Starting phenix.real_space_refine on Sun Jun 29 22:30:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz3_15033/06_2025/7zz3_15033.cif" } resolution = 2.41 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= 0.003 sd= 0.026 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 21 5.49 5 Mg 8 5.21 5 S 133 5.16 5 C 21644 2.51 5 N 5913 2.21 5 O 6704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34427 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 8922 Classifications: {'peptide': 1138} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 1089} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8318 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1011} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8325 Classifications: {'peptide': 1058} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1012} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8325 Classifications: {'peptide': 1058} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1012} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 110 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ATP': 1, 'BCT': 1, 'BTN': 1, 'PYR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 87 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'PYR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 87 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'PYR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 87 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'PYR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 21.45, per 1000 atoms: 0.62 Number of scatterers: 34427 At special positions: 0 Unit cell: (180.2, 157.94, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 133 16.00 P 21 15.00 Mg 8 11.99 O 6704 8.00 N 5913 7.00 C 21644 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 4.3 seconds 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7928 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 31 sheets defined 48.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.854A pdb=" N ALA A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.119A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 4.341A pdb=" N ASP A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 172 through 192 Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.114A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.647A pdb=" N GLY A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.854A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.456A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.502A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.577A pdb=" N TYR A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.530A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.606A pdb=" N ALA A 838 " --> pdb=" O LYS A 834 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 860 removed outlier: 3.598A pdb=" N ILE A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 851 " --> pdb=" O ASP A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.543A pdb=" N VAL A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.776A pdb=" N TYR A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.636A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 removed outlier: 3.734A pdb=" N ILE A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 958 Processing helix chain 'A' and resid 962 through 972 removed outlier: 3.582A pdb=" N ILE A 967 " --> pdb=" O ASP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 removed outlier: 3.537A pdb=" N LEU A 991 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'B' and resid 9 through 23 removed outlier: 3.749A pdb=" N ALA B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.188A pdb=" N PHE B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 175 through 191 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 294 through 303 removed outlier: 4.280A pdb=" N THR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.832A pdb=" N GLY B 350 " --> pdb=" O PRO B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.721A pdb=" N LEU B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.526A pdb=" N VAL B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 Processing helix chain 'B' and resid 545 through 551 removed outlier: 3.987A pdb=" N GLY B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.711A pdb=" N TYR B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 596 Processing helix chain 'B' and resid 617 through 632 Processing helix chain 'B' and resid 645 through 658 removed outlier: 4.491A pdb=" N LYS B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 695 removed outlier: 3.522A pdb=" N TYR B 685 " --> pdb=" O ASN B 681 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 739 through 751 Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 770 through 778 removed outlier: 3.739A pdb=" N TYR B 776 " --> pdb=" O GLN B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 804 removed outlier: 3.556A pdb=" N HIS B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR B 798 " --> pdb=" O GLN B 794 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 804 " --> pdb=" O GLU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 810 Proline residue: B 808 - end of helix No H-bonds generated for 'chain 'B' and resid 805 through 810' Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 826 through 841 Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 845 through 860 removed outlier: 3.847A pdb=" N ARG B 854 " --> pdb=" O LYS B 850 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.664A pdb=" N VAL B 872 " --> pdb=" O PRO B 868 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 881 " --> pdb=" O ALA B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 894 Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 919 through 927 removed outlier: 3.544A pdb=" N LYS B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 962 through 972 removed outlier: 3.816A pdb=" N MET B 971 " --> pdb=" O ILE B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 986 Processing helix chain 'B' and resid 988 through 992 removed outlier: 3.651A pdb=" N LEU B 991 " --> pdb=" O ALA B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1000 Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.880A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 74 Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 172 through 190 Processing helix chain 'C' and resid 247 through 266 Processing helix chain 'C' and resid 294 through 303 removed outlier: 4.150A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 346 through 350 removed outlier: 4.017A pdb=" N GLY C 350 " --> pdb=" O PRO C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 414 Processing helix chain 'C' and resid 422 through 432 Processing helix chain 'C' and resid 432 through 438 Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.503A pdb=" N ASN C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 511 through 521 Processing helix chain 'C' and resid 533 through 540 Processing helix chain 'C' and resid 545 through 551 Processing helix chain 'C' and resid 552 through 560 Processing helix chain 'C' and resid 572 through 580 removed outlier: 3.770A pdb=" N TYR C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 596 Processing helix chain 'C' and resid 617 through 632 Processing helix chain 'C' and resid 644 through 647 Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 681 through 695 Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 759 through 763 Processing helix chain 'C' and resid 770 through 778 removed outlier: 3.578A pdb=" N LEU C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 804 removed outlier: 3.562A pdb=" N HIS C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 804 " --> pdb=" O GLU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 810 Proline residue: C 808 - end of helix No H-bonds generated for 'chain 'C' and resid 805 through 810' Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 826 through 840 removed outlier: 3.585A pdb=" N VAL C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 860 Processing helix chain 'C' and resid 868 through 883 removed outlier: 3.506A pdb=" N VAL C 872 " --> pdb=" O PRO C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 894 Processing helix chain 'C' and resid 900 through 908 Processing helix chain 'C' and resid 919 through 927 Processing helix chain 'C' and resid 945 through 958 Processing helix chain 'C' and resid 962 through 972 Processing helix chain 'C' and resid 972 through 987 Processing helix chain 'C' and resid 988 through 992 removed outlier: 3.598A pdb=" N LEU C 991 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.798A pdb=" N ALA D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.106A pdb=" N PHE D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 62 through 73 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 173 through 190 removed outlier: 4.542A pdb=" N HIS D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 266 removed outlier: 3.551A pdb=" N VAL D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 removed outlier: 4.116A pdb=" N THR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.963A pdb=" N GLY D 350 " --> pdb=" O PRO D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 432 through 438 Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 459 through 475 Processing helix chain 'D' and resid 502 through 510 Processing helix chain 'D' and resid 511 through 522 removed outlier: 3.503A pdb=" N VAL D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 540 Processing helix chain 'D' and resid 545 through 560 removed outlier: 3.902A pdb=" N GLY D 551 " --> pdb=" O GLN D 547 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN D 554 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 removed outlier: 3.764A pdb=" N TYR D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 596 Processing helix chain 'D' and resid 606 through 610 Processing helix chain 'D' and resid 617 through 632 Processing helix chain 'D' and resid 645 through 658 removed outlier: 4.767A pdb=" N LYS D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER D 651 " --> pdb=" O GLN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 695 Processing helix chain 'D' and resid 710 through 725 Processing helix chain 'D' and resid 739 through 751 Processing helix chain 'D' and resid 759 through 763 Processing helix chain 'D' and resid 770 through 778 removed outlier: 3.670A pdb=" N LEU D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 804 removed outlier: 3.509A pdb=" N HIS D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 798 " --> pdb=" O GLN D 794 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 804 " --> pdb=" O GLU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 810 Proline residue: D 808 - end of helix No H-bonds generated for 'chain 'D' and resid 805 through 810' Processing helix chain 'D' and resid 819 through 824 Processing helix chain 'D' and resid 826 through 840 removed outlier: 4.140A pdb=" N SER D 835 " --> pdb=" O THR D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 845 through 860 Processing helix chain 'D' and resid 868 through 883 removed outlier: 3.558A pdb=" N VAL D 872 " --> pdb=" O PRO D 868 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 881 " --> pdb=" O ALA D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 893 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 900 through 908 Processing helix chain 'D' and resid 919 through 927 Processing helix chain 'D' and resid 945 through 958 Processing helix chain 'D' and resid 962 through 972 Processing helix chain 'D' and resid 972 through 987 Processing helix chain 'D' and resid 988 through 992 removed outlier: 3.660A pdb=" N LEU D 991 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.086A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS A 3 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N HIS A 79 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 5 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 288 removed outlier: 5.781A pdb=" N PHE A 284 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A 276 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 286 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS A 207 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP A 227 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 209 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 225 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 15.464A pdb=" N GLN A 235 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N THR A 343 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER A 336 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE A 396 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 338 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS A 394 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS A 340 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS A 392 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 342 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.888A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 604 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 570 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1005 through 1012 removed outlier: 3.959A pdb=" N GLU A1005 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A1015 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU A1021 " --> pdb=" O ASN A1038 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN A1038 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1023 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1078 through 1082 removed outlier: 7.681A pdb=" N VAL A1098 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1082 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N LEU A1096 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1078 through 1082 removed outlier: 7.681A pdb=" N VAL A1098 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1082 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N LEU A1096 " --> pdb=" O ILE A1082 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A1108 " --> pdb=" O LEU A1096 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB2, first strand: chain 'B' and resid 46 through 49 removed outlier: 4.090A pdb=" N VAL B 30 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B 3 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N HIS B 79 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 5 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 167 through 170 removed outlier: 3.534A pdb=" N LYS B 157 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 288 removed outlier: 5.080A pdb=" N PHE B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 278 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE B 284 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 276 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 286 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N HIS B 207 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP B 227 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU B 209 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 225 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLN B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG B 226 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 241 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS B 228 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU B 239 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL B 230 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 15.486A pdb=" N GLN B 235 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 12.081A pdb=" N THR B 343 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 237 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 341 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 529 removed outlier: 6.827A pdb=" N LEU B 527 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU B 567 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 529 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TRP B 569 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 566 " --> pdb=" O GLN B 602 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU B 604 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N MET B 568 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE B 601 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ARG B 637 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N MET B 603 " --> pdb=" O ARG B 637 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE B 639 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE B 605 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE B 636 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 665 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 638 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 662 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 701 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 664 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 6.952A pdb=" N LYS B1015 " --> pdb=" O ILE B1011 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B1021 " --> pdb=" O ASN B1038 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B1038 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 46 through 49 removed outlier: 4.057A pdb=" N VAL C 30 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS C 3 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 79 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 5 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 168 through 170 Processing sheet with id=AC2, first strand: chain 'C' and resid 281 through 288 removed outlier: 5.513A pdb=" N PHE C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS C 278 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 284 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU C 276 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 286 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N HIS C 207 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS C 224 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU C 213 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS C 222 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER C 229 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE C 238 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN C 231 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS C 236 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 15.559A pdb=" N GLN C 235 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 12.126A pdb=" N THR C 343 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL C 237 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 341 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER C 336 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 396 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 338 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS C 394 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS C 340 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS C 392 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 342 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 362 removed outlier: 3.710A pdb=" N THR C 360 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 417 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 526 through 529 removed outlier: 6.824A pdb=" N LEU C 527 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU C 567 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP C 529 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TRP C 569 " --> pdb=" O ASP C 529 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA C 566 " --> pdb=" O GLN C 602 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU C 604 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N MET C 568 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 636 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 665 " --> pdb=" O PHE C 636 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 638 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N CYS C 667 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 662 " --> pdb=" O ILE C 699 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA C 701 " --> pdb=" O ALA C 662 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA C 664 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N KCX C 703 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 666 " --> pdb=" O KCX C 703 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 526 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 757 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR C 528 " --> pdb=" O VAL C 757 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 6.761A pdb=" N LYS C1015 " --> pdb=" O ILE C1011 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU C1021 " --> pdb=" O ASN C1038 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN C1038 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C1023 " --> pdb=" O PHE C1036 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 46 through 49 removed outlier: 3.952A pdb=" N VAL D 30 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'D' and resid 282 through 288 removed outlier: 5.770A pdb=" N PHE D 284 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 276 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 286 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N HIS D 207 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP D 227 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU D 209 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU D 225 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN D 211 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER D 229 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE D 238 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN D 231 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS D 236 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 15.215A pdb=" N GLN D 235 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N THR D 343 " --> pdb=" O GLN D 235 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 237 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 341 " --> pdb=" O VAL D 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AD2, first strand: chain 'D' and resid 360 through 362 removed outlier: 3.591A pdb=" N THR D 360 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 529 removed outlier: 6.712A pdb=" N LEU D 527 " --> pdb=" O SER D 565 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLU D 567 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP D 529 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TRP D 569 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA D 566 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU D 604 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N MET D 568 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE D 636 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR D 665 " --> pdb=" O PHE D 636 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 638 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N CYS D 667 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D 662 " --> pdb=" O ILE D 699 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA D 701 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA D 664 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N KCX D 703 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE D 666 " --> pdb=" O KCX D 703 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 526 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL D 757 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR D 528 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1005 through 1012 removed outlier: 3.907A pdb=" N GLU D1005 " --> pdb=" O LEU D1021 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS D1015 " --> pdb=" O ILE D1011 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU D1021 " --> pdb=" O ASN D1038 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN D1038 " --> pdb=" O LEU D1021 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D1023 " --> pdb=" O PHE D1036 " (cutoff:3.500A) 1571 hydrogen bonds defined for protein. 4476 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: 16.68 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5896 1.31 - 1.44: 8864 1.44 - 1.57: 19902 1.57 - 1.70: 37 1.70 - 1.83: 237 Bond restraints: 34936 Sorted by residual: bond pdb=" C5A ACO C1205 " pdb=" N7A ACO C1205 " ideal model delta sigma weight residual 1.387 1.521 -0.134 1.00e-02 1.00e+04 1.78e+02 bond pdb=" C5A ACO D1205 " pdb=" N7A ACO D1205 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.76e+02 bond pdb=" C5A ACO B1205 " pdb=" N7A ACO B1205 " ideal model delta sigma weight residual 1.387 1.519 -0.132 1.00e-02 1.00e+04 1.75e+02 bond pdb=" C5A ACO A1206 " pdb=" N7A ACO A1206 " ideal model delta sigma weight residual 1.387 1.518 -0.131 1.00e-02 1.00e+04 1.72e+02 bond pdb=" C6A ACO B1205 " pdb=" N6A ACO B1205 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.29e+02 ... (remaining 34931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 46906 3.69 - 7.38: 305 7.38 - 11.07: 72 11.07 - 14.77: 27 14.77 - 18.46: 6 Bond angle restraints: 47316 Sorted by residual: angle pdb=" C4A ACO C1205 " pdb=" N9A ACO C1205 " pdb=" C8A ACO C1205 " ideal model delta sigma weight residual 105.72 122.33 -16.61 1.00e+00 1.00e+00 2.76e+02 angle pdb=" C4A ACO D1205 " pdb=" N9A ACO D1205 " pdb=" C8A ACO D1205 " ideal model delta sigma weight residual 105.72 122.30 -16.58 1.00e+00 1.00e+00 2.75e+02 angle pdb=" C4A ACO B1205 " pdb=" N9A ACO B1205 " pdb=" C8A ACO B1205 " ideal model delta sigma weight residual 105.72 122.25 -16.53 1.00e+00 1.00e+00 2.73e+02 angle pdb=" C4A ACO A1206 " pdb=" N9A ACO A1206 " pdb=" C8A ACO A1206 " ideal model delta sigma weight residual 105.72 122.25 -16.53 1.00e+00 1.00e+00 2.73e+02 angle pdb=" P1A ACO A1206 " pdb=" O3A ACO A1206 " pdb=" P2A ACO A1206 " ideal model delta sigma weight residual 136.83 123.67 13.16 1.00e+00 1.00e+00 1.73e+02 ... (remaining 47311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 20166 32.62 - 65.24: 886 65.24 - 97.86: 84 97.86 - 130.48: 1 130.48 - 163.10: 2 Dihedral angle restraints: 21139 sinusoidal: 8742 harmonic: 12397 Sorted by residual: dihedral pdb=" C5' ADP C1203 " pdb=" O5' ADP C1203 " pdb=" PA ADP C1203 " pdb=" O2A ADP C1203 " ideal model delta sinusoidal sigma weight residual 300.00 136.91 163.10 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP D1203 " pdb=" O5' ADP D1203 " pdb=" PA ADP D1203 " pdb=" O2A ADP D1203 " ideal model delta sinusoidal sigma weight residual 300.00 155.90 144.10 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O1B ADP B1203 " pdb=" O3A ADP B1203 " pdb=" PB ADP B1203 " pdb=" PA ADP B1203 " ideal model delta sinusoidal sigma weight residual -60.00 -175.59 115.58 1 2.00e+01 2.50e-03 3.44e+01 ... (remaining 21136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4009 0.050 - 0.101: 933 0.101 - 0.151: 245 0.151 - 0.201: 14 0.201 - 0.252: 12 Chirality restraints: 5213 Sorted by residual: chirality pdb=" C2B ACO A1206 " pdb=" C1B ACO A1206 " pdb=" C3B ACO A1206 " pdb=" O2B ACO A1206 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2B ACO D1205 " pdb=" C1B ACO D1205 " pdb=" C3B ACO D1205 " pdb=" O2B ACO D1205 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3B ACO C1205 " pdb=" C2B ACO C1205 " pdb=" C4B ACO C1205 " pdb=" O3B ACO C1205 " both_signs ideal model delta sigma weight residual False -2.76 -2.51 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 5210 not shown) Planarity restraints: 6185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 152 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO D 153 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 201 " -0.013 2.00e-02 2.50e+03 1.77e-02 6.26e+00 pdb=" CG TYR D 201 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR D 201 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 201 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 201 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 201 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT A1208 " -0.039 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" O1 BCT A1208 " 0.010 2.00e-02 2.50e+03 pdb=" O2 BCT A1208 " 0.014 2.00e-02 2.50e+03 pdb=" O3 BCT A1208 " 0.015 2.00e-02 2.50e+03 ... (remaining 6182 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 589 2.63 - 3.20: 29686 3.20 - 3.77: 59803 3.77 - 4.33: 82176 4.33 - 4.90: 131031 Nonbonded interactions: 303285 Sorted by model distance: nonbonded pdb=" O3A ADP B1203 " pdb="MG MG B1204 " model vdw 2.065 2.170 nonbonded pdb=" OE1 GLU B 274 " pdb="MG MG B1204 " model vdw 2.077 2.170 nonbonded pdb=" OD1 ASP B 753 " pdb="MG MG B1201 " model vdw 2.086 2.170 nonbonded pdb=" OE2 GLU B 286 " pdb="MG MG B1204 " model vdw 2.090 2.170 nonbonded pdb=" O3A ADP D1203 " pdb="MG MG D1204 " model vdw 2.102 2.170 ... (remaining 303280 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 0 through 1056) selection = (chain 'B' and resid 0 through 1056) selection = (chain 'C' and resid 0 through 1056) selection = (chain 'D' and resid 0 through 1056) } 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=1.00 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: 1.490 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: 0.040 Extract box with map and model: 1.160 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 85.350 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.140 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 : 0.006 0.199 34937 Z= 0.424 Angle : 0.860 18.457 47316 Z= 0.497 Chirality : 0.047 0.252 5213 Planarity : 0.005 0.110 6185 Dihedral : 17.239 163.097 13211 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.75 % Allowed : 19.34 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % 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: -1.03 (0.12), residues: 4291 helix: -0.63 (0.11), residues: 1885 sheet: -0.17 (0.20), residues: 695 loop : -0.76 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 644 HIS 0.008 0.001 HIS D 222 PHE 0.014 0.001 PHE C 624 TYR 0.043 0.001 TYR D 201 ARG 0.018 0.001 ARG B 854 Details of bonding type rmsd hydrogen bonds : bond 0.18530 ( 1568) hydrogen bonds : angle 7.76334 ( 4476) covalent geometry : bond 0.00637 (34936) covalent geometry : angle 0.85991 (47316) Misc. bond : bond 0.10973 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 3.873 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 49 residues processed: 243 average time/residue: 1.4387 time to fit residues: 422.9347 Evaluate side-chains 224 residues out of total 3604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 651 SER Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 752 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 967 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.9051 > 50: distance: 65 - 142: 29.470 distance: 68 - 139: 28.326 distance: 111 - 114: 22.948 distance: 114 - 115: 36.277 distance: 116 - 118: 44.287 distance: 118 - 119: 23.493 distance: 119 - 120: 23.803 distance: 119 - 122: 27.251 distance: 120 - 121: 40.420 distance: 120 - 130: 8.545 distance: 122 - 123: 18.163 distance: 123 - 124: 9.730 distance: 123 - 125: 12.944 distance: 124 - 126: 11.943 distance: 125 - 127: 12.989 distance: 126 - 128: 3.461 distance: 128 - 129: 26.329 distance: 130 - 131: 20.542 distance: 131 - 132: 31.884 distance: 131 - 134: 30.499 distance: 132 - 133: 26.143 distance: 132 - 139: 39.801 distance: 134 - 135: 31.919 distance: 135 - 136: 18.551 distance: 136 - 137: 20.786 distance: 136 - 138: 24.594 distance: 139 - 140: 50.727 distance: 140 - 141: 60.534 distance: 140 - 143: 48.534 distance: 141 - 142: 42.666 distance: 141 - 146: 32.221 distance: 143 - 144: 27.685 distance: 143 - 145: 12.839 distance: 146 - 147: 16.691 distance: 147 - 148: 41.048 distance: 148 - 149: 40.468 distance: 148 - 153: 48.554 distance: 150 - 151: 25.216 distance: 150 - 152: 40.746 distance: 153 - 154: 41.471 distance: 153 - 159: 38.475 distance: 154 - 155: 25.678 distance: 154 - 157: 36.511 distance: 155 - 156: 9.816 distance: 155 - 160: 18.064 distance: 157 - 158: 21.290 distance: 158 - 159: 43.160 distance: 160 - 161: 30.409 distance: 161 - 162: 12.574 distance: 161 - 164: 13.225 distance: 162 - 163: 44.906 distance: 164 - 165: 28.715 distance: 165 - 166: 13.257 distance: 165 - 167: 8.080 distance: 166 - 168: 11.899 distance: 167 - 169: 24.117 distance: 168 - 170: 18.507 distance: 169 - 170: 19.711 distance: 170 - 171: 9.916 distance: 172 - 173: 41.942 distance: 173 - 174: 40.965 distance: 173 - 176: 18.878 distance: 174 - 175: 9.642 distance: 174 - 183: 45.790 distance: 177 - 178: 21.398 distance: 177 - 179: 7.151 distance: 178 - 180: 26.646 distance: 179 - 181: 22.600 distance: 180 - 182: 15.534 distance: 181 - 182: 23.445 distance: 183 - 184: 43.757 distance: 184 - 185: 27.640 distance: 185 - 186: 32.704 distance: 185 - 191: 18.439 distance: 187 - 188: 4.246 distance: 188 - 189: 33.276 distance: 188 - 190: 34.740 distance: 191 - 192: 15.556 distance: 192 - 193: 50.522 distance: 192 - 195: 4.428 distance: 193 - 194: 7.511 distance: 193 - 197: 24.337 distance: 195 - 196: 52.298