------------------------ 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 = 6) 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_/TEMP0 Directory for STOPWIZARD will be AutoBuild_run_1_/TEMP0/ >freer_if_present Only writing out FreeR_flag if present >hklin TEMP_working_best_denmod_map_coeffs.mtz Data to be read from mtz file: TEMP_working_best_denmod_map_coeffs.mtz >labin FP=FWT PHIB=PHWT Current value of "LABIN" is: labin FP=FWT PHIB=PHWT >solvent_content 0.5 Fraction of unit cell assumed to be solvent is: 0.5000000 >no_build Model will not be built >resolution 1000. 4.0 Resolution range (A) is: 4.000000 to 1000.000 >ha_file NONE Heavy atom sites will be read from file: NONE The file does not exist...ignoring it >find_centers Looking for high rms regions to find molecule >wang_radius 10.0 Wang radius for solvent mask identification for each mask cycle: will be 10.00000 >use_wang Wang method for solvent mask will be used >ha_file None Heavy atom sites will be read from file: None The file does not exist...ignoring it >mask_cycles 1 Number of mask/image cycles: 1 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >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 >no_create_free Will not create FREE (test) set >use_all_for_test Will use all data for testing solvent content and histograms 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 TEMP_working_best_denmod_map_coeffs.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 TEMP_working_best_denmod_map_coeffs.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 : FWT DATA# 5 PHIB : PHWT DATA# 6 FOM DATA# 7 HLA DATA# 8 HLB DATA# 9 HLC DATA# 10 HLD DATA# 11 FC DATA# 12 PHIC DATA# 13 SIGFP DATA# 14 FWT DATA# 15 FreeR_flag FP taken from column 12 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 13 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 4063 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 4063 reflections in test set High-resolution limit of input phased data: 4.00 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 4.00 max: 4.00 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: 2977 Not separating out FREE set from other reflections for main cycles. Using all data. Expected resolution-corrected F at d = 2.9A : 786.325 Results of wilson scaling: Scale on I = 164.893 B-value = 7.895 Scaling data with value of 164.893 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: 59 53 18 nu nv nw: 60 54 72 Number of grid points in au: 58320 Mean fom of this map was: 1.00 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 32.49 1.00 1.00 15 21.93 1.00 1.00 28 16.66 1.00 1.00 49 13.10 1.00 1.00 87 11.06 1.00 1.00 81 9.54 1.00 1.00 149 8.32 1.00 1.00 168 7.46 1.00 1.00 191 6.80 1.00 1.00 217 6.29 1.00 1.00 225 5.84 1.00 1.00 302 5.47 1.00 1.00 255 5.17 1.00 1.00 322 4.88 1.00 1.00 388 4.59 1.00 1.00 514 4.33 1.00 1.00 476 4.11 1.00 1.00 596 Mean fom of this map was: 1.00 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Starting smoothing radius will be 10.00000 Smoothing radius for all cycles after the first will be 10.00000 Solvent content will be 0.50 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: 0.50 Smoothing radius: 10.00 New Wang averaging radius = 10.00 Mean +/- SD of density in protein region : 0.05 +/- 0.50 Mean +/- SD of density in solvent region : -0.05 +/- 0.21 Guessing molecular centers... Found 4 peaks peak 42.14 6.6676 3.62458 0.221665 rho: 0.221665 min dist: 43.2564 peak 71.0361 65.3424 1.20819 0.220936 rho: 0.220936 min dist: 42.7131 peak 4.81609 68.0095 13.2901 0.216521 rho: 0.216521 min dist: 40.9297 peak 43.344 17.3358 12.0819 0.213535 rho: 0.213535 min dist: 43.345 Total of 4 peaks written to center_peaks.pdb Writing out 13 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