------------------------ 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_/ >write_if_present Only writing out HL coeffs and FreeR_flag if present >hklin refinement_PHX.mtz Data to be read from mtz file: refinement_PHX.mtz >labin FP=FOBS SIGFP=SIGFOBS FreeR_flag=R-free-flags Current value of "LABIN" is: labin FP=FOBS SIGFP=SIGFOBS FreeR_flag=R-free-flags >hklout exptl_fobs_phases_freeR_flags.mtz Data to be written to mtz file: exptl_fobs_phases_freeR_flags.mtz >solvent_content 0.47 Fraction of unit cell assumed to be solvent is: 0.4700000 >no_build Model will not be built >mask_cycles 1 Number of mask/image cycles: 1 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >ha_file NONE Heavy atom sites will be read from file: NONE The file does not exist...ignoring it >keep_missing All reflections kept, even with missing F >use_wang Wang method for solvent mask will be used >no_ha no_ha: heavy-atoms not written out in pdb files >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 >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 refinement_PHX.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 refinement_PHX.mtz Space group name: P212121 Point group: 222 Space group number : 19 Symmetry operators: 4 Number of columns: 6 H K L FOBS SIGFOBS R-free-flags Column assignments: PROGRAM INPUT_MTZ DATA# 1 H DATA# 2 K DATA# 3 L DATA# 4 FP : FOBS 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 : SIGFOBS DATA# 14 FWT DATA# 15 FreeR_flag : R-free-flags 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 Reading in FreeR_flag Total of 28288 reflections read from file Guessing FreeR_flag corresponding to free reflections This can be set with free_id xx Free R reflections are those with FreeR_flag= 0 Total of 2807 of 28288 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 MATRICES: SYMMETRY ELEMENT 0 1 0 0 0 0 1 0 0 0 0 1 0 SYMMETRY ELEMENT 1 1 0 0 0.5 0 -1 0 0.5 0 0 -1 0 SYMMETRY ELEMENT 2 -1 0 0 0 0 1 0 0.5 0 0 -1 0.5 SYMMETRY ELEMENT 3 -1 0 0 0.5 0 -1 0 0 0 0 1 0.5 SPACE GROUP SYMBOL: P 21 21 21 CHECK ON SPACE GROUP SYMBOL: P 21 21 21 HALL SYMBOL : P 2ac 2ab Standard grids used for FFT 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 = 139.499 B-value = 16.868 Scaling data with value of 139.499 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 Note: need data in at least 3 res shells in find_b Summary of starting FOM vs resolution RES FOM FOM-smoothed N No phased data... 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" 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 NO YES NO 0 Mask cycle 1 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.47 Smoothing radius: 4.00 Using Wang mask (highest SD points) New Wang averaging radius = 4.00 sorry, this map has no density. sorry, this map has no density. Mean +/- SD of density in protein region : 0.00 +/- 0.00 Mean +/- SD of density in solvent region : 0.00 +/- 0.00 sorry, this map has no density. sorry, this map has no density. MEAN SD PROT for SQ-SM : 0.00 +/- 0.00 MEAN SD SOLV for SQ-SM : 0.00 +/- 0.00 N: 0 518400 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 .................................................. . + . . + . . + . . + . . + . . + . p(protein) .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.5 . + . . + . . + . . + . . + . . + . . + . 0.0 ........................+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Range of P(protein) and percentiles used for histograms of protein and solvent: P(protein) Percentile Low High Low High Protein: 0.53 1.00 72 100 Solvent: 0.00 0.53 0 24 Plot 2 ------------------------------------------------------------------------------- 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 .................................................. . + . . + . . + . . + . . + . . + . p(protein) .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.5 . + . . + . . + . . + . . + . . + . . + . 0.0 ........................+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Writing out 10 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