------------------------ 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 >density_radius 10.0 Radius for density search will be: 10 >delta_phi 20.0 Angular grid (degrees) for image search: 20.00000 >density_peaks 20 Maximum peaks in density search will be: 20 >coarse_grid FFT grid will be coarse (same as version 2.02) >ha_file None Heavy atom sites will be read from file: None The file does not exist...ignoring it >dist_min_image 15.0 Minimum distance (A) between adjacent copies of an image is 15.00000 >min_ratio_density 0.75 Min ratio of CC to second peak in density search will be: 0.75 >density_search Carrying out density search >verbose Verbose output will be printed >mask_cycles 1 Number of mask/image cycles: 1 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >center_density 42.14 6.67 3.62 Center of density x y z: 42.14000 6.670000 3.620000 >fraction_ncs_min 0.050 Minimum fraction of a.u. following NCS to keep it: 5.0000001E-02 >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: ------------------------------------------- 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 Number of datasets: 2 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 Coarse grids used for FFT Cell translation in grid units= 40 36 48 Maximum values of h k l found 18 17 21 Cell volume 452522.2 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 Default fraction SOLVENT CONTENT: 0.50 Protein avg density: 0.33 Solvent avg density: 0.19 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: 39 35 12 nu nv nw: 40 36 48 Number of grid points in au: 17280 Mean fom of this map was: 1.00 Copy to group 1 0 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") Estimating optimal initial smoothing radius using the function: R=2.41 * (dmin**0.90) * (fom**-0.26) with dmin = 4.000867 and fom = 1.000000 Leading to R= 8.393744 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... Template search: rotation about X is from 0.0 to 379.0 with increment of 20.0 RMSD min= 3.42 RANGE: 10.00 10.00 10.00 MEAN, SD of D for rotations 4.946829 0.6340200 4.769491 476.0000 Total rotations: 477 MAX of 20 peaks to be kept in template search MAX of 20 peaks to be kept after refinement Total of 477 rotations considered Number of peaks in final unrefined list = 20 Total peaks: 16 Analysis of local correlations within 10 A of centers and between 10 and 11 A. Both should have high CC for correct NCS copies peak CC-near CC-far rotx roty rotx X Y Z 1 0.999357: 0.999455 :: 0 0 0 42.1006 6.70605 3.62458 2 0.568092: 0.358896 :: 12.4444 161.954 118.374 2.89679 69.1482 20.8806 3 0.478745: 0.316001 :: 160 20 57.2375 0.239576 60.2395 80.647 4 0.431714: 0.307882 :: 162.885 77.9516 136.905 25.6125 58.8126 31.1548 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 42.10 6.71 3.62 and as input by user is, 42.10 6.71 3.62 Operator # 2 New X-prime= -0.9508 X + 0.0668 Y + 0.3025 Z + 41.3822 New Y-prime= 0.2726 X + -0.2838 Y + 0.9193 Z + 56.2437 New Z-prime= 0.1472 X + 0.9566 Y + 0.2516 Z + 7.3559 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.90 69.15 20.88 and as input by user is, 2.90 69.15 20.88 Operator # 3 New X-prime= 0.9397 X + 0.1170 Y + -0.3214 Z + -38.9416 New Y-prime= 0.2876 X + -0.7788 Y + 0.5575 Z + 51.3329 New Z-prime= -0.1851 X + -0.6163 Y + -0.7655 Z + 95.3466 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 0.24 60.24 80.65 and as input by user is, 0.24 60.24 80.65 Operator # 4 New X-prime= 0.2087 X + 0.2878 Y + -0.9347 Z + 18.2822 New Y-prime= 0.6682 X + 0.6559 Y + 0.3512 Z + 25.0109 New Z-prime= 0.7141 X + -0.6978 Y + -0.0554 Z + 5.9698 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 25.61 58.81 31.15 and as input by user is, 25.61 58.81 31.15 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= -0.9508 X + 0.2726 Y + 0.1472 Z + 22.9332 New Y-prime= 0.0668 X + -0.2838 Y + 0.9566 Z + 6.1620 New Z-prime= 0.3025 X + 0.9193 Y + 0.2516 Z + -66.0761 Operator # 3 New X-prime= 0.9397 X + 0.2876 Y + -0.1851 Z + 39.4765 New Y-prime= 0.1170 X + -0.7788 Y + -0.6163 Z + 103.2932 New Z-prime= -0.3214 X + 0.5575 Y + -0.7655 Z + 31.8527 Operator # 4 New X-prime= 0.2087 X + 0.6682 Y + 0.7141 Z + -24.7909 New Y-prime= 0.2878 X + 0.6559 Y + -0.6978 Z + -17.5007 New Z-prime= -0.9347 X + 0.3512 Y + -0.0554 Z + 8.6349 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 42.1006 6.7060 3.6246 rota_matrix -0.9508 0.2726 0.1472 rota_matrix 0.0668 -0.2838 0.9566 rota_matrix 0.3025 0.9193 0.2516 tran_orth 22.9332 6.1620 -66.0761 center_orth 2.8968 69.1482 20.8806 rota_matrix 0.9397 0.2876 -0.1851 rota_matrix 0.1170 -0.7788 -0.6163 rota_matrix -0.3214 0.5575 -0.7655 tran_orth 39.4765 103.2932 31.8527 center_orth 0.2396 60.2395 80.6470 rota_matrix 0.2087 0.6682 0.7141 rota_matrix 0.2878 0.6559 -0.6978 rota_matrix -0.9347 0.3512 -0.0554 tran_orth -24.7909 -17.5007 8.6349 center_orth 25.6125 58.8126 31.1548 Analysis of NC symmetry using cutoff of 2.00 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 ----------------------------------------------------------------- ----------------------------------------------------------------- -------------------------------------- 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 YES YES 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: 8.39 Using Wang mask (highest SD points) New Wang averaging radius = 8.39 Mean +/- SD of density in protein region : 0.06 +/- 0.50 Mean +/- SD of density in solvent region : -0.06 +/- 0.19 MEAN SD PROT for SQ-SM : 0.14 +/- 0.03 MEAN SD SOLV for SQ-SM : 0.05 +/- 0.03 N: 8640 8640 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 ................................xxxxxxxxxxxxxxxxxx . + x . . + x . . + x . . + . . + x . . + x . p(protein) . + . 0.5 . +x . . x . . + . . x+ . . x + . . xx + . . xxx + . 0.0 .xxxxxxxxxxxxxxxxx.......+........................ 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: 0.87 1.00 62 100 Solvent: 0.00 0.14 0 44 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 ................................xxxxxxxxxxxxxxxxxx . + x . . + x . . + x . . + . . + x . . + x . p(protein) . + . 0.5 . +x . . x . . + . . x+ . . x + . . xx + . . xxx + . 0.0 .xxxxxxxxxxxxxxxxx.......+........................ 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- -------------------------------------- Getting NCS mask 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 42.10 6.71 3.62 and as input by user is, 42.10 6.71 3.62 Operator # 2 New X-prime= -0.9508 X + 0.0668 Y + 0.3025 Z + 41.3822 New Y-prime= 0.2726 X + -0.2838 Y + 0.9193 Z + 56.2437 New Z-prime= 0.1472 X + 0.9566 Y + 0.2516 Z + 7.3559 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.90 69.15 20.88 and as input by user is, 2.90 69.15 20.88 Operator # 3 New X-prime= 0.9397 X + 0.1170 Y + -0.3214 Z + -38.9416 New Y-prime= 0.2876 X + -0.7788 Y + 0.5575 Z + 51.3329 New Z-prime= -0.1851 X + -0.6163 Y + -0.7655 Z + 95.3466 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 0.24 60.24 80.65 and as input by user is, 0.24 60.24 80.65 Operator # 4 New X-prime= 0.2087 X + 0.2878 Y + -0.9347 Z + 18.2822 New Y-prime= 0.6682 X + 0.6559 Y + 0.3512 Z + 25.0109 New Z-prime= 0.7141 X + -0.6978 Y + -0.0554 Z + 5.9698 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 25.61 58.81 31.15 and as input by user is, 25.61 58.81 31.15 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= -0.9508 X + 0.2726 Y + 0.1472 Z + 22.9332 New Y-prime= 0.0668 X + -0.2838 Y + 0.9566 Z + 6.1620 New Z-prime= 0.3025 X + 0.9193 Y + 0.2516 Z + -66.0761 Operator # 3 New X-prime= 0.9397 X + 0.2876 Y + -0.1851 Z + 39.4765 New Y-prime= 0.1170 X + -0.7788 Y + -0.6163 Z + 103.2932 New Z-prime= -0.3214 X + 0.5575 Y + -0.7655 Z + 31.8527 Operator # 4 New X-prime= 0.2087 X + 0.6682 Y + 0.7141 Z + -24.7909 New Y-prime= 0.2878 X + 0.6559 Y + -0.6978 Z + -17.5007 New Z-prime= -0.9347 X + 0.3512 Y + -0.0554 Z + 8.6349 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 42.1006 6.7060 3.6246 rota_matrix -0.9508 0.2726 0.1472 rota_matrix 0.0668 -0.2838 0.9566 rota_matrix 0.3025 0.9193 0.2516 tran_orth 22.9332 6.1620 -66.0761 center_orth 2.8968 69.1482 20.8806 rota_matrix 0.9397 0.2876 -0.1851 rota_matrix 0.1170 -0.7788 -0.6163 rota_matrix -0.3214 0.5575 -0.7655 tran_orth 39.4765 103.2932 31.8527 center_orth 0.2396 60.2395 80.6470 rota_matrix 0.2087 0.6682 0.7141 rota_matrix 0.2878 0.6559 -0.6978 rota_matrix -0.9347 0.3512 -0.0554 tran_orth -24.7909 -17.5007 8.6349 center_orth 25.6125 58.8126 31.1548 Analysis of NC symmetry using cutoff of 2.00 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 ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 18.86044 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 0.583 0.093 0.042 42.1 6.7 3.6 2.78 645 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 6.4 3.01 396 11.9 0.99 1452 17.4 0.13 3238 23.1 0.03 5742 28.7 0.08 8935 34.3 0.14 12576 39.9 0.09 13217 45.4 0.10 10716 51.0 0.08 5915 56.3 0.06 1770 61.2 -0.00 198 The mean overlap of NCS-related molecules near the molecular center is 0.23 which is low but could be ok. The fall-off of the overlap has a characteristic length of 31.0 A which is consistent with the distance between molecular centers of 18.9 A. Estimated fraction of A.U. in unique part of NCS is 0.1250000 Creating NCS mask... Number of NCS operators in std crystal to use: 4 Total of 48.9% of asymmetric unit used in NCS with 12.4% within molecule 1 and 36.6% in NCS-related molecules. Cutoff in used in identifying NCS = 0.31 Asymmetric unit of NCS contains 2137 points (plus the 2242 border points) which can be represented by 453 continuous rows along x with mean length of 9.7 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.26 Final overall correlation of NCS is: 0.30 Refined NCS 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 42.10 6.71 3.62 and as input by user is, 42.10 6.71 3.62 Operator # 2 New X-prime= -0.9455 X + -0.1209 Y + 0.3023 Z + 42.0409 New Y-prime= 0.3250 X + -0.2975 Y + 0.8977 Z + 54.0768 New Z-prime= -0.0186 X + 0.9470 Y + 0.3206 Z + 14.3821 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.52 69.02 21.11 and as input by user is, 2.90 69.15 20.88 Operator # 3 New X-prime= 0.9397 X + 0.1170 Y + -0.3214 Z + -38.9416 New Y-prime= 0.2876 X + -0.7788 Y + 0.5575 Z + 51.3329 New Z-prime= -0.1851 X + -0.6163 Y + -0.7655 Z + 95.3466 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 0.24 60.24 80.65 and as input by user is, 0.24 60.24 80.65 Operator # 4 New X-prime= 0.2087 X + 0.2878 Y + -0.9347 Z + 18.2822 New Y-prime= 0.6682 X + 0.6559 Y + 0.3512 Z + 25.0109 New Z-prime= 0.7141 X + -0.6978 Y + -0.0554 Z + 5.9698 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 25.61 58.81 31.15 and as input by user is, 25.61 58.81 31.15 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= -0.9455 X + 0.3250 Y + -0.0186 Z + 22.4426 New Y-prime= -0.1209 X + -0.2975 Y + 0.9470 Z + 7.5523 New Z-prime= 0.3023 X + 0.8977 Y + 0.3206 Z + -65.8625 Operator # 3 New X-prime= 0.9397 X + 0.2876 Y + -0.1851 Z + 39.4765 New Y-prime= 0.1170 X + -0.7788 Y + -0.6163 Z + 103.2932 New Z-prime= -0.3214 X + 0.5575 Y + -0.7655 Z + 31.8527 Operator # 4 New X-prime= 0.2087 X + 0.6682 Y + 0.7141 Z + -24.7909 New Y-prime= 0.2878 X + 0.6559 Y + -0.6978 Z + -17.5008 New Z-prime= -0.9347 X + 0.3512 Y + -0.0554 Z + 8.6349 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 42.1006 6.7060 3.6246 rota_matrix -0.9455 0.3250 -0.0186 rota_matrix -0.1209 -0.2975 0.9470 rota_matrix 0.3023 0.8977 0.3206 tran_orth 22.4426 7.5523 -65.8625 center_orth 2.5184 69.0189 21.1104 rota_matrix 0.9397 0.2876 -0.1851 rota_matrix 0.1170 -0.7788 -0.6163 rota_matrix -0.3214 0.5575 -0.7655 tran_orth 39.4765 103.2932 31.8527 center_orth 0.2396 60.2395 80.6470 rota_matrix 0.2087 0.6682 0.7141 rota_matrix 0.2878 0.6559 -0.6978 rota_matrix -0.9347 0.3512 -0.0554 tran_orth -24.7909 -17.5008 8.6349 center_orth 25.6125 58.8126 31.1548 Analysis of NC symmetry using cutoff of 2.00 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 ----------------------------------------------------------------- ----------------------------------------------------------------- Defining NCS regions automatically Finding region around center of mass of molecule 1 where NCS exists Minimum distance between any centers-of-mass: 18.86044 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 0.583 0.093 0.042 42.1 6.7 3.6 2.99 645 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 6.4 3.30 396 11.9 1.13 1452 17.4 0.22 3238 23.1 0.11 5742 28.7 0.12 8935 34.3 0.14 12576 39.9 0.10 13217 45.4 0.10 10716 51.0 0.10 5915 56.3 0.07 1770 61.2 0.00 198 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 0.36 which is very good. The fall-off of the overlap has a characteristic length of 25.8 A which is consistent with the distance between molecular centers of 18.9 A. Estimated fraction of A.U. in unique part of NCS is 0.1250000 Creating NCS mask... Number of NCS operators in std crystal to use: 4 Total of 49.3% of asymmetric unit used in NCS with 12.5% within molecule 1 and 36.8% in NCS-related molecules. Cutoff in used in identifying NCS = 0.39 Asymmetric unit of NCS contains 2162 points (plus the 2231 border points) which can be represented by 447 continuous rows along x with mean length of 9.8 Writing out NCS average map to ncs_au_map_coeffs.mtz CC among all NCS copies: CC 1 2 : 0.226951 CC 1 3 : 0.153368 CC 1 4 : 0.187212 CC 2 3 : 0.363642 CC 2 4 : 0.180435 CC 3 4 : 0.150332 Optimizing members in NCS group with 4 members Final average NCS CC: 0.210323 Keeping member 1 as nc operator 1 Keeping member 2 as nc operator 2 Keeping member 3 as nc operator 3 Keeping member 4 as nc operator 4 Final operators : 4 FILL: Total number of missing reflections added (to dmin = 4.000867 ) is: 10760 for new total of : 14824 : ncs_au_map_coeffs.mtz with 14824 reflections BOUNDS OF NCS AU: 5 41 -14 20 -19 24 BOUNDS OF NCS AU (A): X: 9.0 74.0 Y: -28.0 40.0 Z: -34.4 43.5 Copy to group 1 4 Total of 1 NCS groups. 4 Restoring group 1 now, with 4 operators Using NCS or image this mask cycle Writing out 13 columns of data CC of prob map with current map: 1.000000 -------------------------------------- Getting Final NCS group 1 Total of 1 NCS groups. 4 Restoring group 1 now, with 4 operators Final refined NCS 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 42.10 6.71 3.62 and as input by user is, 42.10 6.71 3.62 Operator # 2 New X-prime= -0.9455 X + -0.1209 Y + 0.3023 Z + 42.0409 New Y-prime= 0.3250 X + -0.2975 Y + 0.8977 Z + 54.0768 New Z-prime= -0.0186 X + 0.9470 Y + 0.3206 Z + 14.3821 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.52 69.02 21.11 and as input by user is, 2.52 69.02 21.11 Operator # 3 New X-prime= 0.9397 X + 0.1170 Y + -0.3214 Z + -38.9416 New Y-prime= 0.2876 X + -0.7788 Y + 0.5575 Z + 51.3329 New Z-prime= -0.1851 X + -0.6163 Y + -0.7655 Z + 95.3466 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 0.24 60.24 80.65 and as input by user is, 0.24 60.24 80.65 Operator # 4 New X-prime= 0.2087 X + 0.2878 Y + -0.9347 Z + 18.2822 New Y-prime= 0.6682 X + 0.6559 Y + 0.3512 Z + 25.0109 New Z-prime= 0.7141 X + -0.6978 Y + -0.0554 Z + 5.9698 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 25.61 58.81 31.15 and as input by user is, 25.61 58.81 31.15 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= -0.9455 X + 0.3250 Y + -0.0186 Z + 22.4426 New Y-prime= -0.1209 X + -0.2975 Y + 0.9470 Z + 7.5523 New Z-prime= 0.3023 X + 0.8977 Y + 0.3206 Z + -65.8625 Operator # 3 New X-prime= 0.9397 X + 0.2876 Y + -0.1851 Z + 39.4765 New Y-prime= 0.1170 X + -0.7788 Y + -0.6163 Z + 103.2932 New Z-prime= -0.3214 X + 0.5575 Y + -0.7655 Z + 31.8527 Operator # 4 New X-prime= 0.2087 X + 0.6682 Y + 0.7141 Z + -24.7909 New Y-prime= 0.2878 X + 0.6559 Y + -0.6978 Z + -17.5008 New Z-prime= -0.9347 X + 0.3512 Y + -0.0554 Z + 8.6349 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 42.1006 6.7060 3.6246 rota_matrix -0.9455 0.3250 -0.0186 rota_matrix -0.1209 -0.2975 0.9470 rota_matrix 0.3023 0.8977 0.3206 tran_orth 22.4426 7.5523 -65.8625 center_orth 2.5184 69.0189 21.1104 rota_matrix 0.9397 0.2876 -0.1851 rota_matrix 0.1170 -0.7788 -0.6163 rota_matrix -0.3214 0.5575 -0.7655 tran_orth 39.4765 103.2932 31.8527 center_orth 0.2396 60.2395 80.6470 rota_matrix 0.2087 0.6682 0.7141 rota_matrix 0.2878 0.6559 -0.6978 rota_matrix -0.9347 0.3512 -0.0554 tran_orth -24.7909 -17.5008 8.6349 center_orth 25.6125 58.8126 31.1548 Analysis of NC symmetry using cutoff of 2.00 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