------------------------ 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 refine_pdb_in.mtz Data to be read from mtz file: refine_pdb_in.mtz >labin FP=2FOFCWT PHIB=PH2FOFCWT Current value of "LABIN" is: labin FP=2FOFCWT PHIB=PH2FOFCWT >hklout map_coeffs.mtz Data to be written to mtz file: map_coeffs.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 >resolution 1.6096 500.0 Resolution range (A) is: 1.609600 to 500.0000 >ha_file NONE Heavy atom sites will be read from file: NONE The file does not exist...ignoring it >no_fill Missing reflections will not be filled in >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 >n_xyz 120 150 180 Grid units x y z: 120 150 180 >database 5 Entry in database of histograms to use: 5 >no_optimize_ncs Not optimizing NCS >spg_name_use P 1 21 1 Space group name for output PDB file only: P 1 21 1 >min_z_value_rho -3.0 Minimum z-value for a segment not matched to sequence: -3.000000 >no_create_free Will not create FREE (test) set >use_all_for_test Will use all data for testing solvent content and histograms >delta_phi 20.00 Angular grid (degrees) for image search: 20.00000 >dist_cut_base 3.0 Tolerance for base pairing (dist_cut_base): 3.000000 >free_id 0 Free R flag ID will be 0 >group_ca_length 4 Minimum # of residues in a group to keep= 4 >group_length 2 Minimum # of segments in a group to keep= 2 >n_random_frag 0 Number of random orientations of start/end of fragments: 0 All done with inputs Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB NONE All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 08-oct-14. Your license is good until 15-dec-96. Opened mtz file refine_pdb_in.mtz Dataset 1 HKL_base HKL_base HKL_base 0 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 0.000000 Dataset 2 project crystal Original-experimenta 1 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Dataset 3 project crystal Experimental-data-us 2 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Dataset 4 project crystal Model-structure-fact 3 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Dataset 5 project crystal Fourier-map-coeffici 4 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Reading SG information from refine_pdb_in.mtz Space group name: P21 Point group: 2 Space group number : 4 Symmetry operators: 2 Number of columns: 16 H K L F-obs SIGF-obs R-free-flags F-obs-filtered SIGF-obs-filtered F-model PHIF-model 2FOFCWT PH2FOFCWT 2FOFCWT_no_fill PH2FOFCWT_no_fill FOFCWT PHFOFCWT Column assignments: PROGRAM INPUT_MTZ DATA# 1 H DATA# 2 K DATA# 3 L DATA# 4 FP : 2FOFCWT DATA# 5 PHIB : PH2FOFCWT DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 11 Dataset information for dataset number 5 and ID= 4 Dataset name:Fourier-map-coeffici Crystal name:crystal Project name:project Cell: 59.554001 79.206001 87.430000 90.000000 92.260002 90.000000 Wavelength: 1.000000 PHIB taken from column 12 WARNING: No SIGFP input data--output SIGFP column will be SIGFP=1.0 for all HKL! No FreeR_flag read in or created Total of 105036 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 105036 reflections in test set High-resolution limit of input phased data: 1.61 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 1.61 max: 1.61 Space group is 4 Using symmetry operations from input MTZ file Transformations from orthogonal to fractional and back: Orthogonal to fractional fractional x= 0.01679 X + -0.00000 Y + 0.00066 Z fractional y= 0.00000 X + 0.01263 Y + -0.00000 Z fractional z= 0.00000 X + 0.00000 Y + 0.01145 Z Fractional to orthogonal Orthogonal X= 59.55400 x + 0.00009 y + -3.44763 z Orthogonal Y= 0.00000 x + 79.20600 y + 0.00010 z Orthogonal Z= 0.00000 x + 0.00000 y + 87.36200 z Estimated # of atoms in au: 5748 Not separating out FREE set from other reflections for main cycles. Using all data. Expected resolution-corrected F at d = 2.9A : 772.557 Results of wilson scaling: Scale on I = 17.941 B-value = -6.056 Scaling data with value of 17.941 Reading model density histograms from /net/chevy/raid1/afonine/sources/solve_resolve/ext_ref_files/segments/rho.list Read total of 10 sets of density functions Highest value of ix, iy, iz in a.u: 119 149 90 nu nv nw: 120 150 180 Number of grid points in au: 1620000 Mean fom of this map was: 1.00 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 14.43 1.00 1.00 384 8.84 1.00 1.00 615 6.66 1.00 1.00 1149 5.25 1.00 1.00 2021 4.44 1.00 1.00 1998 3.84 1.00 1.00 3580 3.35 1.00 1.00 4341 3.00 1.00 1.00 4837 2.73 1.00 1.00 5570 2.53 1.00 1.00 5767 2.35 1.00 1.00 7653 2.20 1.00 1.00 6612 2.08 1.00 1.00 8298 1.96 1.00 1.00 10457 1.84 1.00 1.00 13417 1.74 1.00 1.00 12716 1.65 1.00 1.00 15621 Mean fom of this map was: 1.00 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Estimating optimal initial smoothing radius using the function: R=2.41 * (dmin**0.90) * (fom**-0.26) with dmin = 1.609600 and fom = 1.000000 Leading to R= 3.698820 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: 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: 3.70 Using Wang mask (highest SD points) New Wang averaging radius = 3.70 Mean +/- SD of density in protein region : 0.01 +/- 1.25 Mean +/- SD of density in solvent region : -0.01 +/- 0.52 MEAN SD PROT for SQ-SM : 0.82 +/- 0.17 MEAN SD SOLV for SQ-SM : 0.29 +/- 0.10 N: 858615 761385 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 .............................xxxxxxxxxxxxxxxxxxxxx . + . . + x . . + x . . + . . + . . + x . p(protein) . + . 0.5 . + . . +x . . + . . x . . + . . x+ . . xx + . 0.0 .xxxxxxxxxxxxxxxxxxxx...+......................... 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: 0.84 1.00 56 100 Solvent: 0.00 0.15 0 46 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 .............................xxxxxxxxxxxxxxxxxxxxx . + . . + x . . + x . . + . . + . . + x . p(protein) . + . 0.5 . + . . +x . . + . . x . . + . . x+ . . xx + . 0.0 .xxxxxxxxxxxxxxxxxxxx...+......................... 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Writing out 9 columns of data CC of prob map with current map: 1.000000 resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/aaa_resolve_main.cpp source_line: 1670 status: 0 EndOfResolve