Starting phenix.real_space_refine on Tue Sep 24 09:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xov_22281/09_2024/6xov_22281.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4935 2.51 5 N 1313 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7699 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7699 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 bond proxies already assigned to first conformer: 7874 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 residue: pdb=" N AASN A 915 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN A 915 " occ=0.41 Time building chain proxies: 8.78, per 1000 atoms: 1.13 Number of scatterers: 7755 At special positions: 0 Unit cell: (86.355, 88.065, 98.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1468 8.00 N 1313 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 52.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.617A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.270A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 366 through 369 removed outlier: 3.748A pdb=" N GLY A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 Processing helix chain 'A' and resid 442 through 456 removed outlier: 5.376A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.547A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 3.674A pdb=" N ASN A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 608 through 612 removed outlier: 3.574A pdb=" N LEU A 611 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 623 removed outlier: 4.553A pdb=" N THR A 623 " --> pdb=" O CYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 643 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.678A pdb=" N GLY A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.758A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 764 through 773 removed outlier: 4.120A pdb=" N HIS A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 877 through 894 removed outlier: 3.775A pdb=" N ALA A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 928 through 944 removed outlier: 3.516A pdb=" N VAL A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 3.813A pdb=" N ILE A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.763A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.526A pdb=" N PHE A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 removed outlier: 3.509A pdb=" N ASP A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 3.671A pdb=" N ASP A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.714A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 53 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.714A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 53 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 removed outlier: 7.175A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA6, first strand: chain 'A' and resid 588 through 589 removed outlier: 5.474A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 649 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 589 removed outlier: 5.474A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.557A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN A 864 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A1017 " --> pdb=" O CYS A 869 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1906 1.33 - 1.45: 1564 1.45 - 1.57: 4416 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7948 Sorted by residual: bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.08e-02 8.57e+03 3.49e+00 bond pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.34e-02 5.57e+03 2.04e+00 bond pdb=" N GLY A 626 " pdb=" CA GLY A 626 " ideal model delta sigma weight residual 1.449 1.470 -0.020 1.45e-02 4.76e+03 1.98e+00 bond pdb=" CB ASN A 136 " pdb=" CG ASN A 136 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.73e+00 ... (remaining 7943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10604 2.48 - 4.96: 149 4.96 - 7.45: 20 7.45 - 9.93: 3 9.93 - 12.41: 1 Bond angle restraints: 10777 Sorted by residual: angle pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 110.80 123.21 -12.41 2.13e+00 2.20e-01 3.39e+01 angle pdb=" C SER A 317 " pdb=" CA SER A 317 " pdb=" CB SER A 317 " ideal model delta sigma weight residual 109.90 118.86 -8.96 1.56e+00 4.11e-01 3.30e+01 angle pdb=" N LYS A 324 " pdb=" CA LYS A 324 " pdb=" C LYS A 324 " ideal model delta sigma weight residual 108.56 117.67 -9.11 1.74e+00 3.30e-01 2.74e+01 angle pdb=" C ASP A 321 " pdb=" N PRO A 322 " pdb=" CA PRO A 322 " ideal model delta sigma weight residual 119.28 124.67 -5.39 1.10e+00 8.26e-01 2.41e+01 angle pdb=" N ILE A 758 " pdb=" CA ILE A 758 " pdb=" C ILE A 758 " ideal model delta sigma weight residual 112.17 108.46 3.71 9.50e-01 1.11e+00 1.52e+01 ... (remaining 10772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4339 17.82 - 35.64: 381 35.64 - 53.46: 62 53.46 - 71.27: 12 71.27 - 89.09: 8 Dihedral angle restraints: 4802 sinusoidal: 1960 harmonic: 2842 Sorted by residual: dihedral pdb=" C PHE A 318 " pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta harmonic sigma weight residual 122.80 134.48 -11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 4799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1156 0.110 - 0.220: 23 0.220 - 0.330: 1 0.330 - 0.440: 0 0.440 - 0.550: 1 Chirality restraints: 1181 Sorted by residual: chirality pdb=" CA PHE A 318 " pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CB PHE A 318 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA THR A 876 " pdb=" N THR A 876 " pdb=" C THR A 876 " pdb=" CB THR A 876 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS A 324 " pdb=" N LYS A 324 " pdb=" C LYS A 324 " pdb=" CB LYS A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1178 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 163 " -0.027 2.00e-02 2.50e+03 1.76e-02 6.17e+00 pdb=" CG TYR A 163 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 163 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 163 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 163 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 163 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 163 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 163 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 146 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C TYR A 146 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR A 146 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 147 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 102 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 103 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.026 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 7612 3.22 - 3.78: 12070 3.78 - 4.34: 16710 4.34 - 4.90: 27480 Nonbonded interactions: 64032 Sorted by model distance: nonbonded pdb=" OD1 ASP A 373 " pdb=" N PHE A 374 " model vdw 2.100 3.120 nonbonded pdb=" O LEU A 365 " pdb=" OG SER A 368 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 997 " pdb=" OD1 ASP A 999 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 50 " pdb=" OD1 ASP A 70 " model vdw 2.234 3.040 nonbonded pdb=" O SER A 190 " pdb=" OH TYR A 538 " model vdw 2.235 3.040 ... (remaining 64027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 32.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7948 Z= 0.296 Angle : 0.758 12.411 10777 Z= 0.433 Chirality : 0.048 0.550 1181 Planarity : 0.006 0.045 1407 Dihedral : 14.282 89.092 2962 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.35 % Allowed : 0.58 % Favored : 99.07 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.27), residues: 969 helix: -0.29 (0.25), residues: 444 sheet: -2.18 (0.37), residues: 174 loop : -1.91 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 455 HIS 0.010 0.001 HIS A 108 PHE 0.022 0.002 PHE B 20 TYR 0.041 0.002 TYR A 163 ARG 0.004 0.000 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8126 (t80) cc_final: 0.7824 (t80) REVERT: A 106 LEU cc_start: 0.8882 (tp) cc_final: 0.8531 (tp) REVERT: A 517 VAL cc_start: 0.8318 (p) cc_final: 0.8008 (p) REVERT: A 520 THR cc_start: 0.8784 (m) cc_final: 0.8509 (p) REVERT: A 884 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8566 (tppt) REVERT: A 925 ASP cc_start: 0.7173 (t0) cc_final: 0.6894 (t0) REVERT: A 953 ASP cc_start: 0.7911 (t70) cc_final: 0.7687 (t0) outliers start: 3 outliers final: 0 residues processed: 94 average time/residue: 0.2314 time to fit residues: 31.4531 Evaluate side-chains 66 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 552 GLN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7948 Z= 0.209 Angle : 0.665 9.042 10777 Z= 0.341 Chirality : 0.044 0.204 1181 Planarity : 0.006 0.048 1407 Dihedral : 5.065 45.023 1043 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.81 % Allowed : 6.96 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 969 helix: 0.58 (0.25), residues: 462 sheet: -1.55 (0.39), residues: 166 loop : -1.49 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 851 HIS 0.005 0.001 HIS A 108 PHE 0.011 0.001 PHE A 344 TYR 0.018 0.002 TYR A 163 ARG 0.011 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8851 (m) cc_final: 0.8650 (p) REVERT: A 917 ILE cc_start: 0.8798 (mm) cc_final: 0.8547 (mm) REVERT: A 925 ASP cc_start: 0.7362 (t0) cc_final: 0.7022 (t0) REVERT: A 953 ASP cc_start: 0.7704 (t70) cc_final: 0.7478 (t0) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.1697 time to fit residues: 21.0388 Evaluate side-chains 74 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7948 Z= 0.191 Angle : 0.605 8.811 10777 Z= 0.307 Chirality : 0.042 0.190 1181 Planarity : 0.005 0.047 1407 Dihedral : 4.744 40.495 1043 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.81 % Allowed : 8.35 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 969 helix: 0.96 (0.25), residues: 469 sheet: -1.02 (0.40), residues: 167 loop : -1.10 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 851 HIS 0.003 0.001 HIS A 186 PHE 0.029 0.001 PHE A 389 TYR 0.012 0.001 TYR A 163 ARG 0.006 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8847 (m) cc_final: 0.8608 (p) REVERT: A 573 GLU cc_start: 0.7587 (pm20) cc_final: 0.7267 (pm20) REVERT: A 659 MET cc_start: 0.7851 (tpp) cc_final: 0.7497 (tpt) REVERT: A 925 ASP cc_start: 0.7520 (t0) cc_final: 0.7173 (t0) outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.1640 time to fit residues: 19.9071 Evaluate side-chains 75 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 0.1980 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 223 ASN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 7948 Z= 0.369 Angle : 0.688 9.408 10777 Z= 0.348 Chirality : 0.045 0.186 1181 Planarity : 0.005 0.048 1407 Dihedral : 5.026 44.402 1043 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.28 % Allowed : 8.82 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 969 helix: 0.87 (0.24), residues: 468 sheet: -1.04 (0.40), residues: 171 loop : -1.14 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 455 HIS 0.005 0.001 HIS A 856 PHE 0.024 0.002 PHE A 389 TYR 0.018 0.002 TYR A 388 ARG 0.004 0.001 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8904 (m) cc_final: 0.8680 (p) REVERT: A 595 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7135 (mtm) REVERT: A 659 MET cc_start: 0.7947 (tpp) cc_final: 0.7507 (tpt) REVERT: A 925 ASP cc_start: 0.7704 (t0) cc_final: 0.7427 (t0) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.1548 time to fit residues: 17.1732 Evaluate side-chains 68 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7948 Z= 0.246 Angle : 0.626 11.601 10777 Z= 0.314 Chirality : 0.043 0.178 1181 Planarity : 0.005 0.048 1407 Dihedral : 4.824 42.244 1043 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.04 % Allowed : 10.44 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 969 helix: 1.13 (0.24), residues: 465 sheet: -1.02 (0.39), residues: 177 loop : -1.04 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 455 HIS 0.004 0.001 HIS A 856 PHE 0.025 0.002 PHE A 389 TYR 0.012 0.002 TYR A 380 ARG 0.004 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 THR cc_start: 0.8895 (m) cc_final: 0.8653 (p) REVERT: A 659 MET cc_start: 0.7935 (tpp) cc_final: 0.7629 (tpp) REVERT: A 925 ASP cc_start: 0.7666 (t0) cc_final: 0.7428 (t0) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.1715 time to fit residues: 17.5233 Evaluate side-chains 66 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7948 Z= 0.165 Angle : 0.580 8.606 10777 Z= 0.291 Chirality : 0.041 0.134 1181 Planarity : 0.005 0.046 1407 Dihedral : 4.560 42.750 1043 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.93 % Allowed : 10.90 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 969 helix: 1.51 (0.25), residues: 465 sheet: -0.72 (0.41), residues: 169 loop : -0.68 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 851 HIS 0.003 0.001 HIS A 186 PHE 0.030 0.001 PHE A 389 TYR 0.008 0.001 TYR A 450 ARG 0.004 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8871 (m) cc_final: 0.8621 (p) REVERT: A 659 MET cc_start: 0.7918 (tpp) cc_final: 0.7695 (tpp) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.1712 time to fit residues: 18.0520 Evaluate side-chains 67 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7948 Z= 0.183 Angle : 0.585 8.502 10777 Z= 0.293 Chirality : 0.041 0.137 1181 Planarity : 0.005 0.044 1407 Dihedral : 4.534 39.315 1043 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.04 % Allowed : 11.14 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 969 helix: 1.60 (0.25), residues: 466 sheet: -0.72 (0.40), residues: 178 loop : -0.77 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 851 HIS 0.003 0.001 HIS A 186 PHE 0.027 0.001 PHE A 389 TYR 0.012 0.001 TYR A 450 ARG 0.004 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8876 (m) cc_final: 0.8652 (p) REVERT: A 550 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7144 (pttm) REVERT: A 573 GLU cc_start: 0.7645 (pm20) cc_final: 0.7408 (pm20) REVERT: A 659 MET cc_start: 0.7934 (tpp) cc_final: 0.7719 (tpp) REVERT: A 927 ASN cc_start: 0.7784 (t0) cc_final: 0.7571 (t0) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1813 time to fit residues: 17.4067 Evaluate side-chains 69 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 705 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7948 Z= 0.180 Angle : 0.600 12.173 10777 Z= 0.297 Chirality : 0.041 0.135 1181 Planarity : 0.005 0.044 1407 Dihedral : 4.485 38.309 1043 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.81 % Allowed : 11.48 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 969 helix: 1.66 (0.25), residues: 467 sheet: -0.58 (0.40), residues: 178 loop : -0.74 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 851 HIS 0.007 0.001 HIS A 108 PHE 0.028 0.001 PHE A 389 TYR 0.011 0.001 TYR A 721 ARG 0.003 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8900 (m) cc_final: 0.8663 (p) REVERT: A 550 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7172 (ptpp) REVERT: A 659 MET cc_start: 0.7893 (tpp) cc_final: 0.7689 (tpp) REVERT: A 927 ASN cc_start: 0.7744 (t0) cc_final: 0.7531 (t0) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1811 time to fit residues: 17.1372 Evaluate side-chains 66 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 705 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7948 Z= 0.198 Angle : 0.604 8.711 10777 Z= 0.300 Chirality : 0.041 0.136 1181 Planarity : 0.005 0.042 1407 Dihedral : 4.463 35.338 1043 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.16 % Allowed : 11.37 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 969 helix: 1.73 (0.25), residues: 463 sheet: -0.47 (0.41), residues: 177 loop : -0.69 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 851 HIS 0.006 0.001 HIS A 108 PHE 0.027 0.001 PHE A 389 TYR 0.012 0.001 TYR A 721 ARG 0.003 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8907 (m) cc_final: 0.8667 (p) REVERT: A 659 MET cc_start: 0.7933 (tpp) cc_final: 0.7718 (tpp) REVERT: A 681 MET cc_start: 0.8025 (mmm) cc_final: 0.7612 (mmm) REVERT: A 927 ASN cc_start: 0.7808 (t0) cc_final: 0.7580 (t0) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1899 time to fit residues: 18.2959 Evaluate side-chains 64 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7948 Z= 0.174 Angle : 0.613 12.407 10777 Z= 0.299 Chirality : 0.040 0.133 1181 Planarity : 0.005 0.042 1407 Dihedral : 4.376 33.163 1043 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.58 % Allowed : 12.06 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 969 helix: 1.77 (0.25), residues: 467 sheet: -0.46 (0.40), residues: 178 loop : -0.71 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 851 HIS 0.006 0.001 HIS A 108 PHE 0.028 0.001 PHE A 389 TYR 0.013 0.001 TYR A 721 ARG 0.004 0.000 ARG A 747 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 520 THR cc_start: 0.8902 (m) cc_final: 0.8666 (p) REVERT: A 659 MET cc_start: 0.7958 (tpp) cc_final: 0.7755 (tpp) REVERT: A 681 MET cc_start: 0.8062 (mmm) cc_final: 0.7762 (mmm) REVERT: A 927 ASN cc_start: 0.7813 (t0) cc_final: 0.7586 (t0) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.1743 time to fit residues: 15.9894 Evaluate side-chains 62 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 647 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058541 restraints weight = 57926.923| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.95 r_work: 0.2864 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7948 Z= 0.202 Angle : 0.610 11.238 10777 Z= 0.299 Chirality : 0.041 0.135 1181 Planarity : 0.005 0.042 1407 Dihedral : 4.435 31.417 1043 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.58 % Allowed : 12.30 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 969 helix: 1.69 (0.25), residues: 475 sheet: -0.41 (0.40), residues: 177 loop : -0.68 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 851 HIS 0.005 0.001 HIS A 108 PHE 0.027 0.001 PHE A 389 TYR 0.016 0.001 TYR A 721 ARG 0.005 0.000 ARG A1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.20 seconds wall clock time: 33 minutes 45.66 seconds (2025.66 seconds total)