------------------------ 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_/TEMP0 Directory for STOPWIZARD will be AutoBuild_run_1_/TEMP0/ >freer_if_present Only writing out FreeR_flag if present >hklin map_coeffs.mtz Data to be read from mtz file: 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 -5.6944 42.8323 65.7655 Center of mass of object 1 is near (orthogonal coordinates): -5.694400 42.83230 65.76550 >rota_matrix -1.0000 0.0074 0.0038 Starting NCS operator 2 >rota_matrix -0.0074 -1.0000 0.0037 >rota_matrix 0.0038 0.0036 1.0000 >tran_orth 82.0864 51.1235 -0.2158 >center_orth 88.0894 7.8801 65.6194 Center of mass of object 2 is near (orthogonal coordinates): 88.08940 7.880100 65.61940 >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 1 21 1 Space group name for output PDB file only: P 1 21 1 >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 2 ------------------------------------------- Summary of NCS groups NCS GROUP 1 OPERATORS READ: 2 DOMAIN FILE: HA FILE: ------------------------------------------- Total of 1 NCS groups. 2 Restoring group 1 now, with 2 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 08-oct-14. Your license is good until 15-dec-96. Opened mtz file map_coeffs.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 Fourier-map-coeffici 1 59.55400 79.20600 87.43000 90.00000 92.26000 90.00000 1.000000 Reading SG information from map_coeffs.mtz Space group name: P21 Point group: PG2 Space group number : 4 Symmetry operators: 2 Number of columns: 9 H K L FP SIGFP PHIM FOMM 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 8 Dataset information for dataset number 2 and ID= 1 Dataset name:Fourier-map-coeffici 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 9 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 105036 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 105036 reflections in test set High-resolution limit of input phased data: 1.61 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 MATRICES: SYMMETRY ELEMENT 0 1 0 0 0 0 1 0 0 0 0 1 0 SYMMETRY ELEMENT 1 -1 0 0 0 0 1 0 0.5 0 0 -1 0 SPACE GROUP SYMBOL: P 1 21 1 CHECK ON SPACE GROUP SYMBOL: P 1 21 1 HALL SYMBOL : P 2yb Standard grids used for FFT 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: 5422 Not separating out FREE set from other reflections for main cycles. Using all data. Expected resolution-corrected F at d = 2.9A : 750.374 Results of wilson scaling: Scale on I = 16.925 B-value = -6.056 Scaling data with value of 16.925 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: 1.00 Copy to group 1 2 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 14.43 1.00 1.00 384 8.84 1.00 1.00 615 6.66 1.00 1.00 1149 5.25 1.00 1.00 2021 4.44 1.00 1.00 1998 3.84 1.00 1.00 3580 3.35 1.00 1.00 4341 3.00 1.00 1.00 4837 2.73 1.00 1.00 5570 2.53 1.00 1.00 5767 2.35 1.00 1.00 7653 2.20 1.00 1.00 6612 2.08 1.00 1.00 8298 1.96 1.00 1.00 10457 1.84 1.00 1.00 13417 1.74 1.00 1.00 12716 1.65 1.00 1.00 15621 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 = 1.609600 and fom = 1.000000 Leading to R= 3.698820 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. 2 Restoring group 1 now, with 2 operators Total of 1 NCS groups. 2 Restoring group 1 now, with 2 operators -------------------------------------- Analysis of NCS for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 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 -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -0.9999 X + -0.0074 Y + 0.0038 Z + 82.4591 New Y-prime= 0.0074 X + -0.9999 Y + 0.0037 Z + 50.5123 New Z-prime= 0.0038 X + 0.0036 Y + 1.0000 Z + -0.2794 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.09 7.88 65.62 and as input by user is, 88.09 7.88 65.62 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= -1.0000 X + 0.0074 Y + 0.0038 Z + 82.0864 New Y-prime= -0.0074 X + -1.0000 Y + 0.0037 Z + 51.1235 New Z-prime= 0.0038 X + 0.0036 Y + 1.0000 Z + -0.2158 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 -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0074 0.0038 rota_matrix -0.0074 -1.0000 0.0037 rota_matrix 0.0038 0.0036 1.0000 tran_orth 82.0864 51.1235 -0.2158 center_orth 88.0885 7.8821 65.6182 Analysis of NC symmetry using cutoff of 0.80 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) = 41.197 25.357 65.692 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.002 0.002 1.000 No additional SG symmetry found to be part of 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: 3.70 Using Wang mask (highest SD points) New Wang averaging radius = 3.70 Mean +/- SD of density in protein region : 0.01 +/- 1.23 Mean +/- SD of density in solvent region : -0.01 +/- 0.52 MEAN SD PROT for SQ-SM : 0.81 +/- 0.16 MEAN SD SOLV for SQ-SM : 0.29 +/- 0.11 N: 810018 809982 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 ..............................xxxxxxxxxxxxxxxxxxxx . + x . . + . . + x . . + . . + x . . + . p(protein) . + . 0.5 . +x . . + . . + . . x . . + . . x+ . . xx + . 0.0 .xxxxxxxxxxxxxxxxxxxxx...+........................ 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 58 100 Solvent: 0.00 0.15 0 48 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 ..............................xxxxxxxxxxxxxxxxxxxx . + x . . + . . + x . . + . . + x . . + . p(protein) . + . 0.5 . +x . . + . . + . . x . . + . . x+ . . xx + . 0.0 .xxxxxxxxxxxxxxxxxxxxx...+........................ 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- -------------------------------------- Getting NCS mask for NCS group 1 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 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 -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -0.9999 X + -0.0074 Y + 0.0038 Z + 82.4591 New Y-prime= 0.0074 X + -0.9999 Y + 0.0037 Z + 50.5123 New Z-prime= 0.0038 X + 0.0036 Y + 1.0000 Z + -0.2794 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.09 7.88 65.62 and as input by user is, 88.09 7.88 65.62 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= -1.0000 X + 0.0074 Y + 0.0038 Z + 82.0864 New Y-prime= -0.0074 X + -1.0000 Y + 0.0037 Z + 51.1235 New Z-prime= 0.0038 X + 0.0036 Y + 1.0000 Z + -0.2158 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 -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0074 0.0038 rota_matrix -0.0074 -1.0000 0.0037 rota_matrix 0.0038 0.0036 1.0000 tran_orth 82.0864 51.1235 -0.2158 center_orth 88.0885 7.8821 65.6182 Analysis of NC symmetry using cutoff of 0.80 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) = 41.197 25.357 65.692 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.002 0.002 1.000 No additional SG symmetry found to be part of 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: 43.16140 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 4.70 95159 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.96 63677 17.3 3.44 231387 25.4 1.34 514760 33.4 1.14 805030 41.5 1.66 908023 49.2 1.54 524858 56.6 1.76 123538 63.3 2.10 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.64 which is very good. The fall-off of the overlap has a characteristic length of 133.1 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2500000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 49.4% of asymmetric unit used in NCS with 24.7% within molecule 1 and 24.7% in NCS-related molecules. Cutoff in used in identifying NCS = 1.37 Asymmetric unit of NCS contains 400173 points (plus the 85787 border points) which can be represented by 15801 continuous rows along x with mean length of 30.8 Refining NCS operators NCS operator refinement. Starting overall correlation is 0.88 Final overall correlation of NCS is: 0.88 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 -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0042 Y + 0.0022 Z + 82.4476 New Y-prime= 0.0042 X + -1.0000 Y + 0.0037 Z + 50.4944 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2884 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.11 7.88 65.62 and as input by user is, 88.09 7.88 65.62 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= -1.0000 X + 0.0042 Y + 0.0022 Z + 82.2376 New Y-prime= -0.0042 X + -1.0000 Y + 0.0037 Z + 50.8440 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0732 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 -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0042 0.0022 rota_matrix -0.0042 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2376 50.8440 -0.0732 center_orth 88.1067 7.8821 65.6182 Analysis of NC symmetry using cutoff of 0.80 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) = 41.206 25.357 65.692 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of 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: 43.15074 A Analysis of NC symmetry near centers of mass. near each center of mass # xyz XYZ MEAN N 1 -0.052 0.541 0.753 -5.7 42.8 65.8 4.69 95093 Analysis of overlap of NCS-related molecules vs distance from mol 1 DIST OVERLAP N 9.3 4.96 63677 17.3 3.44 231387 25.4 1.35 514760 33.4 1.17 805030 41.5 1.73 908023 49.2 1.63 524858 56.6 1.90 123538 63.3 2.22 2576 The approximate extrapolated overlap of NCS-related molecules near the molecular center is 1.62 which is very good. The fall-off of the overlap has a characteristic length of 7348.9 A which is a little surprising considering the distance between molecular centers of 43.2 A (but is probably ok) Estimated fraction of A.U. in unique part of NCS is 0.2500000 Creating NCS mask... Number of NCS operators in std crystal to use: 2 Total of 49.5% of asymmetric unit used in NCS with 24.7% within molecule 1 and 24.7% in NCS-related molecules. Cutoff in used in identifying NCS = 1.37 Asymmetric unit of NCS contains 400695 points (plus the 90965 border points) which can be represented by 17255 continuous rows along x with mean length of 28.5 Copy to group 1 2 Total of 1 NCS groups. 2 Restoring group 1 now, with 2 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. 2 Restoring group 1 now, with 2 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 -5.69 42.83 65.77 and as input by user is, -5.69 42.83 65.77 Operator # 2 New X-prime= -1.0000 X + -0.0042 Y + 0.0022 Z + 82.4476 New Y-prime= 0.0042 X + -1.0000 Y + 0.0037 Z + 50.4944 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.2884 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 88.11 7.88 65.62 and as input by user is, 88.11 7.88 65.62 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= -1.0000 X + 0.0042 Y + 0.0022 Z + 82.2376 New Y-prime= -0.0042 X + -1.0000 Y + 0.0037 Z + 50.8440 New Z-prime= 0.0022 X + 0.0036 Y + 1.0000 Z + -0.0732 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 -5.6944 42.8323 65.7655 rota_matrix -1.0000 0.0042 0.0022 rota_matrix -0.0042 -1.0000 0.0037 rota_matrix 0.0022 0.0036 1.0000 tran_orth 82.2376 50.8440 -0.0732 center_orth 88.1067 7.8821 65.6182 Analysis of NC symmetry using cutoff of 0.80 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) = 41.206 25.357 65.692 xyz (fractional)= 0.735 0.320 0.752 in the direction of xyz (orthogonal A) = 0.001 0.002 1.000 No additional SG symmetry found to be part of point group 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