------------------------ 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 1.9501 500.0 Resolution range (A) is: 1.950100 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 >n_xyz 120 120 144 Grid units x y z: 120 120 144 >database 5 Entry in database of histograms to use: 5 >no_optimize_ncs Not optimizing NCS >spg_name_use P 21 21 21 Space group name for output PDB file only: P 21 21 21 >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 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 07-oct-14. Your license is good until 15-dec-96. Opened mtz file image.mtz Dataset 1 HKL_base HKL_base HKL_base 0 72.24000 72.01000 86.99000 90.00000 90.00000 90.00000 0.000000 Dataset 2 project crystal dataset 1 72.24000 72.01000 86.99000 90.00000 90.00000 90.00000 1.000000 Reading SG information from image.mtz Space group name: P212121 Point group: PG222 Space group number : 19 Symmetry operators: 4 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: 72.239998 72.010002 86.989998 90.000000 90.000000 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 27465 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 27465 reflections in test set High-resolution limit of input phased data: 1.95 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 1.95 max: 1.95 Space group is 19 Using symmetry operations from input MTZ file Transformations from orthogonal to fractional and back: Orthogonal to fractional fractional x= 0.01384 X + -0.00000 Y + -0.00000 Z fractional y= 0.00000 X + 0.01389 Y + -0.00000 Z fractional z= 0.00000 X + 0.00000 Y + 0.01150 Z Fractional to orthogonal Orthogonal X= 72.24000 x + 0.00008 y + 0.00010 z Orthogonal Y= 0.00000 x + 72.01000 y + 0.00010 z Orthogonal Z= 0.00000 x + 0.00000 y + 86.99000 z Estimated # of atoms in au: 3156 Warning -- Total of 1296 centric phases off by > 0.5000000 degrees Not separating out FREE set from other reflections for main cycles. Using all data. Expected resolution-corrected F at d = 2.9A : 809.571 Results of wilson scaling: Scale on I = 138.385 B-value = 12.090 Scaling data with value of 138.385 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: 119 119 36 nu nv nw: 120 120 144 Number of grid points in au: 518400 Mean fom of this map was: 0.17 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 17.28 0.49 0.55 137 10.73 0.48 0.53 212 8.09 0.40 0.49 383 6.37 0.36 0.45 675 5.37 0.46 0.41 653 4.65 0.50 0.37 1161 4.06 0.43 0.32 1375 3.63 0.36 0.28 1539 3.31 0.29 0.24 1764 3.06 0.21 0.21 1781 2.85 0.15 0.17 2357 2.67 0.11 0.15 2019 2.52 0.09 0.13 2467 2.38 0.07 0.10 3068 2.24 0.05 0.08 3727 2.11 0.04 0.07 2305 2.01 0.02 0.05 1842 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 = 1.950131 and fom = 0.1747942 Leading to R= 6.918588 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" Solvent content will be 0.47 Using database entry 5 for histograms (" 3 A dehalogenase model ") Total mask cycles: 5 Total density modification mask cycles: 5 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 NO NO NO NO YES NO 10 2 NO NO NO NO YES NO 10 3 NO NO NO NO YES NO 10 4 NO NO NO NO YES NO 10 5 NO NO 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: 6.92 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 ......................................xxxxxxxxxxxx . + xxxx . . + xxx . . + xx . . + xx . . + x . . +x . p(protein) . x . 0.5 . + . . xx+ . . x + . . xx + . . xxxx + . . xx + . . xxxx + . 0.0 .xxxxxxxx...............+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Minor cycle 1 of 10 Resolution = 1.95 Offset for s_rho_cur: -3.08288e-09 Values of m, alpha, s Centric: 0.12675708763757287 6.6054255E-02 0.1367571 Acentric: 0.17988339913331150 9.1953367E-02 0.1898834 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.04.................................................. . . . . . . . xxxo. . . xx xo . . x xo . . xx .xo . p(rho) . x . xx . . x . xx . . x . oxx . . x . xxx . . x . ooxxxx . . x . ooxxxo . . x . xxxoo . . xx . xxxxxo . 0.0 xxxxxxxo....................................xxxxxx -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.................................................. . . . . . . . xxx . . x.ox . . x . x . . o . ox . p(rho) . x . o . . x . x . . x . x . . o . ox . . x . ox . . xx . x . . x . ox . . xx . xxo . 0.0 xxxxxxxxxxxxxx..............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 0.14 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.45 and 0.18 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 = 0.73 offset is -0.06 and sigma is a random variable with rms value of 0.14 Mean starting figure of merit this cycle Overall Centric Acentric 0.17 0.13 0.18 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.41 0.49 0.41 24833 2631 27464 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: 0.18 0.54 0.56 0.63 0.26 0.56 24834 5.6 0.46 0.89 0.90 0.77 0.13 0.90 1146 3.5 0.46 0.89 0.90 0.83 0.13 0.90 3881 2.8 0.23 0.73 0.75 0.71 0.18 0.75 4913 2.4 0.10 0.50 0.52 0.62 0.24 0.52 4891 2.1 0.06 0.32 0.35 0.55 0.28 0.35 7639 2.0 0.02 0.19 0.20 0.37 0.31 0.20 2364 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: 0.13 0.60 0.61 0.29 0.16 0.61 2631 5.6 0.23 0.82 0.82 0.35 0.17 0.82 403 3.5 0.21 0.82 0.82 0.34 0.15 0.82 633 2.8 0.12 0.64 0.65 0.28 0.14 0.65 560 2.4 0.06 0.45 0.46 0.27 0.10 0.46 451 2.1 0.03 0.31 0.32 0.25 0.09 0.32 500 2.0 0.01 0.16 0.17 0.14 0.06 0.17 84 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 0.55 0.56 0.60 0.25 0.56 27465 5.6 0.40 0.87 0.88 0.66 0.14 0.88 1549 3.5 0.43 0.88 0.89 0.76 0.13 0.89 4514 2.8 0.22 0.72 0.74 0.67 0.17 0.74 5473 2.4 0.10 0.49 0.51 0.59 0.22 0.51 5342 2.1 0.05 0.32 0.35 0.53 0.27 0.35 8139 2.0 0.02 0.19 0.20 0.37 0.30 0.20 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.56 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.25 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.75 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.31 * * * * 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 70 0.57 0.88 65 0.76 0.88 13.00 144 0.79 0.86 68 0.67 0.86 9.39 285 0.78 0.83 98 0.73 0.83 7.22 529 0.71 0.80 146 0.69 0.80 5.78 536 0.82 0.76 117 0.72 0.76 5.06 981 0.86 0.72 180 0.85 0.72 4.33 1195 0.81 0.67 180 0.75 0.68 3.83 1350 0.75 0.63 189 0.67 0.63 3.47 1567 0.69 0.59 197 0.58 0.59 3.18 1597 0.61 0.55 184 0.42 0.55 2.96 2136 0.49 0.50 221 0.46 0.50 2.74 1849 0.42 0.47 170 0.39 0.47 2.60 2267 0.41 0.43 200 0.45 0.43 2.46 2844 0.36 0.39 224 0.44 0.40 2.31 3489 0.31 0.35 238 0.30 0.36 2.17 2214 0.24 0.32 91 0.18 0.32 2.06 1781 0.24 0.28 61 0.18 0.28 1.95 Overall average CC: 0.48397523658669223 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 2.153 B-value to apply to Fc= 23.263 Overall R-factor for FC vs FP: 0.386 for 27463 reflections Writing overall R-factor of 0.386 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 24834 0.08 0.08 2631 0.64 0.74 27465 5.6 0.80 0.83 1146 0.08 0.08 403 0.61 0.65 1549 3.5 0.85 0.88 3881 0.01 0.02 633 0.73 0.77 4514 2.8 0.75 0.82 4913 0.09 0.12 560 0.68 0.76 5473 2.4 0.69 0.80 4891 0.09 0.13 451 0.64 0.75 5342 2.1 0.64 0.78 7639 0.14 0.15 500 0.61 0.74 8139 2.0 0.52 0.67 2364 0.10 0.12 84 0.51 0.65 2448 End of first cycle ____________________________________________________________ Minor cycle 2 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0601502 Values of m, alpha, s Centric: 0.60641934589508351 0.3351355 0.4825677 Acentric: 0.55736236014667739 0.3473624 0.4629450 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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.................................................. . . . . . . . xxxxxo . . . ox xx. . . xx xx . . x xx . p(rho) . x .xx . . x . ox . . x . oxxx . . x . oxxxx . . xo . oooxxxxx . . xxo . oooooxxxxx . . xoo . oooxxxxoooooo . . xxo . xxxxxxoo 0.0 xxoo...........................................xxx -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.................................................. . . . . . . . ooo . . o.o . . o xxo . . ox.xo . p(rho) . ox . xx . . x . x . . x . xx . . x . o x . . xo . ox . . xo . ox . . xoo . ox . . xxo . ooxx . 0.0 xxxxxxxxxxxoo...............ooxxxxxxxxxxxxxxxxxxxx -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 0.19 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.69 and 0.20 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 = 0.88 offset is -0.24 and sigma is a random variable with rms value of 0.19 Mean starting figure of merit this cycle Overall Centric Acentric 0.56 0.61 0.56 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.22 0.21 0.22 24833 2631 27464 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: 0.18 0.55 0.56 0.68 0.26 0.56 24834 5.6 0.46 0.84 0.86 0.82 0.18 0.86 1146 3.5 0.46 0.85 0.86 0.86 0.17 0.86 3881 2.8 0.23 0.70 0.72 0.75 0.20 0.72 4913 2.4 0.10 0.51 0.53 0.67 0.23 0.53 4891 2.1 0.06 0.37 0.39 0.60 0.25 0.39 7639 2.0 0.02 0.22 0.23 0.43 0.29 0.23 2364 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: 0.13 0.59 0.60 0.33 0.16 0.60 2631 5.6 0.23 0.79 0.80 0.37 0.18 0.80 403 3.5 0.21 0.76 0.77 0.37 0.17 0.77 633 2.8 0.12 0.60 0.61 0.34 0.15 0.61 560 2.4 0.06 0.47 0.48 0.33 0.10 0.48 451 2.1 0.03 0.37 0.38 0.27 0.08 0.38 500 2.0 0.01 0.21 0.22 0.20 0.04 0.22 84 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 0.55 0.57 0.64 0.25 0.57 27465 5.6 0.40 0.83 0.84 0.70 0.18 0.84 1549 3.5 0.43 0.84 0.85 0.79 0.17 0.85 4514 2.8 0.22 0.69 0.71 0.70 0.19 0.71 5473 2.4 0.10 0.51 0.53 0.64 0.22 0.53 5342 2.1 0.05 0.37 0.39 0.58 0.24 0.39 8139 2.0 0.02 0.22 0.23 0.43 0.28 0.23 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.57 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.25 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.75 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.70 * * * * 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 0.19 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.69 and 0.20 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 = 0.88 offset is -0.24 and sigma is a random variable with rms value of 0.19 Mean starting figure of merit this cycle Overall Centric Acentric 0.56 0.61 0.56 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.17 0.16 0.17 24834 2631 27465 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: 0.18 0.55 0.55 0.68 0.26 0.55 24834 5.6 0.46 0.84 0.85 0.82 0.18 0.85 1146 3.5 0.46 0.85 0.86 0.86 0.17 0.86 3881 2.8 0.23 0.70 0.71 0.75 0.20 0.71 4913 2.4 0.10 0.51 0.52 0.67 0.23 0.52 4891 2.1 0.06 0.37 0.37 0.60 0.25 0.37 7639 2.0 0.02 0.22 0.22 0.43 0.29 0.22 2364 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: 0.13 0.59 0.58 0.33 0.16 0.58 2631 5.6 0.23 0.79 0.77 0.37 0.18 0.77 403 3.5 0.21 0.76 0.74 0.37 0.17 0.74 633 2.8 0.12 0.60 0.59 0.34 0.15 0.59 560 2.4 0.06 0.47 0.46 0.33 0.10 0.46 451 2.1 0.03 0.37 0.36 0.27 0.08 0.36 500 2.0 0.01 0.21 0.20 0.20 0.04 0.20 84 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 0.55 0.55 0.64 0.25 0.55 27465 5.6 0.40 0.83 0.82 0.70 0.18 0.82 1549 3.5 0.43 0.84 0.84 0.79 0.17 0.84 4514 2.8 0.22 0.69 0.70 0.70 0.19 0.70 5473 2.4 0.10 0.51 0.51 0.64 0.22 0.51 5342 2.1 0.05 0.37 0.37 0.58 0.24 0.37 8139 2.0 0.02 0.22 0.22 0.43 0.28 0.22 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.55 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.25 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.75 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 6.70 * * * * 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 70 0.80 1.00 64 0.79 1.00 13.00 144 0.93 0.98 68 0.63 0.98 9.39 285 0.92 0.96 98 0.81 0.96 7.22 529 0.87 0.94 145 0.80 0.94 5.78 536 0.94 0.91 117 0.81 0.91 5.06 978 0.95 0.88 179 0.82 0.88 4.33 1194 0.93 0.84 178 0.76 0.84 3.83 1350 0.91 0.80 189 0.76 0.80 3.47 1567 0.88 0.76 197 0.70 0.76 3.18 1597 0.82 0.73 184 0.68 0.73 2.96 2136 0.74 0.69 221 0.61 0.69 2.74 1849 0.66 0.65 170 0.58 0.65 2.60 2267 0.62 0.62 200 0.64 0.62 2.46 2844 0.58 0.59 224 0.55 0.59 2.31 3489 0.52 0.54 238 0.45 0.55 2.17 2214 0.44 0.51 91 0.38 0.51 2.06 1781 0.32 0.47 61 0.47 0.47 1.95 Overall average CC: 0.66799919454864887 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.321 B-value to apply to Fc= 14.313 Overall R-factor for FC vs FP: 0.327 for 27454 reflections Writing overall R-factor of 0.327 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.75 0.87 24834 0.12 0.11 2631 0.69 0.80 27465 5.6 0.85 0.90 1146 0.06 0.09 403 0.64 0.71 1549 3.5 0.89 0.93 3881 0.05 0.05 633 0.78 0.83 4514 2.8 0.80 0.88 4913 0.15 0.14 560 0.73 0.81 5473 2.4 0.74 0.85 4891 0.16 0.18 451 0.69 0.80 5342 2.1 0.69 0.83 7639 0.20 0.18 500 0.66 0.79 8139 2.0 0.58 0.75 2364 0.07 0.06 84 0.57 0.72 2448 Small cycle 2 of 2 Error estimate for map on this cycle The estimated error in this map is 0.19 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.69 and 0.20 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 = 0.88 offset is -0.24 and sigma is a random variable with rms value of 0.19 Mean starting figure of merit this cycle Overall Centric Acentric 0.55 0.58 0.55 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.07 0.07 0.07 24833 2631 27464 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: 0.18 0.57 0.57 0.71 0.25 0.57 24834 5.6 0.46 0.86 0.86 0.82 0.17 0.86 1146 3.5 0.46 0.87 0.87 0.88 0.15 0.87 3881 2.8 0.23 0.73 0.73 0.78 0.18 0.73 4913 2.4 0.10 0.53 0.54 0.70 0.22 0.54 4891 2.1 0.06 0.39 0.40 0.64 0.24 0.40 7639 2.0 0.02 0.24 0.24 0.48 0.28 0.24 2364 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: 0.13 0.61 0.60 0.35 0.15 0.60 2631 5.6 0.23 0.80 0.79 0.36 0.18 0.79 403 3.5 0.21 0.78 0.77 0.38 0.17 0.77 633 2.8 0.12 0.63 0.63 0.36 0.14 0.63 560 2.4 0.06 0.49 0.49 0.31 0.09 0.49 451 2.1 0.03 0.40 0.39 0.32 0.07 0.39 500 2.0 0.01 0.22 0.22 0.31 0.04 0.22 84 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 0.58 0.68 0.24 0.58 27465 5.6 0.40 0.84 0.84 0.70 0.17 0.84 1549 3.5 0.43 0.86 0.86 0.81 0.15 0.86 4514 2.8 0.22 0.72 0.72 0.73 0.18 0.72 5473 2.4 0.10 0.53 0.54 0.67 0.21 0.54 5342 2.1 0.05 0.39 0.40 0.62 0.23 0.40 8139 2.0 0.02 0.24 0.24 0.47 0.27 0.24 2448 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: 6.78 * * * * 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 70 0.78 0.99 64 0.83 0.99 13.00 144 0.94 0.98 68 0.87 0.98 9.39 285 0.93 0.97 98 0.88 0.97 7.22 529 0.89 0.95 146 0.90 0.95 5.78 536 0.94 0.93 117 0.91 0.93 5.06 980 0.96 0.91 178 0.94 0.91 4.33 1195 0.94 0.88 179 0.90 0.88 3.83 1350 0.92 0.85 189 0.88 0.85 3.47 1567 0.90 0.83 197 0.83 0.83 3.18 1597 0.85 0.80 184 0.79 0.80 2.96 2136 0.81 0.77 221 0.73 0.77 2.74 1849 0.75 0.75 170 0.73 0.75 2.60 2267 0.73 0.72 200 0.74 0.72 2.46 2844 0.70 0.69 224 0.68 0.69 2.31 3489 0.65 0.66 238 0.63 0.66 2.17 2214 0.57 0.63 91 0.46 0.63 2.06 1781 0.48 0.60 61 0.40 0.60 1.95 Overall average CC: 0.75296452977411765 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.330 B-value to apply to Fc= 13.125 Overall R-factor for FC vs FP: 0.270 for 27458 reflections Writing overall R-factor of 0.270 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.13 0.11 2631 0.71 0.80 27465 5.6 0.85 0.90 1146 0.08 0.08 403 0.65 0.70 1549 3.5 0.90 0.93 3881 0.06 0.05 633 0.78 0.82 4514 2.8 0.81 0.88 4913 0.17 0.14 560 0.75 0.82 5473 2.4 0.76 0.86 4891 0.15 0.15 451 0.70 0.81 5342 2.1 0.72 0.85 7639 0.20 0.18 500 0.69 0.81 8139 2.0 0.63 0.78 2364 0.10 0.03 84 0.61 0.76 2448 Minor cycle 3 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.060579 Values of m, alpha, s Centric: 0.60328712922250249 0.3326297 0.4813148 Acentric: 0.57266767687608866 0.3626676 0.4690671 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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.................................................. . . . . . . . xxxxo . . . oxx xxo. . . x xx . . ox xx . p(rho) . xx .xx . . x . ox . . xx . oxxx . . xo . ooxxxx . . o . oooxxxxx . . xxo . oooooxxxxx . . xoo . oooxxxoooooooo. .xxxoo . xxxxxxxoo 0.0 xooo...........................................xxx -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 0.15.................................................. . . . . . . . o . . o.o . . .o . . . . p(rho) . o. . . . o . . o . . . xxxxx . . xx . x . . xo . oxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.71 and 0.15 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 = 0.88 offset is -0.27 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.58 0.60 0.57 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 24833 2631 27464 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: 0.18 0.57 0.58 0.71 0.25 0.58 24834 5.6 0.46 0.86 0.86 0.82 0.17 0.86 1146 3.5 0.46 0.87 0.88 0.88 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.55 0.70 0.21 0.55 4891 2.1 0.06 0.40 0.41 0.64 0.24 0.41 7639 2.0 0.02 0.24 0.25 0.49 0.28 0.25 2364 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: 0.13 0.62 0.62 0.34 0.15 0.62 2631 5.6 0.23 0.80 0.80 0.37 0.18 0.80 403 3.5 0.21 0.78 0.78 0.36 0.17 0.78 633 2.8 0.12 0.64 0.64 0.37 0.14 0.64 560 2.4 0.06 0.50 0.50 0.32 0.09 0.50 451 2.1 0.03 0.41 0.41 0.30 0.07 0.41 500 2.0 0.01 0.23 0.23 0.30 0.04 0.23 84 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 0.68 0.24 0.59 27465 5.6 0.40 0.84 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.86 0.81 0.16 0.86 4514 2.8 0.22 0.72 0.73 0.73 0.17 0.73 5473 2.4 0.10 0.53 0.55 0.67 0.20 0.55 5342 2.1 0.05 0.40 0.41 0.62 0.23 0.41 8139 2.0 0.02 0.24 0.25 0.48 0.27 0.25 2448 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: 6.75 * * * * 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 70 0.79 1.00 64 0.85 1.00 13.00 144 0.94 0.99 68 0.88 0.99 9.39 285 0.93 0.98 98 0.89 0.98 7.22 529 0.90 0.96 146 0.91 0.96 5.78 536 0.95 0.94 117 0.92 0.94 5.06 981 0.96 0.92 178 0.95 0.92 4.33 1195 0.94 0.90 179 0.91 0.90 3.83 1350 0.93 0.87 189 0.89 0.87 3.47 1567 0.90 0.85 197 0.85 0.85 3.18 1597 0.86 0.82 184 0.82 0.82 2.96 2136 0.82 0.80 221 0.76 0.79 2.74 1849 0.77 0.77 170 0.75 0.77 2.60 2267 0.76 0.75 200 0.77 0.75 2.46 2844 0.73 0.72 224 0.71 0.72 2.31 3489 0.69 0.69 238 0.65 0.69 2.17 2214 0.62 0.66 91 0.53 0.66 2.06 1781 0.53 0.63 61 0.46 0.63 1.95 Overall average CC: 0.77774634005905408 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.359 B-value to apply to Fc= 11.964 Overall R-factor for FC vs FP: 0.259 for 27459 reflections Writing overall R-factor of 0.259 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.13 0.10 2631 0.71 0.80 27465 5.6 0.84 0.89 1146 0.07 0.08 403 0.64 0.69 1549 3.5 0.90 0.93 3881 0.05 0.05 633 0.78 0.82 4514 2.8 0.81 0.88 4913 0.19 0.14 560 0.75 0.81 5473 2.4 0.76 0.86 4891 0.13 0.14 451 0.70 0.81 5342 2.1 0.73 0.85 7639 0.20 0.18 500 0.69 0.81 8139 2.0 0.63 0.79 2364 0.12 0.02 84 0.62 0.77 2448 Minor cycle 4 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0601806 Values of m, alpha, s Centric: 0.61554790176687824 0.3424383 0.4862191 Acentric: 0.58184344911298369 0.3718434 0.4727374 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . xxxxx . . . xxx xo. . . x xo . . oxx xo . p(rho) . x .xx . . x . ox . . x . oxxx . . xx . ooxxxx . . xo . ooo xxxx . . xoo . oooooooxxxx . . xo . ooxxxxooooooo. .xxxo . xxxxxx o 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxxx . . xx . x . . xo . xxx . . xx o . o xx . . xx o . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.15 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 -0.27 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.62 0.58 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.02 0.02 24833 2631 27464 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: 0.18 0.57 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.82 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.88 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.78 0.18 0.74 4913 2.4 0.10 0.54 0.55 0.70 0.21 0.55 4891 2.1 0.06 0.40 0.42 0.65 0.24 0.42 7639 2.0 0.02 0.25 0.26 0.50 0.27 0.26 2364 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: 0.13 0.62 0.62 0.35 0.15 0.62 2631 5.6 0.23 0.80 0.80 0.37 0.18 0.80 403 3.5 0.21 0.78 0.78 0.37 0.17 0.78 633 2.8 0.12 0.65 0.65 0.38 0.13 0.65 560 2.4 0.06 0.50 0.51 0.32 0.09 0.51 451 2.1 0.03 0.41 0.42 0.31 0.07 0.42 500 2.0 0.01 0.24 0.24 0.25 0.04 0.24 84 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 0.68 0.24 0.59 27465 5.6 0.40 0.84 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.86 0.81 0.15 0.86 4514 2.8 0.22 0.72 0.73 0.73 0.17 0.73 5473 2.4 0.10 0.53 0.55 0.67 0.20 0.55 5342 2.1 0.05 0.40 0.42 0.63 0.23 0.42 8139 2.0 0.02 0.25 0.26 0.49 0.27 0.26 2448 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: 6.74 * * * * 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 70 0.79 0.98 65 0.88 0.98 13.00 144 0.94 0.98 68 0.89 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.95 146 0.92 0.95 5.78 536 0.95 0.94 117 0.93 0.94 5.06 981 0.96 0.92 178 0.95 0.92 4.33 1195 0.95 0.90 179 0.92 0.90 3.83 1350 0.93 0.88 189 0.89 0.88 3.47 1567 0.91 0.85 197 0.86 0.85 3.18 1597 0.87 0.83 184 0.83 0.83 2.96 2136 0.83 0.81 221 0.77 0.81 2.74 1849 0.78 0.79 170 0.78 0.79 2.60 2267 0.78 0.77 200 0.78 0.77 2.46 2844 0.76 0.74 224 0.73 0.74 2.31 3489 0.71 0.72 238 0.68 0.72 2.17 2214 0.65 0.69 91 0.58 0.69 2.06 1781 0.56 0.66 61 0.46 0.66 1.95 Overall average CC: 0.79302954862609187 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.367 B-value to apply to Fc= 11.266 Overall R-factor for FC vs FP: 0.249 for 27460 reflections Writing overall R-factor of 0.249 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.12 0.10 2631 0.71 0.80 27465 5.6 0.84 0.89 1146 0.07 0.08 403 0.64 0.69 1549 3.5 0.90 0.93 3881 0.05 0.05 633 0.78 0.82 4514 2.8 0.81 0.88 4913 0.17 0.14 560 0.74 0.81 5473 2.4 0.76 0.86 4891 0.12 0.13 451 0.70 0.81 5342 2.1 0.73 0.86 7639 0.20 0.17 500 0.70 0.81 8139 2.0 0.64 0.80 2364 0.12 0.01 84 0.62 0.78 2448 Minor cycle 5 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0600258 Values of m, alpha, s Centric: 0.62272029058663492 0.3481762 0.4890881 Acentric: 0.58624351880042169 0.3762435 0.4744974 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . xxxxo . . . xxx xxo. . . x xo . . oxx xo . p(rho) . x .xx . . x . ox . . x . oxxx . . xo . ooxxxx . . xo . oooxxxxx . . xoo . ooooooxxxxx . . xo . ooxxxxoooooooo .xxxo . xxxxxxoo 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxx . . xx . x . . xx . xxx . . xx o . o xx . . xx o . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.15 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 -0.27 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.62 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 24833 2631 27464 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.88 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.42 0.65 0.24 0.42 7639 2.0 0.02 0.25 0.26 0.50 0.27 0.26 2364 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: 0.13 0.62 0.63 0.34 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.36 0.18 0.81 403 3.5 0.21 0.78 0.78 0.36 0.17 0.78 633 2.8 0.12 0.65 0.65 0.36 0.13 0.65 560 2.4 0.06 0.51 0.51 0.31 0.09 0.51 451 2.1 0.03 0.41 0.42 0.31 0.07 0.42 500 2.0 0.01 0.24 0.24 0.30 0.04 0.24 84 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 0.68 0.23 0.59 27465 5.6 0.40 0.84 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.72 0.73 0.73 0.17 0.73 5473 2.4 0.10 0.54 0.55 0.67 0.20 0.55 5342 2.1 0.05 0.41 0.42 0.63 0.23 0.42 8139 2.0 0.02 0.25 0.26 0.49 0.26 0.26 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.59 * * 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: 6.71 * * * * 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 70 0.80 0.99 65 0.88 0.99 13.00 144 0.94 0.98 68 0.89 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.96 146 0.92 0.96 5.78 536 0.95 0.94 117 0.93 0.94 5.06 981 0.96 0.93 178 0.95 0.93 4.33 1195 0.95 0.90 179 0.92 0.90 3.83 1350 0.93 0.88 189 0.90 0.88 3.47 1567 0.91 0.86 197 0.86 0.86 3.18 1597 0.87 0.84 184 0.84 0.84 2.96 2136 0.84 0.82 221 0.79 0.82 2.74 1849 0.79 0.79 170 0.79 0.79 2.60 2267 0.78 0.77 200 0.79 0.77 2.46 2844 0.77 0.75 224 0.75 0.75 2.31 3489 0.73 0.72 238 0.69 0.72 2.17 2214 0.66 0.69 91 0.61 0.70 2.06 1781 0.58 0.67 61 0.47 0.67 1.95 Overall average CC: 0.80086047780596248 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.371 B-value to apply to Fc= 10.873 Overall R-factor for FC vs FP: 0.244 for 27460 reflections Writing overall R-factor of 0.244 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.12 0.10 2631 0.71 0.80 27465 5.6 0.84 0.89 1146 0.08 0.07 403 0.64 0.69 1549 3.5 0.89 0.93 3881 0.04 0.05 633 0.77 0.82 4514 2.8 0.81 0.88 4913 0.17 0.14 560 0.74 0.81 5473 2.4 0.76 0.86 4891 0.13 0.13 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.19 0.17 500 0.70 0.82 8139 2.0 0.64 0.80 2364 0.07 0.00 84 0.62 0.78 2448 Minor cycle 6 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0599456 Values of m, alpha, s Centric: 0.62681485352758814 0.3514519 0.4907259 Acentric: 0.58845800870522924 0.3784580 0.4753832 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . xxxxoo . . . xxx xxo. . . ox xo . . ox xx . p(rho) . x .xx . . x . ox . . x . oxxx . . xo . ooxxxx . . xo . ooo xxxx . . xo . ooooooxxxxx . . xo . ooxxxxoooooooo .xxxo . xxxxxx o 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxo . . xx . xx . . xx . xxx . . xx o . o xx . . xx o . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.15 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 -0.27 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24833 2630 27463 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.42 0.65 0.24 0.42 7639 2.0 0.02 0.25 0.26 0.50 0.27 0.26 2364 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: 0.13 0.62 0.63 0.34 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.37 0.18 0.81 403 3.5 0.21 0.78 0.78 0.36 0.17 0.78 633 2.8 0.12 0.65 0.66 0.37 0.13 0.66 560 2.4 0.06 0.51 0.52 0.31 0.09 0.52 451 2.1 0.03 0.42 0.42 0.32 0.07 0.42 500 2.0 0.01 0.24 0.25 0.30 0.04 0.25 84 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 0.68 0.23 0.59 27465 5.6 0.40 0.84 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.72 0.73 0.73 0.17 0.73 5473 2.4 0.10 0.54 0.55 0.67 0.20 0.55 5342 2.1 0.05 0.41 0.42 0.63 0.23 0.42 8139 2.0 0.02 0.25 0.26 0.49 0.26 0.26 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.59 * * 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: 6.69 * * * * 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 70 0.80 0.98 65 0.88 0.98 13.00 144 0.94 0.98 68 0.90 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.95 146 0.92 0.95 5.78 536 0.95 0.94 117 0.93 0.94 5.06 981 0.96 0.92 178 0.95 0.92 4.33 1195 0.95 0.90 179 0.92 0.90 3.83 1350 0.93 0.88 189 0.90 0.88 3.47 1567 0.91 0.86 197 0.87 0.86 3.18 1597 0.87 0.84 184 0.85 0.84 2.96 2136 0.84 0.82 221 0.80 0.82 2.74 1849 0.80 0.80 170 0.79 0.80 2.60 2267 0.79 0.78 200 0.80 0.78 2.46 2844 0.77 0.76 224 0.75 0.76 2.31 3489 0.73 0.73 238 0.69 0.74 2.17 2214 0.67 0.71 91 0.63 0.71 2.06 1781 0.59 0.68 61 0.47 0.68 1.95 Overall average CC: 0.80584452237014081 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.375 B-value to apply to Fc= 10.662 Overall R-factor for FC vs FP: 0.241 for 27460 reflections Writing overall R-factor of 0.241 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.12 0.10 2631 0.71 0.80 27465 5.6 0.84 0.88 1146 0.08 0.07 403 0.64 0.68 1549 3.5 0.89 0.93 3881 0.05 0.05 633 0.77 0.81 4514 2.8 0.81 0.88 4913 0.18 0.14 560 0.74 0.81 5473 2.4 0.76 0.86 4891 0.13 0.13 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.19 0.17 500 0.70 0.82 8139 2.0 0.64 0.81 2364 0.10 0.00 84 0.63 0.78 2448 Minor cycle 7 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0599005 Values of m, alpha, s Centric: 0.62933815321396558 0.3534705 0.4917352 Acentric: 0.58977340528211442 0.3797734 0.4759094 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . oxxxxxo . . . xx xo. . . ox xo . . ox xo . p(rho) . x .xx . . x . ox . . x . oxxx . . xo . ooxxxx . . xo . ooo xxxx . . xo . ooooooxxxxx . . xo . oxxxxoooooooo .xxxo . xxxxxxxo 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxo . . xx . xx . . xx . xxx . . xx o . o xx . . xx o . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.15 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 -0.27 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24833 2631 27464 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.43 0.65 0.24 0.43 7639 2.0 0.02 0.25 0.27 0.50 0.27 0.27 2364 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: 0.13 0.63 0.63 0.34 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.37 0.18 0.81 403 3.5 0.21 0.78 0.78 0.36 0.17 0.78 633 2.8 0.12 0.66 0.66 0.36 0.13 0.66 560 2.4 0.06 0.51 0.52 0.30 0.09 0.52 451 2.1 0.03 0.42 0.43 0.33 0.07 0.43 500 2.0 0.01 0.24 0.25 0.30 0.04 0.25 84 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 0.68 0.23 0.59 27465 5.6 0.40 0.84 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.72 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.54 0.55 0.67 0.20 0.55 5342 2.1 0.05 0.41 0.43 0.63 0.23 0.43 8139 2.0 0.02 0.25 0.26 0.50 0.26 0.26 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.59 * * 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: 6.68 * * * * 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 70 0.80 0.99 65 0.88 0.99 13.00 144 0.94 0.98 68 0.90 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.96 146 0.92 0.96 5.78 536 0.95 0.94 117 0.94 0.94 5.06 981 0.96 0.93 178 0.95 0.93 4.33 1195 0.95 0.91 179 0.92 0.91 3.83 1350 0.93 0.89 189 0.90 0.89 3.47 1567 0.91 0.87 197 0.87 0.87 3.18 1597 0.87 0.85 184 0.85 0.85 2.96 2136 0.85 0.82 221 0.81 0.82 2.74 1849 0.80 0.80 170 0.80 0.80 2.60 2267 0.79 0.78 200 0.80 0.78 2.46 2844 0.78 0.76 224 0.76 0.76 2.31 3489 0.74 0.74 238 0.70 0.74 2.17 2214 0.68 0.71 91 0.64 0.71 2.06 1781 0.59 0.68 61 0.47 0.69 1.95 Overall average CC: 0.80912856636195829 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.378 B-value to apply to Fc= 10.541 Overall R-factor for FC vs FP: 0.239 for 27460 reflections Writing overall R-factor of 0.239 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.12 0.10 2631 0.71 0.80 27465 5.6 0.84 0.88 1146 0.07 0.07 403 0.64 0.68 1549 3.5 0.89 0.92 3881 0.04 0.04 633 0.77 0.81 4514 2.8 0.81 0.87 4913 0.17 0.14 560 0.74 0.81 5473 2.4 0.75 0.86 4891 0.12 0.12 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.19 0.17 500 0.70 0.81 8139 2.0 0.64 0.81 2364 0.07 0.00 84 0.62 0.78 2448 Minor cycle 8 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0598593 Values of m, alpha, s Centric: 0.63113900594431005 0.3549112 0.4924556 Acentric: 0.59056449728395044 0.3805645 0.4762258 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . oxxxxxo . . . xx xo. . . ox xo . . ox xx . p(rho) . x . x . . x . ox . . x . oxxx . . xo . o xxx . . xo . ooo xxxxx . . xo . oooooooxxxx . . xo . ooxxxxooooooo .xxxo . xxxxxxo 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxo . . xx . xx . . xx . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.14 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 -0.26 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.59 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24833 2631 27464 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.43 0.65 0.24 0.43 7639 2.0 0.02 0.25 0.27 0.50 0.27 0.27 2364 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: 0.13 0.63 0.63 0.35 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.37 0.18 0.81 403 3.5 0.21 0.78 0.79 0.36 0.17 0.79 633 2.8 0.12 0.66 0.66 0.37 0.13 0.66 560 2.4 0.06 0.51 0.52 0.30 0.09 0.52 451 2.1 0.03 0.42 0.43 0.33 0.07 0.43 500 2.0 0.01 0.24 0.25 0.30 0.04 0.25 84 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 0.68 0.23 0.60 27465 5.6 0.40 0.85 0.85 0.70 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.72 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.54 0.56 0.67 0.20 0.56 5342 2.1 0.05 0.41 0.43 0.63 0.23 0.43 8139 2.0 0.02 0.25 0.27 0.50 0.26 0.27 2448 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: 6.66 * * * * 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 70 0.80 0.99 65 0.88 0.99 13.00 144 0.94 0.98 68 0.90 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.96 146 0.92 0.96 5.78 536 0.95 0.94 117 0.94 0.94 5.06 981 0.96 0.93 178 0.95 0.93 4.33 1195 0.95 0.91 179 0.92 0.91 3.83 1350 0.93 0.89 189 0.90 0.89 3.47 1567 0.91 0.87 197 0.87 0.87 3.18 1597 0.88 0.85 184 0.85 0.85 2.96 2136 0.85 0.83 221 0.81 0.83 2.74 1849 0.80 0.81 170 0.80 0.81 2.60 2267 0.79 0.79 200 0.81 0.79 2.46 2844 0.78 0.76 224 0.76 0.76 2.31 3489 0.74 0.74 238 0.70 0.74 2.17 2214 0.68 0.71 91 0.65 0.71 2.06 1781 0.60 0.69 61 0.47 0.69 1.95 Overall average CC: 0.81109590725532343 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.371 B-value to apply to Fc= 10.433 Overall R-factor for FC vs FP: 0.238 for 27460 reflections Writing overall R-factor of 0.238 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.88 24834 0.11 0.10 2631 0.71 0.80 27465 5.6 0.83 0.88 1146 0.07 0.07 403 0.63 0.68 1549 3.5 0.89 0.92 3881 0.05 0.04 633 0.77 0.81 4514 2.8 0.80 0.87 4913 0.17 0.14 560 0.74 0.80 5473 2.4 0.75 0.86 4891 0.11 0.12 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.18 0.17 500 0.69 0.81 8139 2.0 0.64 0.81 2364 0.07 0.00 84 0.62 0.78 2448 Minor cycle 9 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0598707 Values of m, alpha, s Centric: 0.63256293003219832 0.3560503 0.4930252 Acentric: 0.59124035450755763 0.3812403 0.4764961 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . oxxxxx . . . xx xo. . . ox xo . . ox xx . p(rho) . x . x . . x . ox . . x . oxxx . . xo . o xxx . . xo . ooo xxxxx . . xo . oooooooxxxx . . xo . ooxxxxooooooo .xxxo . xxxxxxo 0.0 xooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxo . . xx . xx . . xx . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.14 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 -0.26 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 24833 2631 27464 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.73 0.74 0.77 0.18 0.74 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.43 0.65 0.24 0.43 7639 2.0 0.02 0.26 0.27 0.50 0.27 0.27 2364 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: 0.13 0.63 0.63 0.35 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.37 0.17 0.81 403 3.5 0.21 0.78 0.79 0.37 0.16 0.79 633 2.8 0.12 0.66 0.66 0.37 0.13 0.66 560 2.4 0.06 0.52 0.52 0.30 0.09 0.52 451 2.1 0.03 0.42 0.43 0.33 0.07 0.43 500 2.0 0.01 0.24 0.25 0.30 0.04 0.25 84 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 0.68 0.23 0.60 27465 5.6 0.40 0.85 0.85 0.69 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.72 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.54 0.56 0.67 0.20 0.56 5342 2.1 0.05 0.41 0.43 0.63 0.23 0.43 8139 2.0 0.02 0.25 0.27 0.50 0.26 0.27 2448 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: 6.65 * * * * 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 70 0.80 0.99 65 0.88 0.99 13.00 144 0.94 0.98 68 0.90 0.98 9.39 285 0.93 0.97 98 0.90 0.97 7.22 529 0.91 0.96 146 0.93 0.96 5.78 536 0.95 0.94 117 0.94 0.94 5.06 981 0.96 0.93 178 0.95 0.93 4.33 1195 0.95 0.91 179 0.92 0.91 3.83 1350 0.93 0.89 189 0.90 0.89 3.47 1567 0.91 0.87 197 0.87 0.87 3.18 1597 0.88 0.85 184 0.85 0.85 2.96 2136 0.85 0.83 221 0.81 0.83 2.74 1849 0.80 0.81 170 0.81 0.81 2.60 2267 0.80 0.79 200 0.81 0.79 2.46 2844 0.78 0.76 224 0.77 0.77 2.31 3489 0.74 0.74 238 0.70 0.74 2.17 2214 0.69 0.71 91 0.66 0.71 2.06 1781 0.60 0.69 61 0.47 0.69 1.95 Overall average CC: 0.81255036968648309 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.373 B-value to apply to Fc= 10.385 Overall R-factor for FC vs FP: 0.237 for 27460 reflections Writing overall R-factor of 0.237 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.87 24834 0.12 0.10 2631 0.71 0.80 27465 5.6 0.83 0.88 1146 0.07 0.07 403 0.63 0.68 1549 3.5 0.89 0.92 3881 0.06 0.04 633 0.77 0.81 4514 2.8 0.80 0.87 4913 0.18 0.14 560 0.74 0.80 5473 2.4 0.75 0.86 4891 0.10 0.12 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.19 0.17 500 0.70 0.81 8139 2.0 0.64 0.81 2364 0.10 0.00 84 0.63 0.78 2448 Minor cycle 10 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0598569 Values of m, alpha, s Centric: 0.63355917794222549 0.3568473 0.4934237 Acentric: 0.59165001526368388 0.3816500 0.4766600 Using all points for histograms Fraction protein = 0.533 276117 Fraction solvent= 0.467 242283 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." 0.03.................................................. . . . . . . . oxxxxxo . . . xx xo. . . ox xo . . ox xx . p(rho) . x . x . . x . ox . . x . oxxx . . xo . o xxxx . . xo . ooo xxxxx . . xxo . oooooooxxxx . . xo . oooxxxxooooooo xxxxo . xxxxxxo 0.0 oooo............................................xx -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 0.16.................................................. . . . . . . . o . . .o . . o. . . .o . p(rho) . o. . . . o . . o . . . xxxo . . xx . xx . . xx . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.72 and 0.14 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 -0.26 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 24833 2631 27464 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: 0.18 0.58 0.59 0.71 0.24 0.59 24834 5.6 0.46 0.86 0.87 0.81 0.17 0.87 1146 3.5 0.46 0.87 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.73 0.75 0.77 0.18 0.75 4913 2.4 0.10 0.54 0.56 0.70 0.21 0.56 4891 2.1 0.06 0.41 0.43 0.65 0.24 0.43 7639 2.0 0.02 0.26 0.27 0.50 0.27 0.27 2364 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: 0.13 0.63 0.63 0.34 0.15 0.63 2631 5.6 0.23 0.81 0.81 0.36 0.17 0.81 403 3.5 0.21 0.79 0.79 0.37 0.16 0.79 633 2.8 0.12 0.66 0.67 0.37 0.13 0.67 560 2.4 0.06 0.52 0.52 0.30 0.09 0.52 451 2.1 0.03 0.42 0.43 0.32 0.07 0.43 500 2.0 0.01 0.24 0.25 0.30 0.04 0.25 84 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 0.67 0.23 0.60 27465 5.6 0.40 0.85 0.85 0.69 0.17 0.85 1549 3.5 0.43 0.86 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.73 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.54 0.56 0.66 0.20 0.56 5342 2.1 0.05 0.41 0.43 0.63 0.23 0.43 8139 2.0 0.02 0.25 0.27 0.50 0.26 0.27 2448 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: 6.64 * * * * 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 70 0.80 0.98 65 0.88 0.98 13.00 144 0.94 0.97 68 0.90 0.97 9.39 285 0.93 0.96 98 0.90 0.96 7.22 529 0.91 0.95 146 0.93 0.95 5.78 536 0.95 0.94 117 0.94 0.94 5.06 981 0.96 0.92 178 0.95 0.92 4.33 1195 0.95 0.90 179 0.92 0.90 3.83 1350 0.93 0.89 189 0.90 0.89 3.47 1567 0.91 0.87 197 0.88 0.87 3.18 1597 0.88 0.85 184 0.85 0.85 2.96 2136 0.85 0.83 221 0.82 0.83 2.74 1849 0.80 0.81 170 0.81 0.81 2.60 2267 0.80 0.79 200 0.81 0.79 2.46 2844 0.78 0.77 224 0.77 0.77 2.31 3489 0.74 0.75 238 0.70 0.75 2.17 2214 0.69 0.72 91 0.66 0.72 2.06 1781 0.60 0.70 61 0.47 0.70 1.95 Overall average CC: 0.81365637245268518 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.374 B-value to apply to Fc= 10.358 Overall R-factor for FC vs FP: 0.237 for 27460 reflections Writing overall R-factor of 0.237 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.87 24834 0.12 0.10 2631 0.71 0.79 27465 5.6 0.83 0.88 1146 0.06 0.07 403 0.63 0.68 1549 3.5 0.89 0.92 3881 0.06 0.04 633 0.77 0.81 4514 2.8 0.80 0.87 4913 0.18 0.14 560 0.74 0.80 5473 2.4 0.75 0.86 4891 0.10 0.12 451 0.69 0.80 5342 2.1 0.73 0.86 7639 0.19 0.17 500 0.69 0.81 8139 2.0 0.65 0.81 2364 0.10 0.00 84 0.63 0.78 2448 Mask cycle 2 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) Minor cycle 1 of 10 Resolution = 1.95 Offset for s_rho_cur: 4.2616e-09 Values of m, alpha, s Centric: 0.63440368714818163 0.3575230 0.4937615 Acentric: 0.59191985622609611 0.3819198 0.4767679 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.22 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.63 0.59 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.04 0.03 0.04 24833 2631 27464 Writing overall R-factor of 0.239 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0698899 Values of m, alpha, s Centric: 0.63691011442305523 0.3595281 0.4947641 Acentric: 0.59542227458067454 0.3854223 0.4781689 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.02 0.01 0.02 24833 2630 27463 Writing overall R-factor of 0.237 to resolve.rfactor Minor cycle 3 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0695445 Values of m, alpha, s Centric: 0.63729939357168874 0.3598396 0.4949198 Acentric: 0.59520214548083927 0.3852021 0.4780809 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24834 2631 27465 Writing overall R-factor of 0.235 to resolve.rfactor Minor cycle 4 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0695159 Values of m, alpha, s Centric: 0.63887627179795381 0.3611010 0.4955505 Acentric: 0.59575023562175911 0.3857502 0.4783001 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.26 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24834 2631 27465 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 5 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.069345 Values of m, alpha, s Centric: 0.63949449668209601 0.3615956 0.4957978 Acentric: 0.59567884969127527 0.3856788 0.4782715 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 24834 2631 27465 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 6 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0693895 Values of m, alpha, s Centric: 0.64045958677633874 0.3623677 0.4961838 Acentric: 0.59603168580252364 0.3860317 0.4784127 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 24833 2631 27464 Writing overall R-factor of 0.233 to resolve.rfactor Minor cycle 7 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.0693399 Values of m, alpha, s Centric: 0.64093512718467571 0.3627481 0.4963740 Acentric: 0.59611978049868186 0.3861198 0.4784479 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24833 2631 27464 Writing overall R-factor of 0.233 to resolve.rfactor Minor cycle 8 of 10 Resolution = 1.95 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0693046 Values of m, alpha, s Centric: 0.64139240466783742 0.3631139 0.4965570 Acentric: 0.59618243966343065 0.3861824 0.4784730 Using all points for histograms Fraction protein = 0.530 274656 Fraction solvent= 0.470 243593 Plot 22 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 . . . oxx xx . . . x xo . . oxx xx . p(rho) . x .xx . . x . xx . . x . oxxx . . xo . ooxxxx . . xo . ooooxxxxx . . xoo . oooooxxxxx . . xo . ooxxxxooooooo xxxxo . xxxxxxo 0.0 oooo.............................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 23 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.16.................................................. . . . . . . . oo . . o . . .o . . o. . p(rho) . . o . . o. . . . . . oxxxo . . xx . xx . . xxo . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24834 2631 27465 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: 0.18 0.58 0.60 0.71 0.24 0.60 24834 5.6 0.46 0.86 0.87 0.82 0.16 0.87 1146 3.5 0.46 0.88 0.88 0.87 0.15 0.88 3881 2.8 0.23 0.74 0.75 0.77 0.17 0.75 4913 2.4 0.10 0.55 0.57 0.70 0.21 0.57 4891 2.1 0.06 0.41 0.43 0.65 0.23 0.43 7639 2.0 0.02 0.26 0.27 0.51 0.27 0.27 2364 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: 0.13 0.64 0.64 0.35 0.14 0.64 2631 5.6 0.23 0.82 0.82 0.37 0.17 0.82 403 3.5 0.21 0.79 0.79 0.37 0.16 0.79 633 2.8 0.12 0.67 0.68 0.36 0.13 0.68 560 2.4 0.06 0.53 0.54 0.31 0.09 0.54 451 2.1 0.03 0.42 0.43 0.30 0.07 0.43 500 2.0 0.01 0.24 0.24 0.32 0.04 0.24 84 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 0.68 0.23 0.60 27465 5.6 0.40 0.85 0.86 0.70 0.17 0.86 1549 3.5 0.43 0.87 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.73 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.55 0.56 0.67 0.20 0.56 5342 2.1 0.05 0.41 0.43 0.63 0.22 0.43 8139 2.0 0.02 0.26 0.27 0.50 0.26 0.27 2448 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: 6.61 * * * * 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 69 0.75 0.98 64 0.88 0.98 13.00 144 0.94 0.97 68 0.91 0.97 9.39 285 0.93 0.96 98 0.91 0.96 7.22 529 0.91 0.95 145 0.91 0.95 5.78 536 0.95 0.94 117 0.94 0.94 5.06 980 0.96 0.92 177 0.95 0.92 4.33 1194 0.95 0.91 178 0.93 0.91 3.83 1350 0.94 0.89 188 0.90 0.89 3.47 1567 0.92 0.87 197 0.89 0.87 3.18 1597 0.89 0.86 184 0.86 0.86 2.96 2136 0.86 0.84 221 0.82 0.84 2.74 1849 0.81 0.82 170 0.83 0.82 2.60 2267 0.81 0.80 200 0.81 0.80 2.46 2844 0.80 0.78 224 0.79 0.78 2.31 3489 0.76 0.76 238 0.71 0.76 2.17 2214 0.71 0.74 91 0.70 0.74 2.06 1781 0.63 0.72 61 0.43 0.72 1.95 Overall average CC: 0.82436110229212012 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.238 B-value to apply to Fc= 11.115 Overall R-factor for FC vs FP: 0.233 for 27452 reflections Writing overall R-factor of 0.233 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.87 24834 0.13 0.10 2631 0.71 0.79 27465 5.6 0.84 0.88 1146 0.06 0.07 403 0.64 0.68 1549 3.5 0.89 0.92 3881 0.09 0.05 633 0.78 0.81 4514 2.8 0.80 0.87 4913 0.17 0.13 560 0.74 0.80 5473 2.4 0.75 0.86 4891 0.13 0.11 451 0.70 0.80 5342 2.1 0.73 0.86 7639 0.18 0.18 500 0.69 0.82 8139 2.0 0.66 0.81 2364 0.17 0.02 84 0.64 0.79 2448 *** Ending these minor cycles as nothing much is happening *** Mask cycle 3 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) Minor cycle 1 of 10 Resolution = 1.95 Offset for s_rho_cur: 2.7277e-09 Values of m, alpha, s Centric: 0.64166530288064816 0.3633322 0.4966661 Acentric: 0.59627028640126312 0.3862703 0.4785081 Using all points for histograms Fraction protein = 0.531 275105 Fraction solvent= 0.469 243146 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 0.73 and 0.11 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 -0.24 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.01 0.01 24834 2631 27465 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.070544 Values of m, alpha, s Centric: 0.64196243372990824 0.3635699 0.4967850 Acentric: 0.59668777752918600 0.3866878 0.4786751 Using all points for histograms Fraction protein = 0.531 275105 Fraction solvent= 0.469 243146 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 0.73 and 0.11 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 -0.25 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.01 0.00 0.01 24834 2630 27464 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 3 of 10 Resolution = 1.95 Offset for s_rho_cur: -0.070526 Values of m, alpha, s Centric: 0.64213978462209154 0.3637119 0.4968559 Acentric: 0.59680509906730428 0.3868051 0.4787220 Using all points for histograms Fraction protein = 0.531 275105 Fraction solvent= 0.469 243146 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 0.73 and 0.11 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 -0.24 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24834 2631 27465 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 4 of 10 Resolution = 1.95 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.070678 Values of m, alpha, s Centric: 0.64222370008572083 0.3637790 0.4968895 Acentric: 0.59700169754088583 0.3870016 0.4788007 Using all points for histograms Fraction protein = 0.531 275105 Fraction solvent= 0.469 243146 Plot 24 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 . . . oxx xxo. . . x xx . . oxx xx . p(rho) . x .xx . . x . ox . . x . oxxx . . xo . ooxxxx . . xo . ooo xxxx . . xoo . oooooxxxxx . . xo . ooxxxxooooooo xxxxo . xxxxxxo 0.0 oooo.............................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 25 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.16.................................................. . . . . . . . oo . . o . . .o . . o. . p(rho) . . o . . o. . . . o . . oxxxx . . xx . xx . . xxo . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.73 and 0.11 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 -0.24 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24834 2631 27465 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: 0.18 0.58 0.60 0.71 0.24 0.60 24834 5.6 0.46 0.86 0.87 0.82 0.16 0.87 1146 3.5 0.46 0.88 0.89 0.87 0.14 0.89 3881 2.8 0.23 0.74 0.75 0.77 0.17 0.75 4913 2.4 0.10 0.55 0.57 0.70 0.21 0.57 4891 2.1 0.06 0.42 0.43 0.65 0.23 0.43 7639 2.0 0.02 0.26 0.27 0.51 0.27 0.27 2364 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: 0.13 0.64 0.64 0.34 0.14 0.64 2631 5.6 0.23 0.82 0.82 0.37 0.17 0.82 403 3.5 0.21 0.79 0.80 0.38 0.16 0.80 633 2.8 0.12 0.67 0.68 0.36 0.13 0.68 560 2.4 0.06 0.53 0.54 0.31 0.09 0.54 451 2.1 0.03 0.42 0.43 0.29 0.07 0.43 500 2.0 0.01 0.24 0.24 0.33 0.04 0.24 84 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 0.68 0.23 0.60 27465 5.6 0.40 0.85 0.86 0.70 0.17 0.86 1549 3.5 0.43 0.87 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.73 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.55 0.56 0.67 0.20 0.56 5342 2.1 0.05 0.42 0.43 0.62 0.22 0.43 8139 2.0 0.02 0.26 0.27 0.50 0.26 0.27 2448 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: 6.59 * * * * 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 69 0.74 0.97 64 0.87 0.97 13.00 144 0.94 0.97 68 0.92 0.97 9.39 285 0.93 0.96 98 0.91 0.96 7.22 529 0.90 0.95 146 0.92 0.95 5.78 536 0.95 0.94 117 0.94 0.94 5.06 980 0.96 0.92 177 0.95 0.92 4.33 1194 0.95 0.91 178 0.93 0.91 3.83 1349 0.94 0.89 188 0.90 0.89 3.47 1567 0.92 0.87 197 0.89 0.87 3.18 1597 0.89 0.86 184 0.85 0.86 2.96 2136 0.85 0.84 221 0.82 0.84 2.74 1849 0.81 0.82 170 0.83 0.82 2.60 2267 0.80 0.80 200 0.80 0.80 2.46 2844 0.80 0.78 224 0.79 0.78 2.31 3489 0.76 0.76 238 0.72 0.76 2.17 2214 0.71 0.74 91 0.71 0.74 2.06 1781 0.63 0.71 61 0.42 0.72 1.95 Overall average CC: 0.82289411346644536 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.243 B-value to apply to Fc= 11.023 Overall R-factor for FC vs FP: 0.233 for 27452 reflections Writing overall R-factor of 0.234 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.87 24834 0.13 0.10 2631 0.71 0.79 27465 5.6 0.85 0.88 1146 0.08 0.07 403 0.65 0.68 1549 3.5 0.89 0.92 3881 0.08 0.05 633 0.77 0.81 4514 2.8 0.80 0.87 4913 0.16 0.13 560 0.73 0.80 5473 2.4 0.75 0.86 4891 0.13 0.11 451 0.70 0.80 5342 2.1 0.73 0.85 7639 0.18 0.18 500 0.69 0.81 8139 2.0 0.65 0.81 2364 0.19 0.02 84 0.64 0.78 2448 *** Ending these minor cycles as nothing much is happening *** 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) Minor cycle 1 of 10 Resolution = 1.95 Offset for s_rho_cur: -1.79292e-09 Values of m, alpha, s Centric: 0.64240543661367200 0.3639244 0.4969622 Acentric: 0.59711790197182424 0.3871179 0.4788471 Using all points for histograms Fraction protein = 0.531 275070 Fraction solvent= 0.469 243181 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 0.73 and 0.11 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 -0.24 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24834 2631 27465 Writing overall R-factor of 0.234 to resolve.rfactor Minor cycle 2 of 10 Resolution = 1.95 ____________________________________________________________ Final cycle Offset for s_rho_cur: -0.0711511 Values of m, alpha, s Centric: 0.64216392059352811 0.3637312 0.4968656 Acentric: 0.59710278636021696 0.3871027 0.4788411 Using all points for histograms Fraction protein = 0.531 275070 Fraction solvent= 0.469 243181 Plot 26 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 . . . oxx xxo. . . x xo . . oxx xx . p(rho) . x .xx . . x . ox . . x . oxxx . . xo . ooxxxx . . xo . oooxxxxx . . xoo . oooooxxxxx . . xo . ooxxxxooooooo .xxxo . xxxxxxo 0.0 xooo.............................................x -2 -1 0 1 2 3 normalized rho (0 = mean of solvent region) ------------------------------------------------------------------------------- Plot 27 Plot of Observed (o) and model (x) electron density distributions for solvent region 0.16.................................................. . . . . . . . oo . . o . . .o . . o. . p(rho) . . o . . o. . . . o . . oxxxx . . xx . xx . . xxo . xxx . . xx o . o xx . . xx oo . oo xx . 0.0 xxxxxxxxxxxxoooo.........ooooxxxxxxxxxxxxxxxxxxxxx -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 0.20 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.73 and 0.11 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 -0.24 and sigma is a random variable with rms value of 0.20 Mean starting figure of merit this cycle Overall Centric Acentric 0.60 0.64 0.60 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.00 0.00 0.00 24834 2631 27465 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: 0.18 0.58 0.60 0.71 0.24 0.60 24834 5.6 0.46 0.86 0.87 0.82 0.17 0.87 1146 3.5 0.46 0.88 0.89 0.87 0.14 0.89 3881 2.8 0.23 0.74 0.75 0.77 0.17 0.75 4913 2.4 0.10 0.55 0.57 0.70 0.21 0.57 4891 2.1 0.06 0.42 0.43 0.65 0.23 0.43 7639 2.0 0.02 0.26 0.27 0.51 0.27 0.27 2364 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: 0.13 0.64 0.64 0.34 0.14 0.64 2631 5.6 0.23 0.82 0.82 0.37 0.17 0.82 403 3.5 0.21 0.79 0.80 0.38 0.16 0.80 633 2.8 0.12 0.67 0.68 0.36 0.13 0.68 560 2.4 0.06 0.53 0.54 0.30 0.09 0.54 451 2.1 0.03 0.42 0.43 0.29 0.07 0.43 500 2.0 0.01 0.24 0.24 0.33 0.04 0.24 84 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 0.67 0.23 0.60 27465 5.6 0.40 0.85 0.86 0.70 0.17 0.86 1549 3.5 0.43 0.87 0.87 0.80 0.15 0.87 4514 2.8 0.22 0.73 0.74 0.73 0.17 0.74 5473 2.4 0.10 0.55 0.56 0.67 0.20 0.56 5342 2.1 0.05 0.42 0.43 0.62 0.22 0.43 8139 2.0 0.02 0.26 0.27 0.50 0.26 0.27 2448 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: 6.58 * * * * 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 69 0.74 0.97 64 0.87 0.97 13.00 144 0.94 0.97 68 0.92 0.97 9.39 285 0.93 0.96 98 0.91 0.96 7.22 529 0.90 0.95 146 0.92 0.95 5.78 536 0.95 0.94 117 0.94 0.94 5.06 979 0.96 0.92 177 0.95 0.92 4.33 1194 0.95 0.91 178 0.93 0.91 3.83 1349 0.94 0.89 188 0.90 0.89 3.47 1567 0.92 0.87 197 0.89 0.87 3.18 1597 0.89 0.85 184 0.85 0.85 2.96 2136 0.85 0.84 221 0.82 0.84 2.74 1849 0.81 0.82 170 0.83 0.82 2.60 2267 0.80 0.80 200 0.80 0.80 2.46 2844 0.80 0.78 224 0.79 0.78 2.31 3489 0.76 0.76 238 0.72 0.76 2.17 2214 0.71 0.74 91 0.71 0.74 2.06 1781 0.63 0.71 61 0.42 0.71 1.95 Overall average CC: 0.82268133780668873 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.245 B-value to apply to Fc= 11.021 Overall R-factor for FC vs FP: 0.234 for 27451 reflections Writing overall R-factor of 0.234 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.77 0.87 24834 0.13 0.10 2631 0.71 0.79 27465 5.6 0.85 0.89 1146 0.08 0.07 403 0.65 0.68 1549 3.5 0.89 0.92 3881 0.08 0.04 633 0.77 0.80 4514 2.8 0.80 0.86 4913 0.16 0.13 560 0.73 0.80 5473 2.4 0.75 0.86 4891 0.14 0.11 451 0.70 0.80 5342 2.1 0.73 0.85 7639 0.18 0.18 500 0.69 0.81 8139 2.0 0.65 0.81 2364 0.17 0.03 84 0.64 0.78 2448 *** Ending these minor cycles as nothing much is happening *** *** Skipping to end as nothing much happened this mask cycle *** Skipping Mask cycle 5 Writing out 13 columns of data CC of prob map with current map: 0.8685082 resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/aaa_resolve_main.cpp source_line: 1670 status: 0 EndOfResolve