------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by Los Alamos National Security, LLC at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- RESOLVE --- * * * * Statistical density modification * * Automated model-building * * * * For on-line help * * see "http://solve.lanl.gov" * * * * This software uses library routines from the * * CCP4 suite (http://www.ccp4.ac.uk) for which * * the author is very thankful! * ******************************************************* (version 2.15 of 20-Mar-2010) (size = 12) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" >workdir AutoBuild_run_1_/TEMP0 Work directory will be : AutoBuild_run_1_/TEMP0/ >outputdir AutoBuild_run_1_ Directory for STOPWIZARD will be AutoBuild_run_1_/ >freer_if_present Only writing out FreeR_flag if present >hklin exptl_phases_and_amplitudes_for_density_modification_aniso.mtz Data to be read from mtz file: exptl_phases_and_amplitudes_for_density_modification_aniso.mtz >labin FP=FP SIGFP=SIGFP Current value of "LABIN" is: labin FP=FP SIGFP=SIGFP >hklout image.mtz Data to be written to mtz file: image.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 >pattern_phase Phasing using prior information and pattern map >cc_map_file combine.map Reading cc map from: combine.map >use_wang Wang 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 exptl_phases_and_amplitudes_for_density_modification_aniso.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 exptl_phases_and_amplitudes_for_density_modification_aniso.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 DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP : SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 4 Dataset information for dataset number 2 and ID= 1 Dataset name:dataset Crystal name:crystal Project name:project Cell: 72.239998 72.010002 86.989998 90.000000 90.000000 90.000000 Wavelength: 1.000000 Note: not using either PHIB or PHIC Reading in SIGFP from column 5 No FreeR_flag read in or created Total of 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 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: 0.00 Mean fom of this map was: 0.00 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Starting smoothing radius will be 4.000000 Setting final smoothing radius to 4.000000 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_finish" Adding extra mask cycle at end to include model information Solvent content will be 0.47 Using database entry 5 for histograms (" 3 A dehalogenase model ") Total mask cycles: 1 Total density modification mask cycles: 1 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 NO NO NO YES YES NO 1 Mask cycle 1 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Scale on input map combine.map is 0.362548 Number of records in input map combine.map is 518400 No FOM in the map file. Using 0.8 Read fstring_struct_4.cc_map_file from combine.map FOM of data used to get CC map: 0.8000000 CC of map file to rho: 0.000000 Using NCS or image this mask cycle Minor cycle 1 of 1 Resolution = 1.95 ____________________________________________________________ Final cycle Offset for s_rho_cur: 0 Just using mask phases and prior this cycle Values of m, alpha, s Centric: 0.0000000000000000 5.9999996E-03 9.9999998E-03 Acentric: 0.0000000000000000 5.9999996E-03 9.9999998E-03 RMS CALC, OBS: 0.1515056 0.000000 518400 Scale on recov to minimize (recov-obs)**2: 0.000000 Actual scale on recov used: 1.000000 Resulting scale * rms obs (recov)= 0.1515056 RMSD_OVERALL set to RMS_RHO_PROT of 0.5681459 Comparison of image and map: RMS map= 0.00 RMSD between image and map is: 0.57 CC of image and map= 0.00 Final RMSD used for image target: 0.568146 Image information used in phasing: Number of points with... image based on model: 518400 image + NCS 0 image only: 0 no information: 0 total in au: 518400 MAP RMS and SIG: 0.152 0.568 518400 Zeroing out reflections and map -- using image only Error estimate for map on this cycle The estimated error in this map is 0.00 based on an analysis of the electron density distributions in the protein and solvent regions with rms values of 0.00 and 0.00 respectively. The value of the scale factor beta relating idealized density distributions P_ideal(rho) to observed ones is: obs_rho = beta * (ideal_rho + offset) + sigma where beta = 1.00 offset is 0.00 and sigma is a random variable with rms value of 0.00 Number of points with image info included: 518400 Mean starting figure of merit this cycle Overall Centric Acentric 0.00 0.00 0.00 27465 2631 24834 Mean normalized structure factor changes this cycle Acentric Centric All 0.18 0.17 0.18 24813 2006 26819 New figure of merit () of phasing based on: (1) experimental phase information, and (2) the probability of the resulting map These are the 2 sources of phase information used in resolve. The phase information from them should be correlated and the phase information from the map should increase during statistical density modification. Correlation between prior and map phase information is measured by , the mean cosine of the phase difference. Best estimate of true figure of merit of map-probability phasing is ratio of correlation to of prior information Fraction of phase information from prior is estimated from of prior, map Acentric reflections only: --Figure of merit-- CC Fraction Total DMIN Prior Map Total Prior-Map from Prior (corrected) N ALL: 0.00 0.18 0.18 0.00 0.00 0.18 24834 5.6 0.00 0.47 0.47 0.00 0.00 0.47 1146 3.5 0.00 0.47 0.47 0.00 0.00 0.47 3881 2.8 0.00 0.23 0.23 0.00 0.00 0.23 4913 2.4 0.00 0.10 0.10 0.00 0.00 0.10 4891 2.1 0.00 0.06 0.06 0.00 0.00 0.06 7639 2.0 0.00 0.02 0.02 0.00 0.00 0.02 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: 0.00 0.13 0.13 0.00 0.01 0.13 2631 5.6 0.00 0.23 0.23 0.00 0.00 0.23 403 3.5 0.00 0.21 0.21 0.00 0.00 0.21 633 2.8 0.00 0.12 0.12 0.00 0.01 0.12 560 2.4 0.00 0.06 0.06 0.00 0.02 0.06 451 2.1 0.00 0.03 0.03 0.00 0.03 0.03 500 2.0 0.00 0.01 0.01 0.00 0.09 0.01 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: 0.00 0.17 0.17 0.00 0.00 0.17 27465 5.6 0.00 0.41 0.41 0.00 0.00 0.41 1549 3.5 0.00 0.43 0.43 0.00 0.00 0.43 4514 2.8 0.00 0.22 0.22 0.00 0.00 0.22 5473 2.4 0.00 0.10 0.10 0.00 0.00 0.10 5342 2.1 0.00 0.05 0.05 0.00 0.00 0.05 8139 2.0 0.00 0.02 0.02 0.00 0.00 0.02 2448 WGT: 1.00 1.00 ********************************************************************** * * * CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.17 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.00 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 1.00 * * NOTE: The fraction from prior will be roughly proportional to * * prior_weight (current value = 1.00) * * * * BIAS RATIO: 0.00 * * * * Bias ratio is given by /(FOMA*FOMB), * * where phiA and FOMA are phase and from prior (model or * * experiment) and phiB and FOMB are from map. * * Bias ratio is about 1 if phiA and phiB are independent, * * >1 if phiB is biased by phiA, * * <1 if FOMA or FOMB are overestimated * * * * If BIAS RATIO <1, CORRECTED FOM = ESTIMATED FOM * BIAS RATIO * ********************************************************************** Analysis of FC CC of FP and FC vs resolution (CALC is fit to the observed CC with a pseudo-B) ACENTRIC CENTRIC N CC CALC N CC CALC DMIN 70 0.82 0.80 67 0.52 0.80 13.00 144 0.92 0.80 68 0.36 0.80 9.39 285 0.85 0.80 98 0.47 0.80 7.22 529 0.82 0.79 146 0.42 0.79 5.78 536 0.89 0.79 117 0.38 0.79 5.06 981 0.91 0.78 180 0.38 0.78 4.33 1195 0.89 0.78 180 0.46 0.78 3.83 1350 0.87 0.77 189 0.34 0.77 3.47 1567 0.86 0.76 197 0.44 0.76 3.18 1597 0.84 0.76 184 0.43 0.76 2.96 2136 0.79 0.75 221 0.47 0.75 2.74 1849 0.77 0.74 170 0.43 0.74 2.60 2267 0.76 0.73 200 0.45 0.73 2.46 2844 0.75 0.72 224 0.23 0.72 2.31 3489 0.75 0.71 238 0.36 0.71 2.17 2214 0.68 0.70 91 0.27 0.70 2.06 1781 0.63 0.69 61 0.12 0.69 1.95 Overall average CC: 0.74205215496485644 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 9.938 B-value to apply to Fc= 13.535 Overall R-factor for FC vs FP: 0.302 for 26913 reflections Leaving out 553 reflections with FC=0 and correcting R-factor to 0.308 from 0.302 as only 98 percent of the reflections are ok Writing overall R-factor of 0.308 to resolve.rfactor Cumulative phase change from start to end of this cycle [] DMIN -----acentric-------- --------centric------- ---------all--------- N N N 0.0 0.00 -0.01 24834 -0.02 0.01 2631 -0.00 -0.01 27465 5.6 -0.01 -0.04 1146 -0.02 0.09 403 -0.01 -0.02 1549 3.5 -0.00 -0.00 3881 -0.02 -0.06 633 -0.00 -0.01 4514 2.8 0.01 -0.01 4913 -0.03 -0.02 560 0.00 -0.01 5473 2.4 0.01 0.00 4891 0.04 0.17 451 0.01 0.01 5342 2.1 -0.01 -0.00 7639 -0.06 -0.03 500 -0.01 -0.01 8139 2.0 -0.01 0.01 2364 0.06 0.31 84 -0.00 0.01 2448 End of first cycle ____________________________________________________________ Writing out 13 columns of data CC of prob map with current map: 0.000000 resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/aaa_resolve_main.cpp source_line: 1670 status: 0 EndOfResolve