------------------------ 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 PHIB=PHIM FOM=FOMM Current value of "LABIN" is: labin FP=FP PHIB=PHIM FOM=FOMM >solvent_content 0.47 Fraction of unit cell assumed to be solvent is: 0.4700000 >no_build Model will not be built >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 >composite_all All files in composite used equally >dump_composite Dumping composite map to dump.map >composite_pdb refine.pdb_ PDB file template for creating composite map: refine.pdb_ >composite_pdb_first 1 First PDB file to consider in composite: 1 >composite_pdb_last 1 Number of last PDB file in composite: 1 >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 Setting up PDB files for composite map Range of file numbers: 1 to 1 File 1 is refine.pdb_1 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 exptl_phases_and_amplitudes_for_density_modification_aniso.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 dataset 1 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Reading SG information from exptl_phases_and_amplitudes_for_density_modification_aniso.mtz Space group name: P21 Point group: PG2 Space group number : 4 Symmetry operators: 2 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 : PHIM DATA# 6 FOM : FOMM 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 4 Dataset information for dataset number 2 and ID= 1 Dataset name:dataset 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 6 FOM taken from column 7 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 84260 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 84260 reflections in test set No useable phase information found in input file 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 = 18.486 B-value = -5.240 Scaling data with value of 18.486 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: 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" Composite map to be derived from 1 pdb files Opening refine.pdb_1 and reading coordinates Center of molecule read in with 6157 atoms is 41.766254 24.949341 65.116585 Read 6157 atoms from PDB file for use in model-based phasing:refine.pdb_1 NOTE: Skipping reordering of residue 631 as it is does not have a complete main chain NOTE: Skipping reordering of residue 430 as it is does not have a complete main chain NOTE: Skipping reordering of residue 632 as it is does not have a complete main chain NOTE: Skipping reordering of residue 430 as it is does not have a complete main chain Getting FCALC from model Overall average CC: 0.66465789467138769 Using average of all 1 useable maps; overall CC estimate: 0.6646579 Correlation of input PDB models used in composite map Weight Map 1 1 0.66 1.00 0.66 Getting FCALC from model Adding solvent model to FCALC Mean of prot, solv in FC map: 0.2177363 2.7791245E-06 Mean of prot, solv in solv map: 2.2198368E-02 0.1579320 Multiplying solvent * 0.6646579 to get solvent density = 0.1049707 CC of composite map with input: 0.000000 CC in recovered region is 0.000000 n= 954668 Scale on map: 0.232279 number of records: 1620000 resolve exit_info: source_file: /net/chevy/raid1/afonine/sources/solve_resolve/resolve/create_composite_map.cpp source_line: 799 status: 0 EndOfResolve