------------------------ 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 NONE Heavy atom sites will be read from file: NONE The file does not exist...ignoring it >solvent_content 0.5 Fraction of unit cell assumed to be solvent is: 0.5000000 >database 5 Entry in database of histograms to use: 5 >mask_cycles 1 Number of mask/image cycles: 1 >fraction_ncs_min 0.050 Minimum fraction of a.u. following NCS to keep it: 5.0000001E-02 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >no_free Using NCS/images from very first cycle; no free estimate of errors (not recommended) >no_build Model will not be built >overlap_min -1.0 Minimum extrapolated correlation to keep NCS after refinement: -1.000000 >new_ncs_group Ignoring new_ncs_group as no NCS read in yet About to start NCS group 1 >rota_matrix 1.0000 0.0000 -0.0000 Starting NCS operator 1 The expectation for NCS operators is that they map from molecule j onto molecule 1.f This is what you get from lsqkab if molecule 1 is xyzin1 (reference) and molecule j is xyzin2 (working) You can input the inverse transformations if you also specify "invert" >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 Center of mass of object 1 is near (orthogonal coordinates): 0.1808000 -11.73180 -6.581700 >rota_matrix -0.5304 -0.5919 0.6069 Starting NCS operator 2 >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 Center of mass of object 2 is near (orthogonal coordinates): 10.68480 13.04700 -12.42940 >rota_matrix -0.9998 -0.0178 -0.0098 Starting NCS operator 3 >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 Center of mass of object 3 is near (orthogonal coordinates): 2.572300 -2.823700 21.28600 >rota_matrix 0.9396 -0.1172 0.3215 Starting NCS operator 4 >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 Center of mass of object 4 is near (orthogonal coordinates): 5.981000 29.18890 -3.848300 >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 4 ------------------------------------------- Summary of NCS groups NCS GROUP 1 OPERATORS READ: 4 DOMAIN FILE: HA FILE: ------------------------------------------- Total of 1 NCS groups. 4 Restoring group 1 now, with 4 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: 2977 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 : 786.325 Results of wilson scaling: Scale on I = 134.725 B-value = 18.580 Scaling data with value of 134.725 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 4 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. 4 Restoring group 1 now, with 4 operators 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 + 0.6850 Y + -0.4995 Z + 15.5286 New Y-prime= -0.5919 X + 0.1226 Y + 0.7967 Z + 19.8361 New Z-prime= 0.6069 X + 0.7182 Y + 0.3404 Z + -1.8728 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 + 0.8256 Y + -0.5638 Z + 3.1542 New Z-prime= -0.0098 X + -0.5641 Y + -0.8256 Z + 9.2353 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.57 -2.82 21.28 and as input by user is, 2.57 -2.82 21.29 Operator # 4 New X-prime= 0.9397 X + 0.2878 Y + -0.1851 Z + 7.9695 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 + -5.4048 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 10.6844 13.0473 -12.4293 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 2.5719 -2.8241 21.2850 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 5.9812 29.1888 -3.8486 Analysis of NC symmetry using cutoff of 0.98 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 1.376 -7.278 7.352 xyz (fractional)= 0.019 -0.101 0.085 in the direction of xyz (orthogonal A) = 0.031 -0.955 0.295 No additional SG symmetry found to be part of point group NC symmetry operator 2 (center at 0.14790156 0.18118811 -0.14288247 ) is not a member of a point group NC symmetry operator 4 (center at 0.082796164 0.40534377 -0.044242028 ) is not a member of a point group 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: 4.40 Using Wang mask (highest SD points) New Wang averaging radius = 4.40 Mean +/- SD of density in protein region : 0.07 +/- 0.65 Mean +/- SD of density in solvent region : -0.07 +/- 0.13 MEAN SD PROT for SQ-SM : 0.11 +/- 0.02 MEAN SD SOLV for SQ-SM : 0.02 +/- 0.02 N: 259203 259197 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 . . + . . + . p(protein) . + . 0.5 . +x . . + . . + . . x . . + . . x+ . . x + . 0.0 .xxxxxxxxxxxxxxxxxxxxxx..+........................ 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: 0.85 1.00 56 100 Solvent: 0.00 0.22 0 50 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 . . + . . + . p(protein) . + . 0.5 . +x . . + . . + . . x . . + . . x+ . . x + . 0.0 .xxxxxxxxxxxxxxxxxxxxxx..+........................ 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 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 + 0.6850 Y + -0.4995 Z + 15.5286 New Y-prime= -0.5919 X + 0.1226 Y + 0.7967 Z + 19.8361 New Z-prime= 0.6069 X + 0.7182 Y + 0.3404 Z + -1.8728 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 + 0.8256 Y + -0.5638 Z + 3.1542 New Z-prime= -0.0098 X + -0.5641 Y + -0.8256 Z + 9.2353 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.57 -2.82 21.28 and as input by user is, 2.57 -2.82 21.29 Operator # 4 New X-prime= 0.9397 X + 0.2878 Y + -0.1851 Z + 7.9695 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 + -5.4048 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 10.6844 13.0473 -12.4293 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 2.5719 -2.8241 21.2850 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 5.9812 29.1888 -3.8486 Analysis of NC symmetry using cutoff of 0.98 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 1.376 -7.278 7.352 xyz (fractional)= 0.019 -0.101 0.085 in the direction of xyz (orthogonal A) = 0.031 -0.955 0.295 No additional SG symmetry found to be part of point group NC symmetry operator 2 (center at 0.14790156 0.18118811 -0.14288247 ) is not a member of a point group NC symmetry operator 4 (center at 0.082796164 0.40534377 -0.044242028 ) is not a member of a point group 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: 18.87601 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 0.003 -0.163 -0.076 0.2 -11.7 -6.6 2.68 19198 2 0.148 0.181 -0.143 10.7 13.0 -12.4 0.06 19172 4 0.083 0.405 -0.044 6.0 29.2 -3.8 0.11 1492 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 5.1 3.73 6073 9.5 1.77 21990 13.9 0.45 48634 18.3 0.09 78291 22.8 0.07 111149 27.4 0.07 149722 31.9 0.09 193462 36.3 0.13 226660 40.8 0.07 204517 45.3 0.08 163709 49.7 0.06 105013 54.1 0.12 51278 58.5 -0.02 15766 62.6 -0.04 2512 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 0.41 which is very good. The fall-off of the overlap has a characteristic length of 21.5 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 48.8% of asymmetric unit used in NCS with 12.5% within molecule 1 and 36.3% in NCS-related molecules. Cutoff in used in identifying NCS = 0.25 Asymmetric unit of NCS contains 64777 points (plus the 72088 border points) which can be represented by 13995 continuous rows along x with mean length of 9.8 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.23 Final overall correlation of NCS is: 0.23 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 0.18 -11.73 -6.58 and as input by user is, 0.18 -11.73 -6.58 Operator # 2 New X-prime= -0.5493 X + 0.6591 Y + -0.5138 Z + 14.7603 New Y-prime= -0.5650 X + 0.1601 Y + 0.8094 Z + 20.3427 New Z-prime= 0.6157 X + 0.7349 Y + 0.2844 Z + -1.8182 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 10.31 13.04 -12.20 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 + 0.8256 Y + -0.5638 Z + 3.1542 New Z-prime= -0.0098 X + -0.5641 Y + -0.8256 Z + 9.2353 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 2.57 -2.82 21.28 and as input by user is, 2.57 -2.82 21.28 Operator # 4 New X-prime= 0.9397 X + 0.2878 Y + -0.1851 Z + 7.9695 New Y-prime= -0.1172 X + 0.7789 Y + 0.6161 Z + 42.4029 New Z-prime= 0.3215 X + -0.5572 Y + 0