------------------------ 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 >no_build Model will not be built >ha_file TEMP.pdb Heavy atom sites will be read from file: TEMP.pdb >ncs_only Just finding NCS and quitting >fraction_ncs_min 0.05 Minimum fraction of a.u. following NCS to keep it: 5.0000001E-02 >ha_ds_window 4.0 Carrying out ha search but assuming it is after a density search Window in ha search will be 4 >window_max 30.0 Carrying out ha search with window_max of 30 >dist_cut_ncs 0.1 Cutoff (A) for considering two points as same by NCS = 0.1000000 >ncs_thorough 8 Relative number of entries in lists for NCS searches (default=8): 8 >force_ncs NCS symmetry will be used whether it appears to exist or not >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 New total number of NCS groups: 1 Copy to group 1 0 ------------------------------------------- Summary of NCS groups NCS GROUP 1 OPERATORS READ: 0 DOMAIN FILE: HA FILE: TEMP.pdb ------------------------------------------- Total of 1 NCS groups. 0 Restoring group 1 now, with 0 operators 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 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 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: 3573 Warning -- Total of 1 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 : 861.376 Results of wilson scaling: Scale on I = 161.669 B-value = 18.580 Scaling data with value of 161.669 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: 1.00 Copy to group 1 0 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 17.28 1.00 1.00 137 10.73 1.00 1.00 212 8.09 1.00 1.00 383 6.37 1.00 1.00 675 5.37 1.00 1.00 653 4.65 1.00 1.00 1161 4.06 1.00 1.00 1375 3.63 1.00 1.00 1539 3.31 1.00 1.00 1764 3.06 1.00 1.00 1781 2.85 1.00 1.00 2357 2.67 1.00 1.00 2019 2.52 1.00 1.00 2467 2.38 1.00 1.00 3068 2.24 1.00 1.00 3727 2.11 1.00 1.00 2305 2.01 1.00 1.00 1842 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 = 1.950131 and fom = 1.000000 Leading to R= 4.396170 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" Total of 1 NCS groups. 0 Restoring group 1 now, with 0 operators NOTE: No NCS in std xl... Opening TEMP.pdb and reading coordinates Center of molecule read in with 12 atoms is 17.572418 48.810917 34.152088 ----------------------------------------------------------------- ----------------------------------------------------------------- Searching for NCS in supplied heavy atom sites from the file: TEMP.pdb NCS: Total of 12 heavy atom sites read in NCS: Points within 0.10 A will be considered close Max distance of an atom to origin: 30.6 A. NCS: Number of expanded coordinates = 155, or 12 per atom NCS: Only included coordinates within 71.73 A of the origin. NCS: (Left out 1141 coordinates ) NCS: Found total of 144 sets of matching distances Considering the first 137 pairs in most applications Dist_cut= 0.1000000 window_max: 4.000000 **** TESTING 4 TRANSFORMS ***** NCS: SYMMETRY FOUND WITH 4 TRANSFORMATIONS: AND RMSD 0F: 0.00 THIS NCS MAY NOT HAVE POINT_GROUP SYMMETRY GROUP 1 RADIUS= 2.65 WITH SITES: 8 9 7 ROTATION/TRANSLATION FROM 1 to 1 : 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 GROUP 2 RADIUS= 2.65 WITH SITES: 11 12 10 ROTATION/TRANSLATION FROM 1 to 2 : -0.530 0.685 -0.500 15.528 -0.592 0.123 0.797 19.836 0.607 0.718 0.340 -1.873 GROUP 3 RADIUS= 2.65 WITH SITES: 5 6 4 ROTATION/TRANSLATION FROM 1 to 3 : -1.000 -0.009 0.018 2.764 -0.018 0.826 -0.564 3.155 -0.010 -0.564 -0.826 9.236 GROUP 4 RADIUS= 2.65 WITH SITES: 2 3 1 ROTATION/TRANSLATION FROM 1 to 4 : 0.940 0.288 -0.185 7.969 -0.117 0.779 0.616 42.403 0.321 -0.557 0.766 -5.404 LIST OF NCS-RELATED SITES (A SYM EQUIV FOR WHICH NCS APPLIES IS LISTED) SITE NCS EQUIV/RMSD XYZ xyz 8 0.36 -12.55 -6.96 0.00 -0.17 -0.08 9 -0.40 -10.66 -7.87 -0.01 -0.15 -0.09 7 0.59 -11.99 -4.91 0.01 -0.17 -0.06 11 8 0.00 10.22 12.54 -13.04 0.14 0.17 -0.15 12 9 0.00 12.38 12.50 -12.45 0.17 0.17 -0.14 10 7 0.00 9.46 14.10 -11.80 0.13 0.20 -0.14 5 8 0.00 2.40 -3.29 22.06 0.03 -0.05 0.25 6 9 0.00 3.12 -1.20 21.75 0.04 -0.02 0.25 4 7 0.00 2.20 -3.99 20.05 0.03 -0.06 0.23 2 8 0.00 5.98 28.30 -3.63 0.08 0.39 -0.04 3 9 0.00 5.98 29.30 -5.62 0.08 0.41 -0.06 1 7 0.00 5.98 29.97 -2.29 0.08 0.42 -0.03 TOTAL SITES (score): 12 ***** RESULT: Best Number of transforms: 4 ***** End of searching for NCS in supplied heavy atom sites ----------------------------------------------------------------- ----------------------------------------------------------------- Copy to group 1 4 Total of 1 NCS groups. 4 Restoring group 1 now, with 4 operators -------------------------------------- Analysis of NCS for NCS group 1 Total of 1 NCS groups. 4 Restoring group 1 now, with 4 operators Non-crystallographic symmetry elements used: (All operating on orthogonal Angstrom coordinates XYZ of molecule 1 to generate new X-prime Yprime Zprime matching molecule j) Operator # 1 New X-prime= 1.0000 X + -0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + 0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + 0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 0.18 -11.73 -6.58 and as input by user is, 0.18 -11.73 -6.58 Operator # 2 New X-prime= -0.5304 X + 0.6849 Y + -0.4995 Z + 15.5283 New Y-prime= -0.5919 X + 0.1226 Y + 0.7966 Z + 19.8355 New Z-prime= 0.6069 X + 0.7182 Y + 0.3404 Z + -1.8727 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 10.68 13.05 -12.43 and as input by user is, 10.68 13.05 -12.43 Operator # 3 New X-prime= -0.9998 X + -0.0092 Y + 0.0181 Z + 2.7644 New Y-prime= -0.0178 X + 0.8257 Y + -0.5639 Z + 3.1546 New Z-prime= -0.0098 X + -0.5641 Y + -0.8257 Z + 9.2357 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.57 -2.82 21.29 and as input by user is, 2.57 -2.82 21.29 Operator # 4 New X-prime= 0.9396 X + 0.2878 Y + -0.1851 Z + 7.9692 New Y-prime= -0.1172 X + 0.7789 Y + 0.6161 Z + 42.4029 New Z-prime= 0.3215 X + -0.5572 Y + 0.7656 Z + -5.4044 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 5.98 29.19 -3.85 and as input by user is, 5.98 29.19 -3.85 Inverses of transformations: (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + -0.0000 Z + -0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + -0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + -0.0000 Operator # 2 New X-prime= -0.5304 X + -0.5919 Y + 0.6069 Z + 21.1139 New Y-prime= 0.6849 X + 0.1226 Y + 0.7182 Z + -11.7224 New Z-prime= -0.4995 X + 0.7966 Y + 0.3404 Z + -7.4074 Operator # 3 New X-prime= -0.9998 X + -0.0178 Y + -0.0098 Z + 2.9105 New Y-prime= -0.0092 X + 0.8257 Y + -0.5641 Z + 2.6306 New Z-prime= 0.0181 X + -0.5639 Y + -0.8257 Z + 9.3542 Operator # 4 New X-prime= 0.9396 X + -0.1172 Y + 0.3215 Z + -0.7809 New Y-prime= 0.2878 X + 0.7789 Y + -0.5572 Z + -38.3328 New Z-prime= -0.1851 X + 0.6161 Y + 0.7656 Z + -20.5113 Transformations formatted for input to resolve: rota_matrix 1.0000 0.0000 -0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -0.0000 -0.0000 -0.0000 center_orth 0.1808 -11.7318 -6.5817 rota_matrix -0.5304 -0.5919 0.6069 rota_matrix 0.6849 0.1226 0.7182 rota_matrix -0.4995 0.7966 0.3404 tran_orth 21.1139 -11.7224 -7.4074 center_orth 10.6848 13.0470 -12.4294 rota_matrix -0.9998 -0.0178 -0.0098 rota_matrix -0.0092 0.8257 -0.5641 rota_matrix 0.0181 -0.5639 -0.8257 tran_orth 2.9105 2.6306 9.3542 center_orth 2.5723 -2.8237 21.2860 rota_matrix 0.9396 -0.1172 0.3215 rota_matrix 0.2878 0.7789 -0.5572 rota_matrix -0.1851 0.6161 0.7656 tran_orth -0.7809 -38.3328 -20.5113 center_orth 5.9810 29.1889 -3.8483 Analysis of NC symmetry using cutoff of 0.10 A as maximum distance between intersecting elements Did not find any NC operator combinations consistent with a point group No point-group symmetry found End of analysis of NCS ----------------------------------------------------------------- ----------------------------------------------------------------- -------------------------------------- resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/aaa_resolve_main.cpp source_line: 1670 status: 0 EndOfResolve