Starting phenix.real_space_refine on Fri Jan 17 05:17:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.map" model { file = "/net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p5x_17456/01_2025/8p5x_17456.cif" } resolution = 2.29 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= 0.020 sd= 1.252 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 222 5.16 5 C 34828 2.51 5 N 9755 2.21 5 O 10523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55346 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 8400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8400 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "H" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "I" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.23, per 1000 atoms: 0.46 Number of scatterers: 55346 At special positions: 0 Unit cell: (227.9, 227.04, 171.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 222 16.00 P 12 15.00 Mg 6 11.99 O 10523 8.00 N 9755 7.00 C 34828 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: 10.37 Conformation dependent library (CDL) restraints added in 5.7 seconds 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13020 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 54 sheets defined 46.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 135 through 152 removed outlier: 3.614A pdb=" N ARG A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.640A pdb=" N ILE A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.928A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 224 " --> pdb=" O THR A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 225 through 242 removed outlier: 3.514A pdb=" N ILE A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.555A pdb=" N TRP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.684A pdb=" N ALA A 387 " --> pdb=" O HIS A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.882A pdb=" N LEU A 407 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.646A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 504 Processing helix chain 'A' and resid 517 through 533 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.627A pdb=" N PHE A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 732 removed outlier: 3.513A pdb=" N ARG A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.503A pdb=" N MET A 755 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 756 " --> pdb=" O PRO A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 752 through 756' Processing helix chain 'A' and resid 759 through 765 removed outlier: 3.976A pdb=" N LEU A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 785 through 804 removed outlier: 3.566A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 860 through 874 removed outlier: 4.223A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.620A pdb=" N GLY A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 949 through 963 removed outlier: 3.509A pdb=" N GLU A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 4.267A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 Processing helix chain 'A' and resid 991 through 997 Processing helix chain 'A' and resid 1021 through 1028 removed outlier: 3.644A pdb=" N PHE A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1055 Processing helix chain 'A' and resid 1068 through 1072 Processing helix chain 'A' and resid 1078 through 1082 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.504A pdb=" N LYS A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1125 removed outlier: 4.219A pdb=" N GLU A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 3.728A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1203 through 1220 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 135 through 152 removed outlier: 3.616A pdb=" N ARG B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.642A pdb=" N ILE B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.928A pdb=" N LYS B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 224 " --> pdb=" O THR B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.514A pdb=" N ILE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.553A pdb=" N TRP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 3.682A pdb=" N ALA B 387 " --> pdb=" O HIS B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 404 through 413 removed outlier: 3.882A pdb=" N LEU B 407 " --> pdb=" O HIS B 404 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU B 410 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 436 through 448 Processing helix chain 'B' and resid 460 through 474 removed outlier: 3.646A pdb=" N LEU B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 504 Processing helix chain 'B' and resid 517 through 533 Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.628A pdb=" N PHE B 702 " --> pdb=" O TYR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.513A pdb=" N ARG B 729 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.504A pdb=" N MET B 755 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 756 " --> pdb=" O PRO B 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 756' Processing helix chain 'B' and resid 759 through 765 removed outlier: 3.977A pdb=" N LEU B 763 " --> pdb=" O LYS B 759 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 765 " --> pdb=" O TYR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 785 through 804 removed outlier: 3.567A pdb=" N ALA B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS B 797 " --> pdb=" O VAL B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 845 Processing helix chain 'B' and resid 846 through 848 No H-bonds generated for 'chain 'B' and resid 846 through 848' Processing helix chain 'B' and resid 860 through 874 removed outlier: 4.226A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.619A pdb=" N GLY B 893 " --> pdb=" O LEU B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 949 through 963 removed outlier: 3.509A pdb=" N GLU B 956 " --> pdb=" O GLY B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 980 removed outlier: 4.268A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 988 Processing helix chain 'B' and resid 991 through 997 Processing helix chain 'B' and resid 1021 through 1028 removed outlier: 3.642A pdb=" N PHE B1025 " --> pdb=" O ARG B1021 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B1028 " --> pdb=" O ARG B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1055 Processing helix chain 'B' and resid 1068 through 1072 Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1099 through 1103 removed outlier: 3.504A pdb=" N LYS B1102 " --> pdb=" O ASP B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1125 removed outlier: 4.219A pdb=" N GLU B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1151 Processing helix chain 'B' and resid 1170 through 1182 removed outlier: 3.726A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1203 through 1220 Processing helix chain 'C' and resid 109 through 121 Processing helix chain 'C' and resid 122 through 124 No H-bonds generated for 'chain 'C' and resid 122 through 124' Processing helix chain 'C' and resid 135 through 152 removed outlier: 3.618A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.632A pdb=" N ILE C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.927A pdb=" N LYS C 223 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 224 " --> pdb=" O THR C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.512A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 320 through 335 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.553A pdb=" N TRP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 384 through 387 removed outlier: 3.683A pdb=" N ALA C 387 " --> pdb=" O HIS C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 387' Processing helix chain 'C' and resid 404 through 413 removed outlier: 3.879A pdb=" N LEU C 407 " --> pdb=" O HIS C 404 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 409 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU C 410 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.645A pdb=" N LEU C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 504 Processing helix chain 'C' and resid 517 through 533 Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 659 Processing helix chain 'C' and resid 685 through 689 Processing helix chain 'C' and resid 698 through 703 removed outlier: 3.627A pdb=" N PHE C 702 " --> pdb=" O TYR C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 732 removed outlier: 3.513A pdb=" N ARG C 729 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 756 removed outlier: 3.503A pdb=" N MET C 755 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 756 " --> pdb=" O PRO C 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 756' Processing helix chain 'C' and resid 759 through 765 removed outlier: 3.976A pdb=" N LEU C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 765 " --> pdb=" O TYR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 779 Processing helix chain 'C' and resid 785 through 804 removed outlier: 3.567A pdb=" N ALA C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 845 Processing helix chain 'C' and resid 846 through 848 No H-bonds generated for 'chain 'C' and resid 846 through 848' Processing helix chain 'C' and resid 860 through 874 removed outlier: 4.224A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.620A pdb=" N GLY C 893 " --> pdb=" O LEU C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 949 through 963 removed outlier: 3.508A pdb=" N GLU C 956 " --> pdb=" O GLY C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 980 removed outlier: 4.266A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 988 Processing helix chain 'C' and resid 991 through 997 Processing helix chain 'C' and resid 1021 through 1028 removed outlier: 3.643A pdb=" N PHE C1025 " --> pdb=" O ARG C1021 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C1028 " --> pdb=" O ARG C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1055 Processing helix chain 'C' and resid 1068 through 1072 Processing helix chain 'C' and resid 1078 through 1082 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.504A pdb=" N LYS C1102 " --> pdb=" O ASP C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1125 removed outlier: 4.218A pdb=" N GLU C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1151 Processing helix chain 'C' and resid 1170 through 1182 removed outlier: 3.728A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1203 through 1220 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 135 through 152 removed outlier: 3.619A pdb=" N ARG D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.638A pdb=" N ILE D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.932A pdb=" N LYS D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET D 224 " --> pdb=" O THR D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.514A pdb=" N ILE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 320 through 335 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.553A pdb=" N TRP D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 383 Processing helix chain 'D' and resid 384 through 387 removed outlier: 3.682A pdb=" N ALA D 387 " --> pdb=" O HIS D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.880A pdb=" N LEU D 407 " --> pdb=" O HIS D 404 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 409 " --> pdb=" O ASP D 406 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU D 410 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 427 through 431 Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 460 through 474 removed outlier: 3.647A pdb=" N LEU D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 504 Processing helix chain 'D' and resid 517 through 533 Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 645 through 651 Processing helix chain 'D' and resid 652 through 659 Processing helix chain 'D' and resid 685 through 689 Processing helix chain 'D' and resid 698 through 703 removed outlier: 3.628A pdb=" N PHE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 732 removed outlier: 3.513A pdb=" N ARG D 729 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 removed outlier: 3.504A pdb=" N MET D 755 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 756 " --> pdb=" O PRO D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 752 through 756' Processing helix chain 'D' and resid 759 through 765 removed outlier: 3.975A pdb=" N LEU D 763 " --> pdb=" O LYS D 759 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 779 Processing helix chain 'D' and resid 785 through 804 removed outlier: 3.567A pdb=" N ALA D 791 " --> pdb=" O GLU D 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS D 797 " --> pdb=" O VAL D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 845 Processing helix chain 'D' and resid 846 through 848 No H-bonds generated for 'chain 'D' and resid 846 through 848' Processing helix chain 'D' and resid 860 through 874 removed outlier: 4.227A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.620A pdb=" N GLY D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 949 through 963 removed outlier: 3.509A pdb=" N GLU D 956 " --> pdb=" O GLY D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 980 removed outlier: 4.266A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 988 Processing helix chain 'D' and resid 991 through 997 Processing helix chain 'D' and resid 1021 through 1028 removed outlier: 3.642A pdb=" N PHE D1025 " --> pdb=" O ARG D1021 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D1028 " --> pdb=" O ARG D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1055 Processing helix chain 'D' and resid 1068 through 1072 Processing helix chain 'D' and resid 1078 through 1082 Processing helix chain 'D' and resid 1099 through 1103 removed outlier: 3.504A pdb=" N LYS D1102 " --> pdb=" O ASP D1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 1112 through 1125 removed outlier: 4.217A pdb=" N GLU D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1151 Processing helix chain 'D' and resid 1170 through 1182 removed outlier: 3.727A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1203 through 1220 Processing helix chain 'E' and resid 109 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 135 through 152 removed outlier: 3.618A pdb=" N ARG E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 174 removed outlier: 3.637A pdb=" N ILE E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.929A pdb=" N LYS E 223 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET E 224 " --> pdb=" O THR E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing helix chain 'E' and resid 225 through 242 removed outlier: 3.514A pdb=" N ILE E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 288 through 292 Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 320 through 335 Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.555A pdb=" N TRP E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 383 Processing helix chain 'E' and resid 384 through 387 removed outlier: 3.683A pdb=" N ALA E 387 " --> pdb=" O HIS E 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 387' Processing helix chain 'E' and resid 404 through 413 removed outlier: 3.882A pdb=" N LEU E 407 " --> pdb=" O HIS E 404 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE E 409 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU E 410 " --> pdb=" O LEU E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 427 through 431 Processing helix chain 'E' and resid 436 through 448 Processing helix chain 'E' and resid 460 through 474 removed outlier: 3.646A pdb=" N LEU E 467 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 504 Processing helix chain 'E' and resid 517 through 533 Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 613 through 629 Processing helix chain 'E' and resid 645 through 651 Processing helix chain 'E' and resid 652 through 659 Processing helix chain 'E' and resid 685 through 689 Processing helix chain 'E' and resid 698 through 703 removed outlier: 3.627A pdb=" N PHE E 702 " --> pdb=" O TYR E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 732 removed outlier: 3.514A pdb=" N ARG E 729 " --> pdb=" O THR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 756 removed outlier: 3.504A pdb=" N MET E 755 " --> pdb=" O ASP E 752 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 756 " --> pdb=" O PRO E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 752 through 756' Processing helix chain 'E' and resid 759 through 765 removed outlier: 3.976A pdb=" N LEU E 763 " --> pdb=" O LYS E 759 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 765 " --> pdb=" O TYR E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 769 through 779 Processing helix chain 'E' and resid 785 through 804 removed outlier: 3.567A pdb=" N ALA E 791 " --> pdb=" O GLU E 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 792 " --> pdb=" O ASP E 788 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS E 797 " --> pdb=" O VAL E 793 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 845 Processing helix chain 'E' and resid 846 through 848 No H-bonds generated for 'chain 'E' and resid 846 through 848' Processing helix chain 'E' and resid 860 through 874 removed outlier: 4.224A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 877 through 893 removed outlier: 3.620A pdb=" N GLY E 893 " --> pdb=" O LEU E 889 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 932 Processing helix chain 'E' and resid 949 through 963 removed outlier: 3.509A pdb=" N GLU E 956 " --> pdb=" O GLY E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 974 through 980 removed outlier: 4.267A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 981 through 988 Processing helix chain 'E' and resid 991 through 997 Processing helix chain 'E' and resid 1021 through 1028 removed outlier: 3.644A pdb=" N PHE E1025 " --> pdb=" O ARG E1021 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E1028 " --> pdb=" O ARG E1024 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1055 Processing helix chain 'E' and resid 1068 through 1072 Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1099 through 1103 removed outlier: 3.503A pdb=" N LYS E1102 " --> pdb=" O ASP E1099 " (cutoff:3.500A) Processing helix chain 'E' and resid 1112 through 1125 removed outlier: 4.218A pdb=" N GLU E1116 " --> pdb=" O LYS E1112 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1151 Processing helix chain 'E' and resid 1170 through 1182 removed outlier: 3.729A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1203 through 1220 Processing helix chain 'F' and resid 109 through 121 Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 135 through 152 removed outlier: 3.622A pdb=" N ARG F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 174 removed outlier: 3.637A pdb=" N ILE F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 179 Processing helix chain 'F' and resid 220 through 224 removed outlier: 3.929A pdb=" N LYS F 223 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 224 " --> pdb=" O THR F 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 220 through 224' Processing helix chain 'F' and resid 225 through 242 removed outlier: 3.514A pdb=" N ILE F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 320 through 335 Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.554A pdb=" N TRP F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 383 Processing helix chain 'F' and resid 384 through 387 removed outlier: 3.686A pdb=" N ALA F 387 " --> pdb=" O HIS F 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 384 through 387' Processing helix chain 'F' and resid 404 through 413 removed outlier: 3.881A pdb=" N LEU F 407 " --> pdb=" O HIS F 404 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE F 409 " --> pdb=" O ASP F 406 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU F 410 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'F' and resid 427 through 431 Processing helix chain 'F' and resid 436 through 448 Processing helix chain 'F' and resid 460 through 474 removed outlier: 3.646A pdb=" N LEU F 467 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 504 Processing helix chain 'F' and resid 517 through 533 Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 557 through 562 Processing helix chain 'F' and resid 613 through 629 Processing helix chain 'F' and resid 645 through 651 Processing helix chain 'F' and resid 652 through 659 Processing helix chain 'F' and resid 685 through 689 Processing helix chain 'F' and resid 698 through 703 removed outlier: 3.627A pdb=" N PHE F 702 " --> pdb=" O TYR F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 732 removed outlier: 3.513A pdb=" N ARG F 729 " --> pdb=" O THR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 756 removed outlier: 3.503A pdb=" N MET F 755 " --> pdb=" O ASP F 752 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR F 756 " --> pdb=" O PRO F 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 752 through 756' Processing helix chain 'F' and resid 759 through 765 removed outlier: 3.976A pdb=" N LEU F 763 " --> pdb=" O LYS F 759 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 765 " --> pdb=" O TYR F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 779 Processing helix chain 'F' and resid 785 through 804 removed outlier: 3.570A pdb=" N ALA F 791 " --> pdb=" O GLU F 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 792 " --> pdb=" O ASP F 788 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS F 797 " --> pdb=" O VAL F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 845 Processing helix chain 'F' and resid 846 through 848 No H-bonds generated for 'chain 'F' and resid 846 through 848' Processing helix chain 'F' and resid 860 through 874 removed outlier: 4.221A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 893 removed outlier: 3.623A pdb=" N GLY F 893 " --> pdb=" O LEU F 889 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 932 Processing helix chain 'F' and resid 949 through 963 removed outlier: 3.507A pdb=" N GLU F 956 " --> pdb=" O GLY F 952 " (cutoff:3.500A) Processing helix chain 'F' and resid 974 through 980 removed outlier: 4.264A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 981 through 988 Processing helix chain 'F' and resid 991 through 997 Processing helix chain 'F' and resid 1021 through 1028 removed outlier: 3.640A pdb=" N PHE F1025 " --> pdb=" O ARG F1021 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F1028 " --> pdb=" O ARG F1024 " (cutoff:3.500A) Processing helix chain 'F' and resid 1041 through 1055 Processing helix chain 'F' and resid 1068 through 1072 Processing helix chain 'F' and resid 1078 through 1082 Processing helix chain 'F' and resid 1099 through 1103 removed outlier: 3.505A pdb=" N LYS F1102 " --> pdb=" O ASP F1099 " (cutoff:3.500A) Processing helix chain 'F' and resid 1112 through 1125 removed outlier: 4.225A pdb=" N GLU F1116 " --> pdb=" O LYS F1112 " (cutoff:3.500A) Processing helix chain 'F' and resid 1141 through 1151 Processing helix chain 'F' and resid 1170 through 1182 removed outlier: 3.727A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1203 through 1220 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 218 removed outlier: 3.705A pdb=" N ALA A 212 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 204 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 201 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 128 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C 267 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.538A pdb=" N HIS A 267 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 128 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 201 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 204 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 212 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 422 through 424 Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.898A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 939 through 944 removed outlier: 6.444A pdb=" N VAL A 896 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR A 943 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 898 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 895 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA A 969 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG A 897 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLU A 971 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 899 " --> pdb=" O GLU A 971 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 968 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU A1005 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP A 970 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A1004 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A1065 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A1006 " --> pdb=" O THR A1065 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AA9, first strand: chain 'A' and resid 1091 through 1092 removed outlier: 6.864A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE A1134 " --> pdb=" O MET A1107 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A1109 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A1193 " --> pdb=" O GLN A1162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A1164 " --> pdb=" O ARG A1193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 211 through 218 removed outlier: 3.706A pdb=" N ALA B 212 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 204 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 201 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 128 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 267 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.533A pdb=" N HIS B 267 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 128 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA D 201 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 204 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 212 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 422 through 424 Processing sheet with id=AB6, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.906A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 939 through 944 removed outlier: 6.444A pdb=" N VAL B 896 " --> pdb=" O LEU B 941 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR B 943 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 898 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 895 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA B 969 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 897 " --> pdb=" O ALA B 969 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU B 971 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 899 " --> pdb=" O GLU B 971 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 968 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU B1005 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP B 970 " --> pdb=" O LEU B1005 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B1004 " --> pdb=" O ILE B1063 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B1065 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B1006 " --> pdb=" O THR B1065 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AB9, first strand: chain 'B' and resid 1091 through 1092 removed outlier: 6.867A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE B1134 " --> pdb=" O MET B1107 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1109 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG B1193 " --> pdb=" O GLN B1162 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B1164 " --> pdb=" O ARG B1193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 211 through 218 removed outlier: 3.703A pdb=" N ALA C 212 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 204 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 201 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 128 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 267 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AC3, first strand: chain 'C' and resid 422 through 424 Processing sheet with id=AC4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.900A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 939 through 944 removed outlier: 6.443A pdb=" N VAL C 896 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TYR C 943 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 898 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 895 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA C 969 " --> pdb=" O LEU C 895 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 897 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU C 971 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA C 899 " --> pdb=" O GLU C 971 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 968 " --> pdb=" O ILE C1003 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU C1005 " --> pdb=" O VAL C 968 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP C 970 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C1004 " --> pdb=" O ILE C1063 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR C1065 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU C1006 " --> pdb=" O THR C1065 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 915 through 916 Processing sheet with id=AC7, first strand: chain 'C' and resid 1091 through 1092 removed outlier: 6.864A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE C1134 " --> pdb=" O MET C1107 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C1109 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C1193 " --> pdb=" O GLN C1162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU C1164 " --> pdb=" O ARG C1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AC9, first strand: chain 'D' and resid 267 through 269 removed outlier: 3.525A pdb=" N HIS D 267 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR F 128 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER F 256 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL F 282 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR F 258 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 201 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU F 204 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 212 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 422 through 424 Processing sheet with id=AD2, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.907A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 939 through 944 removed outlier: 6.444A pdb=" N VAL D 896 " --> pdb=" O LEU D 941 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N TYR D 943 " --> pdb=" O VAL D 896 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 898 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 895 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA D 969 " --> pdb=" O LEU D 895 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG D 897 " --> pdb=" O ALA D 969 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU D 971 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA D 899 " --> pdb=" O GLU D 971 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 968 " --> pdb=" O ILE D1003 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU D1005 " --> pdb=" O VAL D 968 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP D 970 " --> pdb=" O LEU D1005 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D1004 " --> pdb=" O ILE D1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR D1065 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU D1006 " --> pdb=" O THR D1065 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 915 through 916 Processing sheet with id=AD5, first strand: chain 'D' and resid 1091 through 1092 removed outlier: 6.866A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE D1134 " --> pdb=" O MET D1107 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D1109 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG D1193 " --> pdb=" O GLN D1162 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU D1164 " --> pdb=" O ARG D1193 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 422 through 424 Processing sheet with id=AD7, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.899A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 939 through 944 removed outlier: 6.445A pdb=" N VAL E 896 " --> pdb=" O LEU E 941 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR E 943 " --> pdb=" O VAL E 896 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU E 898 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU E 895 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA E 969 " --> pdb=" O LEU E 895 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 897 " --> pdb=" O ALA E 969 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU E 971 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA E 899 " --> pdb=" O GLU E 971 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 968 " --> pdb=" O ILE E1003 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU E1005 " --> pdb=" O VAL E 968 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E 970 " --> pdb=" O LEU E1005 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU E1004 " --> pdb=" O ILE E1063 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E1065 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU E1006 " --> pdb=" O THR E1065 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 915 through 916 Processing sheet with id=AE1, first strand: chain 'E' and resid 1091 through 1092 removed outlier: 6.864A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE E1134 " --> pdb=" O MET E1107 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E1109 " --> pdb=" O ILE E1134 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG E1193 " --> pdb=" O GLN E1162 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU E1164 " --> pdb=" O ARG E1193 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 422 through 424 Processing sheet with id=AE3, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.899A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 939 through 944 removed outlier: 6.441A pdb=" N VAL F 896 " --> pdb=" O LEU F 941 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR F 943 " --> pdb=" O VAL F 896 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU F 898 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU F 895 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA F 969 " --> pdb=" O LEU F 895 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG F 897 " --> pdb=" O ALA F 969 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLU F 971 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA F 899 " --> pdb=" O GLU F 971 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL F 968 " --> pdb=" O ILE F1003 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F1005 " --> pdb=" O VAL F 968 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP F 970 " --> pdb=" O LEU F1005 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F1004 " --> pdb=" O ILE F1063 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR F1065 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU F1006 " --> pdb=" O THR F1065 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 915 through 916 Processing sheet with id=AE6, first strand: chain 'F' and resid 1091 through 1092 removed outlier: 6.858A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F1134 " --> pdb=" O MET F1107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL F1109 " --> pdb=" O ILE F1134 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG F1193 " --> pdb=" O GLN F1162 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU F1164 " --> pdb=" O ARG F1193 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG G 134 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR G 110 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 78 through 79 removed outlier: 8.880A pdb=" N ILE G 78 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR G 69 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.918A pdb=" N ARG H 134 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR H 110 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 78 through 79 removed outlier: 8.880A pdb=" N ILE H 78 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR H 69 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG I 134 " --> pdb=" O LYS I 52 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR I 110 " --> pdb=" O ARG I 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 78 through 79 removed outlier: 8.882A pdb=" N ILE I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR I 69 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG J 134 " --> pdb=" O LYS J 52 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR J 110 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 78 through 79 removed outlier: 8.881A pdb=" N ILE J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR J 69 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG K 134 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR K 110 " --> pdb=" O ARG K 117 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 78 through 79 removed outlier: 8.881A pdb=" N ILE K 78 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR K 69 " --> pdb=" O ILE K 78 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 60 through 63 removed outlier: 6.918A pdb=" N ARG L 134 " --> pdb=" O LYS L 52 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR L 110 " --> pdb=" O ARG L 117 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 78 through 79 removed outlier: 8.882A pdb=" N ILE L 78 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR L 69 " --> pdb=" O ILE L 78 " (cutoff:3.500A) 2526 hydrogen bonds defined for protein. 6930 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: 28.84 Time building geometry restraints manager: 12.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10298 1.32 - 1.44: 13840 1.44 - 1.57: 31916 1.57 - 1.69: 24 1.69 - 1.82: 420 Bond restraints: 56498 Sorted by residual: bond pdb=" CA SER D 869 " pdb=" CB SER D 869 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.56e-02 4.11e+03 2.42e+01 bond pdb=" CA SER B 869 " pdb=" CB SER B 869 " ideal model delta sigma weight residual 1.531 1.455 0.077 1.56e-02 4.11e+03 2.41e+01 bond pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" N VAL E 401 " pdb=" CA VAL E 401 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.33e+01 bond pdb=" N VAL A 401 " pdb=" CA VAL A 401 " ideal model delta sigma weight residual 1.460 1.495 -0.036 7.50e-03 1.78e+04 2.25e+01 ... (remaining 56493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 48382 1.56 - 3.12: 22046 3.12 - 4.68: 5542 4.68 - 6.25: 559 6.25 - 7.81: 68 Bond angle restraints: 76597 Sorted by residual: angle pdb=" CA GLY D 670 " pdb=" C GLY D 670 " pdb=" O GLY D 670 " ideal model delta sigma weight residual 122.22 118.06 4.16 6.50e-01 2.37e+00 4.10e+01 angle pdb=" CA GLY B 670 " pdb=" C GLY B 670 " pdb=" O GLY B 670 " ideal model delta sigma weight residual 122.22 118.08 4.14 6.50e-01 2.37e+00 4.05e+01 angle pdb=" CA GLY C 670 " pdb=" C GLY C 670 " pdb=" O GLY C 670 " ideal model delta sigma weight residual 122.22 118.13 4.09 6.50e-01 2.37e+00 3.97e+01 angle pdb=" CA GLY E 670 " pdb=" C GLY E 670 " pdb=" O GLY E 670 " ideal model delta sigma weight residual 122.22 118.14 4.08 6.50e-01 2.37e+00 3.93e+01 angle pdb=" CA GLY F 670 " pdb=" C GLY F 670 " pdb=" O GLY F 670 " ideal model delta sigma weight residual 122.22 118.15 4.07 6.50e-01 2.37e+00 3.92e+01 ... (remaining 76592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 30859 17.45 - 34.90: 2277 34.90 - 52.35: 589 52.35 - 69.80: 145 69.80 - 87.25: 45 Dihedral angle restraints: 33915 sinusoidal: 13611 harmonic: 20304 Sorted by residual: dihedral pdb=" CA LYS C 156 " pdb=" C LYS C 156 " pdb=" N ILE C 157 " pdb=" CA ILE C 157 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LYS F 156 " pdb=" C LYS F 156 " pdb=" N ILE F 157 " pdb=" CA ILE F 157 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LYS D 156 " pdb=" C LYS D 156 " pdb=" N ILE D 157 " pdb=" CA ILE D 157 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 33912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4450 0.073 - 0.147: 3077 0.147 - 0.220: 859 0.220 - 0.294: 26 0.294 - 0.367: 18 Chirality restraints: 8430 Sorted by residual: chirality pdb=" CA PRO E 714 " pdb=" N PRO E 714 " pdb=" C PRO E 714 " pdb=" CB PRO E 714 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA PRO C 714 " pdb=" N PRO C 714 " pdb=" C PRO C 714 " pdb=" CB PRO C 714 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA PRO F 714 " pdb=" N PRO F 714 " pdb=" C PRO F 714 " pdb=" CB PRO F 714 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 8427 not shown) Planarity restraints: 10121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' TPP E1301 " -0.002 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" C4' TPP E1301 " 0.017 2.00e-02 2.50e+03 pdb=" C5' TPP E1301 " 0.027 2.00e-02 2.50e+03 pdb=" C6' TPP E1301 " 0.034 2.00e-02 2.50e+03 pdb=" C7' TPP E1301 " -0.067 2.00e-02 2.50e+03 pdb=" CM2 TPP E1301 " -0.042 2.00e-02 2.50e+03 pdb=" N1' TPP E1301 " 0.018 2.00e-02 2.50e+03 pdb=" N3' TPP E1301 " 0.002 2.00e-02 2.50e+03 pdb=" N4' TPP E1301 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' TPP F1301 " -0.004 2.00e-02 2.50e+03 2.68e-02 1.61e+01 pdb=" C4' TPP F1301 " 0.015 2.00e-02 2.50e+03 pdb=" C5' TPP F1301 " 0.025 2.00e-02 2.50e+03 pdb=" C6' TPP F1301 " 0.029 2.00e-02 2.50e+03 pdb=" C7' TPP F1301 " -0.057 2.00e-02 2.50e+03 pdb=" CM2 TPP F1301 " -0.034 2.00e-02 2.50e+03 pdb=" N1' TPP F1301 " 0.013 2.00e-02 2.50e+03 pdb=" N3' TPP F1301 " 0.001 2.00e-02 2.50e+03 pdb=" N4' TPP F1301 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' TPP A1301 " -0.004 2.00e-02 2.50e+03 2.64e-02 1.57e+01 pdb=" C4' TPP A1301 " 0.014 2.00e-02 2.50e+03 pdb=" C5' TPP A1301 " 0.024 2.00e-02 2.50e+03 pdb=" C6' TPP A1301 " 0.029 2.00e-02 2.50e+03 pdb=" C7' TPP A1301 " -0.057 2.00e-02 2.50e+03 pdb=" CM2 TPP A1301 " -0.032 2.00e-02 2.50e+03 pdb=" N1' TPP A1301 " 0.014 2.00e-02 2.50e+03 pdb=" N3' TPP A1301 " -0.002 2.00e-02 2.50e+03 pdb=" N4' TPP A1301 " 0.014 2.00e-02 2.50e+03 ... (remaining 10118 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6033 2.78 - 3.31: 50639 3.31 - 3.84: 79202 3.84 - 4.37: 110980 4.37 - 4.90: 177562 Nonbonded interactions: 424416 Sorted by model distance: nonbonded pdb=" OD1 ASN B 678 " pdb="MG MG B1302 " model vdw 2.250 2.170 nonbonded pdb=" OD1 ASN D 678 " pdb="MG MG D1302 " model vdw 2.253 2.170 nonbonded pdb=" OD1 ASN F 678 " pdb="MG MG F1302 " model vdw 2.283 2.170 nonbonded pdb=" OD1 ASN C 678 " pdb="MG MG C1301 " model vdw 2.295 2.170 nonbonded pdb=" OD1 ASN A 678 " pdb="MG MG A1302 " model vdw 2.297 2.170 ... (remaining 424411 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 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'B' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'C' and resid 102 through 1221) selection = (chain 'D' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'E' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'F' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.200 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: 0.090 Extract box with map and model: 1.960 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 107.920 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.013 0.077 56498 Z= 0.865 Angle : 1.762 7.807 76597 Z= 1.303 Chirality : 0.091 0.367 8430 Planarity : 0.005 0.033 10121 Dihedral : 14.212 87.247 20895 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.21 % Allowed : 3.60 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.93 (0.08), residues: 7062 helix: -1.45 (0.08), residues: 2562 sheet: -0.06 (0.14), residues: 1116 loop : -1.50 (0.09), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP C 417 HIS 0.016 0.004 HIS D 643 PHE 0.030 0.004 PHE F1082 TYR 0.046 0.006 TYR C 856 ARG 0.013 0.001 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1256 time to evaluate : 4.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8781 (mmt) cc_final: 0.8029 (mmt) REVERT: A 156 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8616 (mtpm) REVERT: A 257 LEU cc_start: 0.9197 (tp) cc_final: 0.8994 (tt) REVERT: A 290 GLU cc_start: 0.8634 (pm20) cc_final: 0.8347 (pm20) REVERT: A 296 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 405 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8291 (mtm180) REVERT: A 617 MET cc_start: 0.8670 (ttp) cc_final: 0.8455 (tmt) REVERT: A 760 MET cc_start: 0.8774 (ttp) cc_final: 0.8552 (ttp) REVERT: A 787 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 902 ASP cc_start: 0.8057 (m-30) cc_final: 0.7754 (m-30) REVERT: A 905 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8479 (ttp80) REVERT: A 909 THR cc_start: 0.8689 (m) cc_final: 0.8477 (m) REVERT: B 235 ASP cc_start: 0.8460 (t70) cc_final: 0.8184 (t0) REVERT: B 290 GLU cc_start: 0.8648 (pm20) cc_final: 0.8349 (pm20) REVERT: B 296 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 405 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8366 (mtm180) REVERT: B 617 MET cc_start: 0.8772 (ttp) cc_final: 0.8545 (tmt) REVERT: B 692 MET cc_start: 0.9113 (mtm) cc_final: 0.8807 (mtp) REVERT: B 787 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8327 (mt-10) REVERT: B 902 ASP cc_start: 0.8099 (m-30) cc_final: 0.7839 (m-30) REVERT: C 227 SER cc_start: 0.8856 (t) cc_final: 0.8632 (p) REVERT: C 405 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8150 (mtm180) REVERT: C 593 MET cc_start: 0.9197 (tpt) cc_final: 0.8991 (tpt) REVERT: C 617 MET cc_start: 0.8650 (ttp) cc_final: 0.8350 (tmt) REVERT: C 692 MET cc_start: 0.9044 (mtm) cc_final: 0.8820 (mtm) REVERT: C 761 TYR cc_start: 0.8875 (m-80) cc_final: 0.8510 (m-80) REVERT: C 902 ASP cc_start: 0.8000 (m-30) cc_final: 0.7703 (m-30) REVERT: C 905 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8490 (ttp80) REVERT: D 227 SER cc_start: 0.8682 (t) cc_final: 0.8435 (p) REVERT: D 579 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7065 (t70) REVERT: D 593 MET cc_start: 0.9213 (tpt) cc_final: 0.8985 (tpt) REVERT: D 606 ASN cc_start: 0.8839 (p0) cc_final: 0.8617 (p0) REVERT: D 617 MET cc_start: 0.8731 (ttp) cc_final: 0.8491 (tmt) REVERT: D 902 ASP cc_start: 0.8077 (m-30) cc_final: 0.7827 (m-30) REVERT: E 118 MET cc_start: 0.8753 (mmt) cc_final: 0.7785 (mmt) REVERT: E 132 ASP cc_start: 0.8554 (p0) cc_final: 0.8304 (p0) REVERT: E 593 MET cc_start: 0.9228 (tpt) cc_final: 0.8939 (tpt) REVERT: E 617 MET cc_start: 0.8607 (ttp) cc_final: 0.8384 (tmt) REVERT: E 761 TYR cc_start: 0.8837 (m-80) cc_final: 0.8619 (m-80) REVERT: E 902 ASP cc_start: 0.7996 (m-30) cc_final: 0.7746 (m-30) REVERT: E 909 THR cc_start: 0.8649 (m) cc_final: 0.8445 (m) REVERT: F 167 MET cc_start: 0.8755 (ttt) cc_final: 0.8313 (ttt) REVERT: F 405 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8119 (mtm180) REVERT: F 593 MET cc_start: 0.9147 (tpt) cc_final: 0.8933 (tpt) REVERT: F 859 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8450 (ttm170) REVERT: F 902 ASP cc_start: 0.8121 (m-30) cc_final: 0.7852 (m-30) outliers start: 12 outliers final: 2 residues processed: 1268 average time/residue: 1.6682 time to fit residues: 2565.5575 Evaluate side-chains 1127 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1124 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 263 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 0.6980 chunk 536 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 361 optimal weight: 0.8980 chunk 286 optimal weight: 0.6980 chunk 554 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 413 optimal weight: 2.9990 chunk 642 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 117 ASN B 276 GLN B 404 HIS B 498 ASN B 589 GLN B 973 GLN B1027 GLN B1213 GLN C 251 GLN C 276 GLN C 973 GLN D 276 GLN D 292 GLN D 316 HIS D 320 GLN D 498 ASN D1027 GLN D1045 HIS E 251 GLN E 276 GLN E 320 GLN E 973 GLN F 276 GLN F 973 GLN F1027 GLN F1045 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.119397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106609 restraints weight = 74164.904| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.50 r_work: 0.3403 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 56498 Z= 0.176 Angle : 0.554 5.855 76597 Z= 0.296 Chirality : 0.043 0.160 8430 Planarity : 0.005 0.093 10121 Dihedral : 5.269 78.000 7782 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.41 % Allowed : 9.02 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.07 (0.09), residues: 7062 helix: 0.94 (0.10), residues: 2622 sheet: 0.54 (0.14), residues: 1200 loop : -0.87 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 466 HIS 0.006 0.001 HIS F 267 PHE 0.023 0.001 PHE F1046 TYR 0.016 0.001 TYR D 761 ARG 0.007 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1207 time to evaluate : 4.915 Fit side-chains REVERT: A 290 GLU cc_start: 0.7930 (pm20) cc_final: 0.7598 (pm20) REVERT: A 405 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8088 (mtm180) REVERT: A 902 ASP cc_start: 0.8133 (m-30) cc_final: 0.7821 (m-30) REVERT: A 909 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 113 SER cc_start: 0.8321 (t) cc_final: 0.8089 (p) REVERT: B 296 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 405 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8220 (mtm180) REVERT: B 442 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8465 (mtt180) REVERT: B 902 ASP cc_start: 0.8203 (m-30) cc_final: 0.7983 (m-30) REVERT: C 167 MET cc_start: 0.8681 (ttt) cc_final: 0.8450 (ttt) REVERT: C 230 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (tp) REVERT: C 405 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7865 (mtm180) REVERT: C 761 TYR cc_start: 0.8624 (m-80) cc_final: 0.8423 (m-80) REVERT: C 902 ASP cc_start: 0.8051 (m-30) cc_final: 0.7787 (m-30) REVERT: C 1027 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: C 1208 GLN cc_start: 0.8154 (mt0) cc_final: 0.7928 (mt0) REVERT: D 113 SER cc_start: 0.8473 (t) cc_final: 0.8264 (p) REVERT: D 286 ASP cc_start: 0.8121 (t0) cc_final: 0.7859 (t0) REVERT: D 579 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6444 (t70) REVERT: D 902 ASP cc_start: 0.8200 (m-30) cc_final: 0.7998 (m-30) REVERT: D 1027 GLN cc_start: 0.8006 (tt0) cc_final: 0.7775 (tt0) REVERT: E 118 MET cc_start: 0.8687 (mmt) cc_final: 0.7983 (mmt) REVERT: E 761 TYR cc_start: 0.8619 (m-80) cc_final: 0.8314 (m-80) REVERT: E 902 ASP cc_start: 0.8084 (m-30) cc_final: 0.7849 (m-30) REVERT: E 1027 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: F 113 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8131 (p) REVERT: F 185 ASP cc_start: 0.7917 (t0) cc_final: 0.7653 (t0) REVERT: F 257 LEU cc_start: 0.8977 (tp) cc_final: 0.8728 (tp) REVERT: F 405 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7991 (mtm180) REVERT: F 763 LEU cc_start: 0.8476 (mt) cc_final: 0.8258 (mt) REVERT: F 902 ASP cc_start: 0.8219 (m-30) cc_final: 0.7997 (m-30) REVERT: F 1027 GLN cc_start: 0.7974 (tt0) cc_final: 0.7741 (tt0) REVERT: I 46 SER cc_start: 0.8682 (p) cc_final: 0.8473 (p) REVERT: I 72 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8538 (ttt-90) REVERT: L 46 SER cc_start: 0.8659 (p) cc_final: 0.8456 (p) outliers start: 82 outliers final: 12 residues processed: 1223 average time/residue: 1.7215 time to fit residues: 2547.1113 Evaluate side-chains 1174 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1156 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 47 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 423 optimal weight: 5.9990 chunk 603 optimal weight: 0.2980 chunk 657 optimal weight: 2.9990 chunk 486 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 317 optimal weight: 0.0030 chunk 380 optimal weight: 7.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A 677 ASN A 944 ASN A 973 GLN B 404 HIS B 498 ASN B 677 ASN B 679 GLN C 251 GLN C 677 ASN C 944 ASN D 292 GLN D 677 ASN E 251 GLN E 316 HIS E 363 ASN E 677 ASN E 944 ASN E 973 GLN E1184 ASN F 677 ASN F 722 GLN F 944 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106436 restraints weight = 73279.335| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.54 r_work: 0.3392 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56498 Z= 0.249 Angle : 0.540 8.400 76597 Z= 0.287 Chirality : 0.045 0.152 8430 Planarity : 0.005 0.058 10121 Dihedral : 4.973 66.364 7780 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.58 % Allowed : 10.99 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.64 (0.10), residues: 7062 helix: 1.60 (0.10), residues: 2634 sheet: 0.79 (0.14), residues: 1272 loop : -0.74 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 466 HIS 0.008 0.001 HIS F 267 PHE 0.027 0.002 PHE F1046 TYR 0.018 0.002 TYR D 761 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1203 time to evaluate : 4.886 Fit side-chains REVERT: A 290 GLU cc_start: 0.8030 (pm20) cc_final: 0.7705 (pm20) REVERT: A 298 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7952 (mmp80) REVERT: A 405 ARG cc_start: 0.8315 (mtm180) cc_final: 0.8038 (mtm180) REVERT: A 755 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: A 1208 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: B 113 SER cc_start: 0.8357 (t) cc_final: 0.8142 (p) REVERT: B 296 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 405 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8159 (mtm180) REVERT: B 902 ASP cc_start: 0.8218 (m-30) cc_final: 0.7957 (m-30) REVERT: C 230 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8436 (tp) REVERT: C 405 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7849 (mtm180) REVERT: C 593 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.7679 (tpt) REVERT: C 617 MET cc_start: 0.8244 (ttp) cc_final: 0.8026 (ppp) REVERT: C 902 ASP cc_start: 0.8059 (m-30) cc_final: 0.7797 (m-30) REVERT: C 1027 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: C 1208 GLN cc_start: 0.8194 (mt0) cc_final: 0.7920 (mt0) REVERT: D 113 SER cc_start: 0.8488 (t) cc_final: 0.8268 (p) REVERT: D 579 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6449 (t70) REVERT: D 1027 GLN cc_start: 0.8024 (tt0) cc_final: 0.7788 (tt0) REVERT: E 118 MET cc_start: 0.8752 (mmt) cc_final: 0.7914 (mmt) REVERT: E 761 TYR cc_start: 0.8644 (m-80) cc_final: 0.8411 (m-80) REVERT: E 803 VAL cc_start: 0.8527 (t) cc_final: 0.8320 (p) REVERT: E 902 ASP cc_start: 0.8080 (m-30) cc_final: 0.7873 (m-30) REVERT: E 993 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: F 185 ASP cc_start: 0.7888 (t0) cc_final: 0.7589 (t0) REVERT: F 257 LEU cc_start: 0.8952 (tp) cc_final: 0.8719 (tp) REVERT: F 405 ARG cc_start: 0.8352 (mtm180) cc_final: 0.7996 (mtm180) REVERT: F 986 ASP cc_start: 0.7940 (m-30) cc_final: 0.7734 (m-30) REVERT: I 72 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8605 (ttt-90) outliers start: 92 outliers final: 25 residues processed: 1228 average time/residue: 1.6979 time to fit residues: 2526.6602 Evaluate side-chains 1219 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1186 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 593 MET Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 993 GLU Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 150 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 515 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 501 optimal weight: 0.1980 chunk 306 optimal weight: 0.7980 chunk 674 optimal weight: 0.9980 chunk 638 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 677 ASN A 973 GLN B 404 HIS B 679 GLN B 944 ASN B 973 GLN C 251 GLN C 677 ASN D 292 GLN D 363 ASN D 677 ASN E 251 GLN E 677 ASN E 944 ASN E 973 GLN F 363 ASN F 677 ASN F 710 ASN F1138 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107663 restraints weight = 73325.143| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.51 r_work: 0.3411 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 56498 Z= 0.186 Angle : 0.493 6.885 76597 Z= 0.260 Chirality : 0.043 0.148 8430 Planarity : 0.004 0.043 10121 Dihedral : 4.806 69.774 7780 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 11.80 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.93 (0.10), residues: 7062 helix: 1.86 (0.10), residues: 2646 sheet: 0.98 (0.14), residues: 1278 loop : -0.63 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 466 HIS 0.004 0.001 HIS F 267 PHE 0.025 0.001 PHE F1046 TYR 0.017 0.001 TYR D 761 ARG 0.008 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1222 time to evaluate : 4.883 Fit side-chains REVERT: A 290 GLU cc_start: 0.8034 (pm20) cc_final: 0.7698 (pm20) REVERT: A 298 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7924 (mmp80) REVERT: A 405 ARG cc_start: 0.8302 (mtm180) cc_final: 0.8095 (mtm180) REVERT: A 1208 GLN cc_start: 0.8093 (mt0) cc_final: 0.7827 (mt0) REVERT: B 113 SER cc_start: 0.8349 (t) cc_final: 0.8132 (p) REVERT: B 296 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 405 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8236 (mtm180) REVERT: B 929 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: C 405 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7820 (mtm180) REVERT: C 902 ASP cc_start: 0.8107 (m-30) cc_final: 0.7876 (m-30) REVERT: C 1027 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: D 579 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6417 (t70) REVERT: D 803 VAL cc_start: 0.8406 (t) cc_final: 0.8170 (p) REVERT: D 1027 GLN cc_start: 0.7998 (tt0) cc_final: 0.7795 (tt0) REVERT: E 118 MET cc_start: 0.8754 (mmt) cc_final: 0.7955 (mmt) REVERT: E 902 ASP cc_start: 0.8053 (m-30) cc_final: 0.7845 (m-30) REVERT: E 949 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: E 993 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: E 1208 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: F 113 SER cc_start: 0.8436 (t) cc_final: 0.8170 (p) REVERT: F 185 ASP cc_start: 0.7891 (t0) cc_final: 0.7609 (t0) REVERT: F 257 LEU cc_start: 0.8913 (tp) cc_final: 0.8683 (tp) REVERT: F 315 ASP cc_start: 0.8125 (t0) cc_final: 0.7925 (t0) REVERT: F 405 ARG cc_start: 0.8349 (mtm180) cc_final: 0.7991 (mtm180) REVERT: F 448 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (p) REVERT: F 986 ASP cc_start: 0.7945 (m-30) cc_final: 0.7720 (m-30) REVERT: I 72 ARG cc_start: 0.8859 (ttt180) cc_final: 0.8579 (ttt-90) outliers start: 87 outliers final: 30 residues processed: 1243 average time/residue: 1.6780 time to fit residues: 2536.9643 Evaluate side-chains 1249 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 1211 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 1096 ASN Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 949 GLU Chi-restraints excluded: chain E residue 993 GLU Chi-restraints excluded: chain E residue 1208 GLN Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 1209 LEU Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 634 optimal weight: 0.7980 chunk 698 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 365 optimal weight: 0.9980 chunk 321 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 537 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 677 ASN A 973 GLN A1184 ASN B 404 HIS C 251 GLN C 677 ASN C 944 ASN C1184 ASN D 677 ASN D1184 ASN E 251 GLN E 677 ASN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 677 ASN F 710 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.120617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107505 restraints weight = 73820.145| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.52 r_work: 0.3413 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 56498 Z= 0.184 Angle : 0.486 7.321 76597 Z= 0.256 Chirality : 0.043 0.148 8430 Planarity : 0.004 0.070 10121 Dihedral : 4.741 70.216 7780 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.20 % Allowed : 12.93 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.08 (0.10), residues: 7062 helix: 2.01 (0.10), residues: 2646 sheet: 1.22 (0.14), residues: 1242 loop : -0.61 (0.10), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.005 0.001 HIS C 267 PHE 0.025 0.001 PHE F1046 TYR 0.018 0.001 TYR E 761 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1222 time to evaluate : 4.862 Fit side-chains REVERT: A 290 GLU cc_start: 0.8053 (pm20) cc_final: 0.7731 (pm20) REVERT: A 405 ARG cc_start: 0.8277 (mtm180) cc_final: 0.8075 (mtm180) REVERT: A 1208 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: B 113 SER cc_start: 0.8357 (t) cc_final: 0.8139 (p) REVERT: B 290 GLU cc_start: 0.7976 (pm20) cc_final: 0.7720 (pm20) REVERT: B 405 ARG cc_start: 0.8503 (mtm180) cc_final: 0.8228 (mtm180) REVERT: C 405 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7823 (mtm180) REVERT: C 902 ASP cc_start: 0.8108 (m-30) cc_final: 0.7883 (m-30) REVERT: C 1027 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: D 579 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6386 (t70) REVERT: D 803 VAL cc_start: 0.8401 (t) cc_final: 0.8187 (p) REVERT: E 118 MET cc_start: 0.8756 (mmt) cc_final: 0.7989 (mmt) REVERT: E 902 ASP cc_start: 0.8082 (m-30) cc_final: 0.7882 (m-30) REVERT: E 993 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: E 1208 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: F 113 SER cc_start: 0.8425 (t) cc_final: 0.8163 (p) REVERT: F 185 ASP cc_start: 0.7919 (t0) cc_final: 0.7650 (t0) REVERT: F 257 LEU cc_start: 0.8900 (tp) cc_final: 0.8678 (tp) REVERT: F 315 ASP cc_start: 0.8089 (t0) cc_final: 0.7881 (t0) REVERT: F 405 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7983 (mtm180) REVERT: F 448 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8292 (p) REVERT: F 722 GLN cc_start: 0.8394 (tt0) cc_final: 0.8124 (tt0) REVERT: F 726 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: F 986 ASP cc_start: 0.7958 (m-30) cc_final: 0.7745 (m-30) REVERT: I 72 ARG cc_start: 0.8869 (ttt180) cc_final: 0.8595 (ttt-90) outliers start: 70 outliers final: 40 residues processed: 1241 average time/residue: 1.6555 time to fit residues: 2495.5609 Evaluate side-chains 1259 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1212 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 1096 ASN Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 880 TRP Chi-restraints excluded: chain E residue 993 GLU Chi-restraints excluded: chain E residue 1073 LYS Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain E residue 1208 GLN Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 381 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 518 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 259 optimal weight: 0.3980 chunk 308 optimal weight: 0.0570 chunk 491 optimal weight: 0.7980 chunk 323 optimal weight: 0.7980 chunk 415 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 404 HIS B 973 GLN C 251 GLN C 363 ASN C 677 ASN C 944 ASN D 677 ASN E 251 GLN E 677 ASN E 944 ASN F 710 ASN F1045 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.123483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110341 restraints weight = 74131.716| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.56 r_work: 0.3454 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 56498 Z= 0.119 Angle : 0.442 7.334 76597 Z= 0.232 Chirality : 0.041 0.140 8430 Planarity : 0.004 0.041 10121 Dihedral : 4.484 66.634 7780 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.01 % Allowed : 13.43 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.32 (0.10), residues: 7062 helix: 2.22 (0.10), residues: 2646 sheet: 1.33 (0.14), residues: 1242 loop : -0.48 (0.10), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 466 HIS 0.003 0.001 HIS F 267 PHE 0.022 0.001 PHE D1046 TYR 0.015 0.001 TYR E 761 ARG 0.007 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1259 time to evaluate : 4.839 Fit side-chains REVERT: A 290 GLU cc_start: 0.8059 (pm20) cc_final: 0.7736 (pm20) REVERT: A 298 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7868 (mmp80) REVERT: A 405 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7949 (mtm180) REVERT: B 290 GLU cc_start: 0.7995 (pm20) cc_final: 0.7707 (pm20) REVERT: B 405 ARG cc_start: 0.8496 (mtm180) cc_final: 0.8223 (mtm180) REVERT: C 405 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7801 (mtm180) REVERT: C 765 THR cc_start: 0.8503 (t) cc_final: 0.8294 (m) REVERT: C 902 ASP cc_start: 0.8109 (m-30) cc_final: 0.7868 (m-30) REVERT: D 579 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6320 (t70) REVERT: D 803 VAL cc_start: 0.8288 (t) cc_final: 0.8084 (p) REVERT: E 118 MET cc_start: 0.8748 (mmt) cc_final: 0.8021 (mmt) REVERT: E 501 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: F 113 SER cc_start: 0.8396 (t) cc_final: 0.8157 (p) REVERT: F 257 LEU cc_start: 0.8841 (tp) cc_final: 0.8622 (tp) REVERT: F 405 ARG cc_start: 0.8323 (mtm180) cc_final: 0.7968 (mtm180) REVERT: F 448 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8140 (p) REVERT: F 593 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: F 722 GLN cc_start: 0.8338 (tt0) cc_final: 0.8048 (tt0) REVERT: F 726 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: F 986 ASP cc_start: 0.7944 (m-30) cc_final: 0.7742 (m-30) REVERT: I 72 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8553 (ttt-90) outliers start: 59 outliers final: 30 residues processed: 1276 average time/residue: 1.6322 time to fit residues: 2538.6866 Evaluate side-chains 1247 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1211 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain D residue 1187 LYS Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 501 GLN Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 1073 LYS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 726 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 10 optimal weight: 0.2980 chunk 655 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 chunk 544 optimal weight: 0.7980 chunk 422 optimal weight: 3.9990 chunk 506 optimal weight: 2.9990 chunk 480 optimal weight: 6.9990 chunk 631 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN A 677 ASN B 404 HIS B 491 ASN B 498 ASN B 710 ASN C 251 GLN C 363 ASN C 677 ASN C 944 ASN C1027 GLN D 677 ASN E 677 ASN E 944 ASN E1027 GLN F 292 GLN F 363 ASN F 710 ASN F 936 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106459 restraints weight = 73448.652| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.53 r_work: 0.3394 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56498 Z= 0.270 Angle : 0.524 8.092 76597 Z= 0.277 Chirality : 0.045 0.154 8430 Planarity : 0.004 0.039 10121 Dihedral : 4.783 70.212 7780 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.05 % Allowed : 13.70 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.15 (0.10), residues: 7062 helix: 2.02 (0.10), residues: 2676 sheet: 1.27 (0.14), residues: 1236 loop : -0.56 (0.10), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 466 HIS 0.007 0.001 HIS C 267 PHE 0.027 0.002 PHE F1046 TYR 0.020 0.002 TYR E 761 ARG 0.010 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1230 time to evaluate : 4.882 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8069 (pm20) cc_final: 0.7734 (pm20) REVERT: A 298 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7862 (mmp80) REVERT: A 405 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7963 (mtm180) REVERT: A 1208 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: B 153 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7421 (mtm-85) REVERT: B 290 GLU cc_start: 0.8014 (pm20) cc_final: 0.7717 (pm20) REVERT: B 1208 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: C 405 ARG cc_start: 0.8236 (mtm180) cc_final: 0.7795 (mtm180) REVERT: C 765 THR cc_start: 0.8583 (t) cc_final: 0.8373 (m) REVERT: C 902 ASP cc_start: 0.8150 (m-30) cc_final: 0.7916 (m-30) REVERT: D 113 SER cc_start: 0.8475 (t) cc_final: 0.8242 (p) REVERT: D 579 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6397 (t70) REVERT: D 803 VAL cc_start: 0.8480 (t) cc_final: 0.8249 (p) REVERT: D 831 LEU cc_start: 0.8176 (tp) cc_final: 0.7967 (tt) REVERT: E 118 MET cc_start: 0.8758 (mmt) cc_final: 0.7950 (mmt) REVERT: E 1208 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: F 113 SER cc_start: 0.8447 (t) cc_final: 0.8169 (p) REVERT: F 257 LEU cc_start: 0.8906 (tp) cc_final: 0.8682 (tp) REVERT: F 405 ARG cc_start: 0.8312 (mtm180) cc_final: 0.7944 (mtm180) REVERT: F 593 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7617 (tpt) REVERT: I 72 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8655 (ttt-90) outliers start: 61 outliers final: 33 residues processed: 1250 average time/residue: 1.6532 time to fit residues: 2513.7594 Evaluate side-chains 1259 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 1220 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1096 ASN Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 1073 LYS Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain E residue 1208 GLN Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 1209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 160 optimal weight: 2.9990 chunk 473 optimal weight: 0.9990 chunk 420 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 528 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 580 optimal weight: 4.9990 chunk 499 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 404 HIS B 679 GLN C 251 GLN C 363 ASN C 677 ASN C 944 ASN C1168 GLN D 404 HIS D 498 ASN D 677 ASN D 973 GLN E 677 ASN E 944 ASN E 973 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106801 restraints weight = 73396.848| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.53 r_work: 0.3401 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 56498 Z= 0.245 Angle : 0.517 8.191 76597 Z= 0.272 Chirality : 0.044 0.149 8430 Planarity : 0.004 0.063 10121 Dihedral : 4.790 70.568 7778 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.27 % Allowed : 13.70 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.12 (0.10), residues: 7062 helix: 1.96 (0.10), residues: 2682 sheet: 1.28 (0.14), residues: 1248 loop : -0.57 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.006 0.001 HIS F 267 PHE 0.027 0.001 PHE F1046 TYR 0.018 0.001 TYR D 761 ARG 0.008 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1232 time to evaluate : 4.902 Fit side-chains REVERT: A 290 GLU cc_start: 0.8080 (pm20) cc_final: 0.7740 (pm20) REVERT: A 298 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7841 (mmp80) REVERT: A 405 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7959 (mtm180) REVERT: A 873 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 1059 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8150 (mtt90) REVERT: A 1208 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: B 153 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: B 290 GLU cc_start: 0.8010 (pm20) cc_final: 0.7698 (pm20) REVERT: C 405 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7787 (mtm180) REVERT: C 501 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: C 765 THR cc_start: 0.8612 (t) cc_final: 0.8398 (m) REVERT: C 902 ASP cc_start: 0.8145 (m-30) cc_final: 0.7927 (m-30) REVERT: D 113 SER cc_start: 0.8488 (t) cc_final: 0.8268 (p) REVERT: D 579 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6387 (t70) REVERT: D 803 VAL cc_start: 0.8451 (t) cc_final: 0.8224 (p) REVERT: D 831 LEU cc_start: 0.8176 (tp) cc_final: 0.7969 (tt) REVERT: E 118 MET cc_start: 0.8753 (mmt) cc_final: 0.7931 (mmt) REVERT: F 113 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8176 (p) REVERT: F 257 LEU cc_start: 0.8913 (tp) cc_final: 0.8685 (tp) REVERT: F 405 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7942 (mtm180) REVERT: F 593 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7589 (tpt) REVERT: I 72 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8614 (ttt-90) outliers start: 74 outliers final: 42 residues processed: 1257 average time/residue: 1.6371 time to fit residues: 2511.6958 Evaluate side-chains 1277 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1227 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 1073 LYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 801 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 686 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 540 optimal weight: 2.9990 chunk 577 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 661 optimal weight: 0.9980 chunk 475 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 682 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 944 ASN B 404 HIS B 679 GLN C 251 GLN C 677 ASN C 944 ASN D 404 HIS D 677 ASN D 973 GLN E 677 ASN E 944 ASN E 973 GLN F 363 ASN F 710 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.107581 restraints weight = 73763.313| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.53 r_work: 0.3418 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 56498 Z= 0.181 Angle : 0.491 7.812 76597 Z= 0.258 Chirality : 0.043 0.148 8430 Planarity : 0.004 0.040 10121 Dihedral : 4.675 67.964 7778 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.06 % Allowed : 14.22 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.22 (0.10), residues: 7062 helix: 2.07 (0.10), residues: 2682 sheet: 1.32 (0.14), residues: 1248 loop : -0.53 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.005 0.001 HIS F 267 PHE 0.025 0.001 PHE F1046 TYR 0.017 0.001 TYR D 761 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1236 time to evaluate : 4.963 Fit side-chains REVERT: A 144 MET cc_start: 0.8317 (mtp) cc_final: 0.8098 (ttm) REVERT: A 290 GLU cc_start: 0.8077 (pm20) cc_final: 0.7737 (pm20) REVERT: A 298 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7827 (mmp80) REVERT: A 405 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7954 (mtm180) REVERT: A 873 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 1059 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8129 (mtt90) REVERT: B 153 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7395 (mtm-85) REVERT: B 290 GLU cc_start: 0.8016 (pm20) cc_final: 0.7695 (pm20) REVERT: C 405 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7768 (mtm180) REVERT: C 765 THR cc_start: 0.8585 (t) cc_final: 0.8368 (m) REVERT: C 902 ASP cc_start: 0.8134 (m-30) cc_final: 0.7895 (m-30) REVERT: D 579 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6380 (t70) REVERT: D 803 VAL cc_start: 0.8398 (t) cc_final: 0.8182 (p) REVERT: E 118 MET cc_start: 0.8748 (mmt) cc_final: 0.7953 (mmt) REVERT: F 113 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8164 (p) REVERT: F 257 LEU cc_start: 0.8891 (tp) cc_final: 0.8656 (tp) REVERT: F 405 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7937 (mtm180) REVERT: F 593 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.7531 (tpt) outliers start: 62 outliers final: 44 residues processed: 1258 average time/residue: 1.6452 time to fit residues: 2526.3511 Evaluate side-chains 1273 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1223 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 629 ASP Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 1073 LYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 801 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 148 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 599 optimal weight: 0.0970 chunk 666 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 565 optimal weight: 0.5980 chunk 309 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 667 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 677 ASN B 404 HIS B 498 ASN B 677 ASN B 710 ASN C 677 ASN C 944 ASN C1138 HIS D 404 HIS D1143 ASN E 677 ASN E 944 ASN F 710 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108577 restraints weight = 74129.635| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.50 r_work: 0.3446 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 56498 Z= 0.137 Angle : 0.469 8.026 76597 Z= 0.244 Chirality : 0.042 0.144 8430 Planarity : 0.004 0.040 10121 Dihedral : 4.533 65.923 7778 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.77 % Allowed : 14.82 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.29 (0.10), residues: 7062 helix: 2.16 (0.10), residues: 2682 sheet: 1.44 (0.14), residues: 1236 loop : -0.55 (0.10), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 466 HIS 0.004 0.001 HIS D 404 PHE 0.023 0.001 PHE D1046 TYR 0.016 0.001 TYR F 761 ARG 0.009 0.000 ARG F 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1247 time to evaluate : 5.795 Fit side-chains REVERT: A 290 GLU cc_start: 0.8054 (pm20) cc_final: 0.7716 (pm20) REVERT: A 298 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7823 (mmp80) REVERT: A 405 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7954 (mtm180) REVERT: B 118 MET cc_start: 0.8811 (mmt) cc_final: 0.8050 (mmt) REVERT: B 153 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: B 290 GLU cc_start: 0.8012 (pm20) cc_final: 0.7697 (pm20) REVERT: C 405 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7745 (mtm180) REVERT: C 765 THR cc_start: 0.8520 (t) cc_final: 0.8313 (m) REVERT: C 902 ASP cc_start: 0.8132 (m-30) cc_final: 0.7886 (m-30) REVERT: D 579 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6300 (t0) REVERT: D 803 VAL cc_start: 0.8319 (t) cc_final: 0.8103 (p) REVERT: E 118 MET cc_start: 0.8768 (mmt) cc_final: 0.8051 (mmt) REVERT: F 113 SER cc_start: 0.8410 (t) cc_final: 0.8158 (p) REVERT: F 257 LEU cc_start: 0.8853 (tp) cc_final: 0.8629 (tp) REVERT: F 405 ARG cc_start: 0.8283 (mtm180) cc_final: 0.7912 (mtm180) REVERT: F 593 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.7616 (tpt) REVERT: F 1185 MET cc_start: 0.8701 (ttp) cc_final: 0.8432 (ttm) REVERT: I 72 ARG cc_start: 0.8777 (ttt180) cc_final: 0.8453 (ttt-90) outliers start: 45 outliers final: 34 residues processed: 1264 average time/residue: 1.6536 time to fit residues: 2545.7102 Evaluate side-chains 1261 residues out of total 5892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1224 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 560 SER Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 71.7525 > 50: distance: 78 - 82: 35.440 distance: 82 - 83: 41.332 distance: 83 - 84: 39.285 distance: 83 - 86: 55.574 distance: 84 - 85: 40.153 distance: 84 - 90: 55.657 distance: 86 - 87: 40.416 distance: 88 - 89: 39.121 distance: 90 - 91: 40.784 distance: 91 - 92: 55.864 distance: 91 - 94: 56.531 distance: 92 - 97: 40.181 distance: 94 - 96: 38.813 distance: 97 - 98: 7.641 distance: 98 - 99: 65.621 distance: 98 - 101: 39.393 distance: 99 - 106: 57.081 distance: 101 - 102: 39.824 distance: 102 - 103: 15.426 distance: 103 - 104: 43.450 distance: 103 - 105: 47.356 distance: 106 - 107: 55.687 distance: 106 - 112: 56.921 distance: 107 - 108: 70.580 distance: 114 - 115: 40.924 distance: 114 - 117: 52.371 distance: 115 - 116: 38.903 distance: 115 - 122: 40.108 distance: 117 - 118: 52.778 distance: 119 - 120: 39.832 distance: 122 - 123: 40.850 distance: 123 - 124: 38.706 distance: 123 - 126: 32.901 distance: 124 - 125: 42.343 distance: 124 - 130: 34.069 distance: 125 - 159: 61.457 distance: 126 - 127: 49.414 distance: 127 - 128: 41.055 distance: 128 - 129: 36.176 distance: 130 - 131: 39.607 distance: 131 - 132: 57.865 distance: 132 - 142: 40.520 distance: 134 - 135: 38.908 distance: 135 - 136: 63.683 distance: 135 - 137: 61.963 distance: 136 - 138: 45.267 distance: 137 - 139: 38.921 distance: 138 - 140: 34.837 distance: 139 - 140: 41.693 distance: 140 - 141: 28.352 distance: 142 - 143: 17.710 distance: 143 - 144: 20.481 distance: 143 - 146: 21.275 distance: 144 - 145: 39.555 distance: 144 - 151: 40.814 distance: 146 - 147: 38.771 distance: 151 - 152: 35.935 distance: 152 - 153: 57.734 distance: 153 - 154: 38.901 distance: 153 - 159: 39.658 distance: 156 - 157: 52.868 distance: 156 - 158: 53.874 distance: 160 - 161: 39.162 distance: 161 - 167: 34.652 distance: 163 - 165: 30.048 distance: 164 - 166: 31.466