.68 95 0.34 0.68 1.61 Overall average CC: 0.78197006731443730 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 0.966 B-value to apply to Fc= 10.906 Overall R-factor for FC vs FP: 0.268 for 84258 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 -0.00 -0.00 81928 0.01 -0.01 2332 -0.00 -0.00 84260 4.6 -0.01 -0.01 4137 -0.01 -0.09 345 -0.01 -0.02 4482 2.9 -0.00 0.00 11903 -0.02 0.01 496 -0.00 0.00 12399 2.3 0.01 0.00 16949 0.04 0.00 534 0.01 0.00 17483 2.0 -0.00 -0.01 14217 0.02 0.01 358 -0.00 -0.01 14575 1.7 -0.01 -0.01 24723 -0.01 0.02 471 -0.01 -0.01 25194 1.6 -0.01 -0.01 9999 0.11 0.15 128 -0.01 -0.01 10127 Minor cycle 3 of 3 Resolution = 1.61 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0240185 Values of m, alpha, s Centric: 0.43991055781426375 0.2339463 0.3939463 Acentric: 0.37524687170366167 0.2101975 0.3551481 Using all points for histograms Fraction protein = 0.529 854714 Fraction solvent= 0.471 760059 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." 0.03.................................................. . . . . xxx . . . xooxxo . . . xo xoo . . xo xoo . . o xoo . p(rho) . ox .xxo . . x . o . . ox . xxx . . x . xxxx . . x . ooxxxxxx . . oxx . ooooxxxxx . . xx . oooxxxxx . . oxx . oxxxxxxo 0.0 xxx..............................................x -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 0.10.................................................. . . . . . . . oo . . oxxo . . x.xx . . xx. x . p(rho) . x . x . . xo . x . . o . x . . xo . ox . . o . ox . . xo . x . . xo . ox . . xo . oxx . 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 = 0.96 RMS in NCS unit : 1: 0.94089329204704275 RMS in NCS unit : 2: 0.93631755266996530 Average RMS ncs in std crystal: 0.93860542774200439 Including ncs au 1 with rms of 0.94154938291436030 Including ncs au 2 with rms of 0.93692280142561180 RMS rho in NCS region: 0.93923894092441385 For NCS pair 1 , 2 : Target CC of rho(i),rho(j)= 0.93 Normalized rms error est from solvent/protein= 0.24 Normalized rms error est of NCS= 0.08 Average SD of NCS targets: 0.3295750 For NCS asym unit 1 the mean target rho is 0.035 +/- 0.936 and the mean uncertainty in it is 0.398 +/- 0.192 For NCS asym unit 2 the mean target rho is 0.034 +/- 0.941 and the mean uncertainty in it is 0.398 +/- 0.192 For a.u. 1 total of 422621 grid points filled in, for 0 unique mappings and 0 attempts to write duplicates and 0 errors out of range and 422621 newly-filled in points and 0 points with lower sigma than prev. For a.u. 2 total of 422643 grid points filled in, for 422609 unique mappings and 3 attempts to write duplicates and 3 errors out of range and 422643 newly-filled in points and 0 points with lower sigma than prev. Done setting up NCS information for group 1 RMS CALC, OBS: 0.8999489 0.8861096 954509 Scale on recov to minimize (recov-obs)**2: 0.9124493 Actual scale on recov used: 0.9124493 Resulting scale * rms obs (recov)= 0.8211578 Comparison of image and map: RMS map= 0.89 RMSD between image and map is: 0.33 CC of image and map= 0.93 Overall CC of model FC and obs FO, corrected for fraction of non-solvent region covered by model: 0.6646579 Overall RMSD estimated from rms of current map * *std::sqrt(1.-cc_overall_est**2) Resulting estimate of RMSD taken from from CC of Fo Fc: 0.6620549 Final RMSD used for image target: 0.662055 Image information used in phasing: Number of points with... image based on model: 190069 image + NCS 764440 image only: 0 no information: 665491 total in au: 1620000 MAP RMS and SIG: 0.395 0.662 190069 Error estimate for map on this cycle The estimated error in this map is 0.23 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.94 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 = 0.94 offset is -0.19 and sigma is a random variable with rms value of 0.23 Number of points with protein histograms included: 1035333 Mean starting figure of merit this cycle Overall Centric Acentric 0.38 0.44 0.38 84260 2332 81928 Mean normalized structure factor changes this cycle Acentric Centric All 0.03 0.03 0.03 81911 2332 84243 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: 0.00 0.38 0.38 0.00 0.00 0.38 81928 4.6 0.00 0.72 0.72 0.00 0.00 0.72 4137 2.9 0.00 0.74 0.74 0.00 0.00 0.74 11903 2.3 0.00 0.52 0.52 0.00 0.00 0.52 16949 2.0 0.00 0.38 0.38 0.00 0.00 0.38 14217 1.7 0.00 0.17 0.17 0.00 0.00 0.17 24723 1.6 0.00 0.07 0.07 0.00 0.00 0.07 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: 0.00 0.45 0.45 0.00 0.00 0.45 2332 4.6 0.00 0.64 0.64 0.00 0.00 0.64 345 2.9 0.00 0.67 0.67 0.00 0.00 0.67 496 2.3 0.00 0.52 0.52 0.00 0.00 0.52 534 2.0 0.00 0.36 0.36 0.00 0.00 0.36 358 1.7 0.00 0.18 0.18 0.00 0.01 0.18 471 1.6 0.00 0.05 0.05 0.00 0.02 0.05 128 WGT: 1.00 1.00 All reflections: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.00 0.38 0.38 0.00 0.00 0.38 84260 4.6 0.00 0.72 0.72 0.00 0.00 0.72 4482 2.9 0.00 0.73 0.73 0.00 0.00 0.73 12399 2.3 0.00 0.52 0.52 0.00 0.00 0.52 17483 2.0 0.00 0.38 0.38 0.00 0.00 0.38 14575 1.7 0.00 0.17 0.17 0.00 0.00 0.17 25194 1.6 0.00 0.07 0.07 0.00 0.00 0.07 10127 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.38 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.00 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 1.00 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 0.00 * * * * 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 0.96 42 0.46 0.96 10.73 507 0.82 0.95 60 0.80 0.95 7.75 1058 0.90 0.94 91 0.90 0.94 5.96 1884 0.92 0.92 131 0.90 0.92 4.77 1881 0.92 0.91 100 0.89 0.91 4.17 1899 0.82 0.89 74 0.80 0.89 3.58 4133 0.89 0.87 173 0.89 0.87 3.16 4651 0.89 0.84 176 0.90 0.84 2.86 5367 0.88 0.82 187 0.87 0.82 2.62 5570 0.87 0.80 178 0.87 0.80 2.44 6624 0.85 0.78 188 0.87 0.78 2.27 4223 0.75 0.75 104 0.78 0.75 2.15 8006 0.84 0.73 205 0.88 0.73 2.03 8584 0.70 0.71 187 0.66 0.71 1.91 10719 0.69 0.68 212 0.60 0.68 1.79 9039 0.61 0.66 129 0.48 0.66 1.70 7523 0.45 0.63 95 0.29 0.63 1.61 Overall average CC: 0.75478575271643489 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 0.713 B-value to apply to Fc= 16.685 Overall R-factor for FC vs FP: 0.312 for 84258 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 -0.00 -0.00 81928 0.03 -0.01 2332 -0.00 -0.00 84260 4.6 -0.01 -0.01 4137 -0.02 -0.09 345 -0.01 -0.02 4482 2.9 -0.00 0.00 11903 -0.01 0.01 496 -0.00 0.00 12399 2.3 0.01 0.00 16949 0.07 0.01 534 0.01 0.00 17483 2.0 -0.00 -0.01 14217 0.02 0.00 358 -0.00 -0.01 14575 1.7 -0.01 -0.02 24723 0.03 0.02 471 -0.01 -0.02 25194 1.6 -0.01 -0.01 9999 0.16 0.14 128 -0.01 -0.01 10127 Writing out 13 columns of data CC of prob map with current map: 0.9336393 -------------------------------------- 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 + -0.0034 Y + 0.0024 Z + 82.3966 New Y-prime= 0.0034 X + -1.0000 Y + 0.0026 Z + 50.5647 New Z-prime= 0.0024 X + 0.0025 Y + 1.0000 Z + -0.2419 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 + 0.0034 Y + 0.0024 Z + 82.2255 New Y-prime= -0.0034 X + -1.0000 Y + 0.0026 Z + 50.8459 New Z-prime= 0.0024 X + 0.0025 Y + 1.0000 Z + -0.0810 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 0.0034 0.0024 rota_matrix -0.0034 -1.0000 0.0026 rota_matrix 0.0024 0.0025 1.0000 tran_orth 82.2255 50.8459 -0.0810 center_orth 88.1034 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 0.001 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