Starting phenix.real_space_refine on Sat Dec 9 17:16:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opd_13016/12_2023/7opd_13016.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 197 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 302 5.16 5 C 38839 2.51 5 N 12055 2.21 5 O 12919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1258": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M GLU 385": "OE1" <-> "OE2" Residue "M ARG 409": "NH1" <-> "NH2" Residue "M GLU 411": "OE1" <-> "OE2" Residue "M GLU 418": "OE1" <-> "OE2" Residue "M ARG 441": "NH1" <-> "NH2" Residue "M ARG 450": "NH1" <-> "NH2" Residue "M GLU 459": "OE1" <-> "OE2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M GLU 544": "OE1" <-> "OE2" Residue "M GLU 548": "OE1" <-> "OE2" Residue "M GLU 630": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "M GLU 704": "OE1" <-> "OE2" Residue "M ARG 707": "NH1" <-> "NH2" Residue "M ARG 759": "NH1" <-> "NH2" Residue "M GLU 802": "OE1" <-> "OE2" Residue "M GLU 824": "OE1" <-> "OE2" Residue "M GLU 827": "OE1" <-> "OE2" Residue "M ARG 855": "NH1" <-> "NH2" Residue "M ARG 918": "NH1" <-> "NH2" Residue "M GLU 947": "OE1" <-> "OE2" Residue "M GLU 952": "OE1" <-> "OE2" Residue "M GLU 953": "OE1" <-> "OE2" Residue "M GLU 968": "OE1" <-> "OE2" Residue "M ARG 995": "NH1" <-> "NH2" Residue "M ARG 1014": "NH1" <-> "NH2" Residue "M GLU 1061": "OE1" <-> "OE2" Residue "M GLU 1129": "OE1" <-> "OE2" Residue "M GLU 1273": "OE1" <-> "OE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "a GLU 306": "OE1" <-> "OE2" Residue "b ARG 516": "NH1" <-> "NH2" Residue "b ARG 538": "NH1" <-> "NH2" Residue "b GLU 564": "OE1" <-> "OE2" Residue "b GLU 584": "OE1" <-> "OE2" Residue "b ARG 593": "NH1" <-> "NH2" Residue "b GLU 608": "OE1" <-> "OE2" Residue "b ARG 637": "NH1" <-> "NH2" Residue "b ARG 652": "NH1" <-> "NH2" Residue "b ARG 666": "NH1" <-> "NH2" Residue "b GLU 771": "OE1" <-> "OE2" Residue "b GLU 792": "OE1" <-> "OE2" Residue "b GLU 829": "OE1" <-> "OE2" Residue "b ARG 876": "NH1" <-> "NH2" Residue "b GLU 903": "OE1" <-> "OE2" Residue "b ARG 915": "NH1" <-> "NH2" Residue "b GLU 946": "OE1" <-> "OE2" Residue "b ARG 950": "NH1" <-> "NH2" Residue "b ARG 985": "NH1" <-> "NH2" Residue "d ARG 50": "NH1" <-> "NH2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ARG 147": "NH1" <-> "NH2" Residue "d ARG 198": "NH1" <-> "NH2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 286": "OE1" <-> "OE2" Residue "d GLU 351": "OE1" <-> "OE2" Residue "d ARG 369": "NH1" <-> "NH2" Residue "d GLU 784": "OE1" <-> "OE2" Residue "d GLU 842": "OE1" <-> "OE2" Residue "d GLU 863": "OE1" <-> "OE2" Residue "d GLU 898": "OE1" <-> "OE2" Residue "d ARG 900": "NH1" <-> "NH2" Residue "d PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 988": "OE1" <-> "OE2" Residue "d ARG 989": "NH1" <-> "NH2" Residue "d GLU 1045": "OE1" <-> "OE2" Residue "d GLU 1079": "OE1" <-> "OE2" Residue "d ARG 1080": "NH1" <-> "NH2" Residue "d ARG 1102": "NH1" <-> "NH2" Residue "d ARG 1138": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64227 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11179 Classifications: {'peptide': 1412} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1342} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9052 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1013 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 6648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6648 Classifications: {'peptide': 810} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 777} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "N" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 727 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "P" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 12, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "R" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 160 Classifications: {'peptide': 40} Incomplete info: {'backbone_only': 40} Link IDs: {'TRANS': 39} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'UNK:plan-1': 40} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 3560 Classifications: {'peptide': 890} Incomplete info: {'backbone_only': 855} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 868} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 3815 Unresolved non-hydrogen angles: 5472 Unresolved non-hydrogen dihedrals: 2486 Unresolved non-hydrogen chiralities: 1072 Planarities with less than four sites: {'GLN:plan1': 59, 'ASP:plan': 50, 'TYR:plan': 46, 'ASN:plan1': 42, 'TRP:plan': 7, 'HIS:plan': 28, 'PHE:plan': 33, 'GLU:plan': 74, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1967 Chain: "T" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 947 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "U" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 416 Classifications: {'peptide': 104} Incomplete info: {'backbone_only': 96} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 256 Chain: "V" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 868 Classifications: {'peptide': 217} Incomplete info: {'backbone_only': 211} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 975 Unresolved non-hydrogen angles: 1393 Unresolved non-hydrogen dihedrals: 639 Unresolved non-hydrogen chiralities: 263 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 509 Chain: "Y" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 1200 Classifications: {'peptide': 300} Incomplete info: {'backbone_only': 275} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1193 Unresolved non-hydrogen angles: 1752 Unresolved non-hydrogen dihedrals: 785 Unresolved non-hydrogen chiralities: 363 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 10, 'ASP:plan': 29, 'PHE:plan': 10, 'GLU:plan': 10, 'HIS:plan': 13} Unresolved non-hydrogen planarities: 586 Chain: "Z" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 172 Classifications: {'peptide': 43} Incomplete info: {'backbone_only': 42} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "a" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2849 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "b" Number of atoms: 4261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4261 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain breaks: 3 Chain: "c" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 564 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 133} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 615 Unresolved non-hydrogen angles: 874 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 290 Chain: "d" Number of atoms: 7443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 7443 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 290} Link IDs: {'PTRANS': 40, 'TRANS': 1055} Chain breaks: 6 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1205 Unresolved non-hydrogen angles: 1763 Unresolved non-hydrogen dihedrals: 743 Unresolved non-hydrogen chiralities: 394 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 525 Chain: "e" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 2845 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 679} Link IDs: {'PTRANS': 19, 'TRANS': 691} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 3093 Unresolved non-hydrogen angles: 4405 Unresolved non-hydrogen dihedrals: 2016 Unresolved non-hydrogen chiralities: 878 Planarities with less than four sites: {'GLN:plan1': 41, 'HIS:plan': 22, 'TYR:plan': 20, 'ASN:plan1': 23, 'TRP:plan': 6, 'ASP:plan': 46, 'PHE:plan': 35, 'GLU:plan': 60, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1482 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 84 Classifications: {'peptide': 21} Incomplete info: {'backbone_only': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 91.096 125.009 171.771 1.00 49.42 S ATOM 486 SG CYS A 74 91.328 128.608 171.634 1.00 43.63 S ATOM 533 SG CYS A 81 92.268 127.215 168.775 1.00 38.41 S ATOM 768 SG CYS A 111 135.869 118.392 185.814 1.00 97.18 S ATOM 1109 SG CYS A 154 138.084 120.328 187.500 1.00111.87 S ATOM 1132 SG CYS A 184 137.756 116.730 188.930 1.00113.84 S ATOM 19801 SG CYS B1119 103.116 136.626 180.029 1.00 41.75 S ATOM 19823 SG CYS B1122 105.366 133.957 178.756 1.00 39.90 S ATOM 19938 SG CYS B1137 102.180 132.866 179.414 1.00 53.56 S ATOM 19959 SG CYS B1140 105.102 134.493 182.033 1.00 51.74 S ATOM 20925 SG CYS C 88 59.673 141.990 113.138 1.00 57.79 S ATOM 20938 SG CYS C 90 59.392 139.290 115.243 1.00 65.42 S ATOM 20973 SG CYS C 94 58.624 139.350 112.186 1.00 49.61 S ATOM 20995 SG CYS C 97 62.443 139.339 112.512 1.00 41.48 S ATOM 28299 SG CYS I 17 167.248 86.113 138.368 1.00100.86 S ATOM 28323 SG CYS I 20 164.228 86.482 140.290 1.00 97.63 S ATOM 28484 SG CYS I 39 165.618 88.851 141.677 1.00103.83 S ATOM 28509 SG CYS I 42 167.529 85.793 141.345 1.00104.25 S ATOM 28861 SG CYS I 86 159.136 106.235 99.458 1.00 61.88 S ATOM 28885 SG CYS I 89 157.987 103.924 97.270 1.00 68.13 S ATOM 29089 SG CYS I 114 155.490 104.855 98.977 1.00 53.57 S ATOM 29124 SG CYS I 119 158.282 102.452 100.174 1.00 64.28 S ATOM 29234 SG CYS J 7 90.259 133.665 99.874 1.00 41.61 S ATOM 29258 SG CYS J 10 88.430 136.178 97.998 1.00 9.72 S ATOM 29522 SG CYS J 44 92.274 135.723 97.711 1.00 9.66 S ATOM 29528 SG CYS J 45 89.835 133.698 96.017 1.00 14.17 S ATOM 30690 SG CYS L 19 77.588 97.793 121.828 1.00 45.95 S ATOM 30709 SG CYS L 22 75.219 96.358 120.113 1.00 51.26 S ATOM 30826 SG CYS L 36 74.536 95.928 123.233 1.00 56.73 S ATOM 30852 SG CYS L 39 77.836 94.212 121.439 1.00 58.50 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N GLY M1173 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY M1173 " occ=0.00 residue: pdb=" N GLY M1227 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY M1227 " occ=0.00 residue: pdb=" N GLY M1235 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY M1235 " occ=0.00 residue: pdb=" N GLY M1238 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY M1238 " occ=0.00 residue: pdb=" N GLY M1260 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY M1260 " occ=0.00 Time building chain proxies: 25.35, per 1000 atoms: 0.39 Number of scatterers: 64227 At special positions: 0 Unit cell: (212.1, 242.55, 303.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 302 16.00 P 103 15.00 Mg 1 11.99 O 12919 8.00 N 12055 7.00 C 38839 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 - 3.50 Amino acid : False - 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: 20.44 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 39 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11980 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 108 sheets defined 42.0% alpha, 17.9% beta 40 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 17.25 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.842A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.743A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.989A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.718A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.568A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.915A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.752A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.989A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.660A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 4.170A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.840A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.845A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.718A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.589A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.000A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 4.094A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.827A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.588A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.719A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.254A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.550A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.569A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.833A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.679A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.819A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.561A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.796A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.530A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.587A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.106A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.505A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.062A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 removed outlier: 4.046A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.727A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.614A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.565A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.215A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.550A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.041A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 285 through 292 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.650A pdb=" N GLN M 299 " --> pdb=" O PRO M 295 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU M 300 " --> pdb=" O GLU M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 311 through 325 Processing helix chain 'M' and resid 356 through 370 Processing helix chain 'M' and resid 372 through 380 Processing helix chain 'M' and resid 380 through 385 Processing helix chain 'M' and resid 389 through 427 removed outlier: 3.777A pdb=" N GLU M 401 " --> pdb=" O TRP M 397 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS M 402 " --> pdb=" O GLN M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 453 removed outlier: 3.505A pdb=" N LEU M 451 " --> pdb=" O ASP M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 471 WARNING: missing atoms! removed outlier: 3.531A pdb=" N TYR M 470 " --> pdb=" O HIS M 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 530 removed outlier: 3.734A pdb=" N CYS M 527 " --> pdb=" O MET M 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA M 530 " --> pdb=" O ILE M 526 " (cutoff:3.500A) Processing helix chain 'M' and resid 532 through 539 Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 565 through 572 removed outlier: 3.582A pdb=" N LEU M 569 " --> pdb=" O GLU M 565 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP M 572 " --> pdb=" O GLU M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 599 Processing helix chain 'M' and resid 599 through 613 Processing helix chain 'M' and resid 621 through 628 removed outlier: 3.959A pdb=" N LYS M 626 " --> pdb=" O LYS M 622 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP M 627 " --> pdb=" O LYS M 623 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 638 removed outlier: 3.961A pdb=" N SER M 636 " --> pdb=" O TYR M 633 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS M 638 " --> pdb=" O TYR M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 648 No H-bonds generated for 'chain 'M' and resid 646 through 648' Processing helix chain 'M' and resid 651 through 662 Processing helix chain 'M' and resid 685 through 691 removed outlier: 3.791A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 720 Processing helix chain 'M' and resid 720 through 754 Processing helix chain 'M' and resid 825 through 843 Processing helix chain 'M' and resid 855 through 869 removed outlier: 3.719A pdb=" N MET M 859 " --> pdb=" O ARG M 855 " (cutoff:3.500A) Processing helix chain 'M' and resid 888 through 896 removed outlier: 3.573A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) Processing helix chain 'M' and resid 896 through 903 removed outlier: 3.874A pdb=" N GLU M 900 " --> pdb=" O SER M 896 " (cutoff:3.500A) Processing helix chain 'M' and resid 907 through 922 Processing helix chain 'M' and resid 922 through 931 Processing helix chain 'M' and resid 933 through 940 removed outlier: 3.868A pdb=" N LEU M 940 " --> pdb=" O ASP M 936 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 Processing helix chain 'M' and resid 972 through 979 Processing helix chain 'M' and resid 981 through 989 removed outlier: 4.075A pdb=" N ALA M 984 " --> pdb=" O TYR M 981 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 986 " --> pdb=" O GLN M 983 " (cutoff:3.500A) Processing helix chain 'M' and resid 993 through 1008 Processing helix chain 'M' and resid 1015 through 1021 Processing helix chain 'M' and resid 1024 through 1033 removed outlier: 4.549A pdb=" N GLY M1033 " --> pdb=" O MET M1029 " (cutoff:3.500A) Processing helix chain 'M' and resid 1051 through 1056 removed outlier: 3.514A pdb=" N GLY M1055 " --> pdb=" O VAL M1052 " (cutoff:3.500A) Processing helix chain 'M' and resid 1059 through 1061 No H-bonds generated for 'chain 'M' and resid 1059 through 1061' Processing helix chain 'M' and resid 1062 through 1074 removed outlier: 3.618A pdb=" N LEU M1074 " --> pdb=" O ALA M1070 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1095 Processing helix chain 'M' and resid 1103 through 1112 Processing helix chain 'M' and resid 1119 through 1132 removed outlier: 3.537A pdb=" N CYS M1132 " --> pdb=" O ALA M1128 " (cutoff:3.500A) Processing helix chain 'M' and resid 1145 through 1154 Processing helix chain 'M' and resid 1241 through 1246 Processing helix chain 'M' and resid 1252 through 1256 removed outlier: 4.444A pdb=" N GLU M1255 " --> pdb=" O ARG M1252 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 Processing helix chain 'R' and resid 11 through 40 removed outlier: 3.831A pdb=" N UNK R 16 " --> pdb=" O UNK R 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 36 removed outlier: 3.539A pdb=" N VAL S 30 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 54 removed outlier: 4.154A pdb=" N TRP S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 67 removed outlier: 3.968A pdb=" N LEU S 64 " --> pdb=" O PHE S 60 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU S 65 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA S 66 " --> pdb=" O LYS S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 99 removed outlier: 4.570A pdb=" N VAL S 94 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG S 98 " --> pdb=" O VAL S 94 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS S 99 " --> pdb=" O GLN S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 124 removed outlier: 5.281A pdb=" N GLN S 112 " --> pdb=" O ASP S 108 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE S 123 " --> pdb=" O MET S 119 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE S 124 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 140 removed outlier: 3.585A pdb=" N LEU S 139 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU S 140 " --> pdb=" O CYS S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 159 Processing helix chain 'S' and resid 163 through 176 removed outlier: 4.177A pdb=" N LYS S 169 " --> pdb=" O ALA S 165 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE S 172 " --> pdb=" O GLY S 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 193 removed outlier: 3.822A pdb=" N TYR S 185 " --> pdb=" O GLY S 181 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS S 188 " --> pdb=" O ALA S 184 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU S 190 " --> pdb=" O TYR S 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG S 191 " --> pdb=" O LYS S 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR S 192 " --> pdb=" O LYS S 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 210 removed outlier: 3.894A pdb=" N GLY S 203 " --> pdb=" O GLU S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 228 Processing helix chain 'S' and resid 231 through 242 removed outlier: 4.609A pdb=" N LEU S 235 " --> pdb=" O CYS S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 255 removed outlier: 3.854A pdb=" N ASN S 253 " --> pdb=" O ASP S 249 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 265 Processing helix chain 'S' and resid 268 through 282 Processing helix chain 'S' and resid 286 through 298 removed outlier: 4.349A pdb=" N LEU S 293 " --> pdb=" O GLN S 289 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS S 294 " --> pdb=" O HIS S 290 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 319 Processing helix chain 'S' and resid 321 through 336 removed outlier: 3.563A pdb=" N GLN S 327 " --> pdb=" O ASP S 323 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA S 336 " --> pdb=" O ALA S 332 " (cutoff:3.500A) Processing helix chain 'S' and resid 341 through 353 removed outlier: 3.543A pdb=" N ILE S 352 " --> pdb=" O GLY S 348 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR S 353 " --> pdb=" O GLN S 349 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 371 removed outlier: 3.880A pdb=" N ALA S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN S 362 " --> pdb=" O GLU S 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS S 366 " --> pdb=" O GLN S 362 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL S 367 " --> pdb=" O CYS S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 374 through 383 removed outlier: 3.965A pdb=" N MET S 378 " --> pdb=" O ASN S 374 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS S 379 " --> pdb=" O TYR S 375 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE S 380 " --> pdb=" O GLU S 376 " (cutoff:3.500A) Processing helix chain 'S' and resid 390 through 405 removed outlier: 4.796A pdb=" N ILE S 396 " --> pdb=" O GLU S 392 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA S 397 " --> pdb=" O LYS S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 413 through 423 removed outlier: 3.942A pdb=" N ILE S 421 " --> pdb=" O GLU S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 426 through 444 removed outlier: 3.875A pdb=" N ALA S 430 " --> pdb=" O ASP S 426 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU S 441 " --> pdb=" O ALA S 437 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN S 442 " --> pdb=" O THR S 438 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU S 443 " --> pdb=" O ARG S 439 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS S 444 " --> pdb=" O ILE S 440 " (cutoff:3.500A) Processing helix chain 'S' and resid 450 through 464 removed outlier: 3.634A pdb=" N LEU S 454 " --> pdb=" O PRO S 450 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG S 463 " --> pdb=" O ALA S 459 " (cutoff:3.500A) Processing helix chain 'S' and resid 466 through 484 Processing helix chain 'S' and resid 491 through 510 Processing helix chain 'S' and resid 512 through 527 Processing helix chain 'S' and resid 531 through 545 removed outlier: 3.737A pdb=" N GLY S 538 " --> pdb=" O TYR S 534 " (cutoff:3.500A) Processing helix chain 'S' and resid 549 through 561 Processing helix chain 'S' and resid 564 through 576 removed outlier: 3.647A pdb=" N GLY S 572 " --> pdb=" O TRP S 568 " (cutoff:3.500A) Processing helix chain 'S' and resid 584 through 589 removed outlier: 3.707A pdb=" N PHE S 588 " --> pdb=" O GLY S 584 " (cutoff:3.500A) Processing helix chain 'S' and resid 600 through 613 Processing helix chain 'S' and resid 623 through 643 Processing helix chain 'S' and resid 646 through 660 removed outlier: 4.223A pdb=" N ALA S 650 " --> pdb=" O ASN S 646 " (cutoff:3.500A) Processing helix chain 'S' and resid 666 through 677 removed outlier: 3.666A pdb=" N VAL S 673 " --> pdb=" O VAL S 669 " (cutoff:3.500A) Processing helix chain 'S' and resid 680 through 694 removed outlier: 3.933A pdb=" N TRP S 684 " --> pdb=" O ILE S 680 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU S 685 " --> pdb=" O SER S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 696 through 708 removed outlier: 5.522A pdb=" N GLN S 702 " --> pdb=" O ILE S 698 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N MET S 703 " --> pdb=" O SER S 699 " (cutoff:3.500A) Processing helix chain 'S' and resid 716 through 724 removed outlier: 3.808A pdb=" N VAL S 720 " --> pdb=" O ASN S 716 " (cutoff:3.500A) Processing helix chain 'S' and resid 733 through 747 removed outlier: 3.665A pdb=" N VAL S 746 " --> pdb=" O LYS S 742 " (cutoff:3.500A) Processing helix chain 'S' and resid 750 through 767 Processing helix chain 'S' and resid 775 through 799 removed outlier: 3.507A pdb=" N VAL S 779 " --> pdb=" O ASN S 775 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS S 784 " --> pdb=" O LEU S 780 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL S 799 " --> pdb=" O TYR S 795 " (cutoff:3.500A) Processing helix chain 'S' and resid 809 through 892 removed outlier: 3.588A pdb=" N GLU S 813 " --> pdb=" O LEU S 809 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA S 829 " --> pdb=" O GLN S 825 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG S 830 " --> pdb=" O TYR S 826 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU S 848 " --> pdb=" O LYS S 844 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU S 883 " --> pdb=" O ALA S 879 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS S 886 " --> pdb=" O VAL S 882 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN S 887 " --> pdb=" O GLU S 883 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR S 892 " --> pdb=" O ILE S 888 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 383 removed outlier: 3.515A pdb=" N SER U 383 " --> pdb=" O ASN U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 408 through 413 removed outlier: 3.603A pdb=" N LEU U 412 " --> pdb=" O GLY U 408 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS U 413 " --> pdb=" O ARG U 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 408 through 413' Processing helix chain 'V' and resid 73 through 79 removed outlier: 3.759A pdb=" N GLN V 79 " --> pdb=" O SER V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 118 Processing helix chain 'V' and resid 182 through 196 removed outlier: 4.067A pdb=" N THR V 187 " --> pdb=" O ASP V 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR V 192 " --> pdb=" O ALA V 188 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE V 193 " --> pdb=" O ILE V 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 228 removed outlier: 4.064A pdb=" N ARG Z 227 " --> pdb=" O ASP Z 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 239 removed outlier: 3.763A pdb=" N LEU Z 238 " --> pdb=" O ARG Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 260 Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.963A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 500 through 507 Processing helix chain 'b' and resid 508 through 525 Processing helix chain 'b' and resid 537 through 553 removed outlier: 3.820A pdb=" N GLN b 541 " --> pdb=" O GLY b 537 " (cutoff:3.500A) Processing helix chain 'b' and resid 574 through 576 No H-bonds generated for 'chain 'b' and resid 574 through 576' Processing helix chain 'b' and resid 577 through 589 Processing helix chain 'b' and resid 606 through 618 removed outlier: 3.803A pdb=" N LEU b 610 " --> pdb=" O LYS b 606 " (cutoff:3.500A) Processing helix chain 'b' and resid 624 through 631 Processing helix chain 'b' and resid 631 through 636 Processing helix chain 'b' and resid 648 through 653 removed outlier: 4.437A pdb=" N ASN b 653 " --> pdb=" O LYS b 650 " (cutoff:3.500A) Processing helix chain 'b' and resid 656 through 663 Processing helix chain 'b' and resid 681 through 693 removed outlier: 3.914A pdb=" N LEU b 685 " --> pdb=" O ASN b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 707 Processing helix chain 'b' and resid 707 through 714 Processing helix chain 'b' and resid 720 through 739 Processing helix chain 'b' and resid 769 through 782 Processing helix chain 'b' and resid 782 through 790 Processing helix chain 'b' and resid 794 through 808 removed outlier: 4.430A pdb=" N GLY b 798 " --> pdb=" O GLN b 794 " (cutoff:3.500A) Processing helix chain 'b' and resid 834 through 837 Processing helix chain 'b' and resid 838 through 854 Processing helix chain 'b' and resid 865 through 878 Processing helix chain 'b' and resid 893 through 904 Processing helix chain 'b' and resid 914 through 918 Processing helix chain 'b' and resid 937 through 946 removed outlier: 3.953A pdb=" N ASP b 941 " --> pdb=" O ASN b 937 " (cutoff:3.500A) Processing helix chain 'b' and resid 967 through 988 removed outlier: 3.619A pdb=" N LYS b 971 " --> pdb=" O THR b 967 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL b 986 " --> pdb=" O LEU b 982 " (cutoff:3.500A) Processing helix chain 'b' and resid 1387 through 1399 removed outlier: 3.737A pdb=" N LEU b1399 " --> pdb=" O ALA b1395 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 14 removed outlier: 3.514A pdb=" N THR c 14 " --> pdb=" O GLU c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 35 Processing helix chain 'c' and resid 36 through 51 removed outlier: 3.533A pdb=" N SER c 40 " --> pdb=" O GLU c 36 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG c 44 " --> pdb=" O SER c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 71 Processing helix chain 'c' and resid 75 through 80 Processing helix chain 'c' and resid 83 through 94 removed outlier: 3.702A pdb=" N ASP c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 124 removed outlier: 4.129A pdb=" N GLU c 122 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 141 Processing helix chain 'd' and resid 250 through 254 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.017A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 986 through 990 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1075 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1097 through 1099 No H-bonds generated for 'chain 'd' and resid 1097 through 1099' Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1138 removed outlier: 3.790A pdb=" N LEU d1129 " --> pdb=" O THR d1125 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 74 removed outlier: 3.691A pdb=" N GLN e 60 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR e 62 " --> pdb=" O TYR e 58 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP e 63 " --> pdb=" O THR e 59 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 75 through 77 No H-bonds generated for 'chain 'e' and resid 75 through 77' Processing helix chain 'e' and resid 83 through 93 Processing helix chain 'e' and resid 98 through 117 Processing helix chain 'e' and resid 118 through 122 removed outlier: 3.560A pdb=" N ARG e 122 " --> pdb=" O LEU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 153 through 158 removed outlier: 3.626A pdb=" N ASP e 157 " --> pdb=" O PHE e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 182 Processing helix chain 'e' and resid 186 through 204 removed outlier: 3.987A pdb=" N SER e 190 " --> pdb=" O LYS e 186 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 224 Processing helix chain 'e' and resid 231 through 254 removed outlier: 3.829A pdb=" N PHE e 235 " --> pdb=" O PHE e 231 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 277 removed outlier: 3.666A pdb=" N GLY e 271 " --> pdb=" O LEU e 267 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP e 272 " --> pdb=" O GLU e 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG e 273 " --> pdb=" O GLU e 269 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 295 removed outlier: 3.859A pdb=" N LYS e 284 " --> pdb=" O HIS e 280 " (cutoff:3.500A) Proline residue: e 285 - end of helix Processing helix chain 'e' and resid 304 through 313 removed outlier: 3.675A pdb=" N LEU e 310 " --> pdb=" O GLY e 306 " (cutoff:3.500A) Processing helix chain 'e' and resid 315 through 326 Processing helix chain 'e' and resid 331 through 353 removed outlier: 3.858A pdb=" N ALA e 335 " --> pdb=" O GLY e 331 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE e 351 " --> pdb=" O PHE e 347 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE e 353 " --> pdb=" O THR e 349 " (cutoff:3.500A) Processing helix chain 'e' and resid 361 through 378 Processing helix chain 'e' and resid 384 through 399 Processing helix chain 'e' and resid 404 through 417 Processing helix chain 'e' and resid 425 through 441 removed outlier: 3.711A pdb=" N LEU e 429 " --> pdb=" O THR e 425 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 462 removed outlier: 3.837A pdb=" N PHE e 449 " --> pdb=" O GLY e 445 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 481 removed outlier: 3.697A pdb=" N HIS e 481 " --> pdb=" O SER e 477 " (cutoff:3.500A) Processing helix chain 'e' and resid 489 through 512 Processing helix chain 'e' and resid 544 through 560 removed outlier: 4.208A pdb=" N GLY e 560 " --> pdb=" O ALA e 556 " (cutoff:3.500A) Processing helix chain 'e' and resid 593 through 605 removed outlier: 3.904A pdb=" N VAL e 598 " --> pdb=" O PHE e 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN e 603 " --> pdb=" O LEU e 599 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU e 604 " --> pdb=" O LEU e 600 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY e 605 " --> pdb=" O MET e 601 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 616 Processing helix chain 'e' and resid 620 through 628 removed outlier: 3.836A pdb=" N ARG e 626 " --> pdb=" O SER e 622 " (cutoff:3.500A) Processing helix chain 'e' and resid 671 through 675 Processing helix chain 'e' and resid 677 through 690 removed outlier: 4.111A pdb=" N VAL e 688 " --> pdb=" O THR e 684 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN e 690 " --> pdb=" O GLU e 686 " (cutoff:3.500A) Processing helix chain 'e' and resid 691 through 707 removed outlier: 4.189A pdb=" N GLN e 695 " --> pdb=" O ASP e 691 " (cutoff:3.500A) Processing helix chain 'e' and resid 711 through 723 removed outlier: 4.172A pdb=" N SER e 717 " --> pdb=" O ASN e 713 " (cutoff:3.500A) Processing helix chain 'e' and resid 728 through 742 Processing helix chain 'e' and resid 749 through 751 No H-bonds generated for 'chain 'e' and resid 749 through 751' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.520A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.850A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.390A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.716A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 6.063A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.994A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.774A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.148A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.148A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.709A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB9, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.812A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.519A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.586A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A1177 " --> pdb=" O PRO A1209 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC4, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 8.315A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.550A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.659A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC8, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.726A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AD1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.654A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.538A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.692A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.692A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.366A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE3, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.903A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AE5, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE6, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.632A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.967A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE9, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.091A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF2, first strand: chain 'G' and resid 149 through 153 removed outlier: 6.807A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF4, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AF5, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.623A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 640 through 644 removed outlier: 5.303A pdb=" N LYS M 641 " --> pdb=" O ILE M 618 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE M 618 " --> pdb=" O LYS M 641 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 805 through 811 removed outlier: 3.641A pdb=" N ASP M 807 " --> pdb=" O LEU M 798 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE M 795 " --> pdb=" O ALA M 785 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 1262 through 1266 removed outlier: 3.898A pdb=" N VAL M1228 " --> pdb=" O ILE M1240 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE M1240 " --> pdb=" O VAL M1228 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR M1237 " --> pdb=" O ALA M1277 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 5 through 8 removed outlier: 4.220A pdb=" N ILE S 6 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU S 19 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE S 17 " --> pdb=" O ILE S 8 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.685A pdb=" N VAL U 376 " --> pdb=" O ILE V 314 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE V 314 " --> pdb=" O VAL U 376 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE V 315 " --> pdb=" O LEU V 326 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 456 through 459 removed outlier: 3.782A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE U 440 " --> pdb=" O VAL V 214 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL V 214 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS U 442 " --> pdb=" O VAL V 212 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 461 through 463 Processing sheet with id=AG5, first strand: chain 'U' and resid 472 through 475 removed outlier: 3.559A pdb=" N ILE U 473 " --> pdb=" O VAL U 484 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN U 475 " --> pdb=" O GLN U 482 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 231 through 232 Processing sheet with id=AG7, first strand: chain 'V' and resid 260 through 261 removed outlier: 4.267A pdb=" N GLN V 260 " --> pdb=" O VAL V 271 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 9 through 11 Processing sheet with id=AG9, first strand: chain 'Y' and resid 19 through 24 removed outlier: 5.805A pdb=" N VAL Y 44 " --> pdb=" O SER Y 59 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER Y 59 " --> pdb=" O VAL Y 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL Y 46 " --> pdb=" O GLN Y 57 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 67 through 72 removed outlier: 5.214A pdb=" N SER Y 83 " --> pdb=" O HIS Y 87 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N HIS Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP Y 92 " --> pdb=" O GLN Y 98 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN Y 98 " --> pdb=" O ASP Y 92 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 112 through 114 removed outlier: 3.504A pdb=" N ALA Y 113 " --> pdb=" O ALA Y 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA Y 122 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR Y 142 " --> pdb=" O ILE Y 132 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY Y 134 " --> pdb=" O LYS Y 140 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS Y 140 " --> pdb=" O GLY Y 134 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 151 through 156 removed outlier: 5.781A pdb=" N ILE Y 172 " --> pdb=" O THR Y 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR Y 185 " --> pdb=" O ILE Y 172 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE Y 174 " --> pdb=" O LEU Y 183 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 195 through 198 removed outlier: 4.076A pdb=" N SER Y 195 " --> pdb=" O ALA Y 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR Y 197 " --> pdb=" O VAL Y 206 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS Y 215 " --> pdb=" O THR Y 207 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP Y 218 " --> pdb=" O LEU Y 224 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU Y 224 " --> pdb=" O ASP Y 218 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 235 through 240 removed outlier: 6.273A pdb=" N SER Y 250 " --> pdb=" O LEU Y 236 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Y 238 " --> pdb=" O VAL Y 248 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL Y 248 " --> pdb=" O VAL Y 238 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE Y 240 " --> pdb=" O HIS Y 246 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS Y 246 " --> pdb=" O PHE Y 240 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP Y 260 " --> pdb=" O CYS Y 266 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS Y 266 " --> pdb=" O ASP Y 260 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 277 through 282 removed outlier: 4.196A pdb=" N GLY Y 279 " --> pdb=" O VAL Y 292 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 30 through 32 Processing sheet with id=AH8, first strand: chain 'a' and resid 37 through 38 removed outlier: 7.252A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.565A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE a 68 " --> pdb=" O ILE a 90 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 102 through 107 removed outlier: 6.650A pdb=" N SER a 118 " --> pdb=" O GLU a 103 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL a 105 " --> pdb=" O THR a 116 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR a 116 " --> pdb=" O VAL a 105 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP a 107 " --> pdb=" O MET a 114 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET a 114 " --> pdb=" O TRP a 107 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN a 133 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 144 through 149 removed outlier: 4.136A pdb=" N HIS a 180 " --> pdb=" O LEU a 170 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP a 172 " --> pdb=" O CYS a 178 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N CYS a 178 " --> pdb=" O ASP a 172 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 189 through 194 Processing sheet with id=AI4, first strand: chain 'a' and resid 250 through 253 removed outlier: 3.640A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'a' and resid 298 through 299 removed outlier: 3.589A pdb=" N THR a 298 " --> pdb=" O PHE a 309 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN a 326 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 491 through 492 Processing sheet with id=AI7, first strand: chain 'b' and resid 528 through 530 removed outlier: 3.759A pdb=" N ILE b 671 " --> pdb=" O VAL b 643 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL b 570 " --> pdb=" O ILE b 644 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASP b 646 " --> pdb=" O VAL b 570 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL b 572 " --> pdb=" O ASP b 646 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR b 569 " --> pdb=" O LEU b 621 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR b 623 " --> pdb=" O THR b 569 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE b 571 " --> pdb=" O THR b 623 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'b' and resid 759 through 766 Processing sheet with id=AI9, first strand: chain 'd' and resid 1004 through 1009 removed outlier: 6.717A pdb=" N GLY d1031 " --> pdb=" O ASN d1005 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE d1007 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU d1029 " --> pdb=" O PHE d1007 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N HIS d1009 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER d1027 " --> pdb=" O HIS d1009 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY d1026 " --> pdb=" O SER d1042 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER d1042 " --> pdb=" O GLY d1026 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU d1039 " --> pdb=" O THR d 8 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR d 8 " --> pdb=" O LEU d1039 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR d1041 " --> pdb=" O VAL d 6 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL d 6 " --> pdb=" O THR d1041 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU d1043 " --> pdb=" O ASN d 4 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN d 4 " --> pdb=" O LEU d1043 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 15 through 21 removed outlier: 6.088A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 61 through 67 removed outlier: 3.856A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 121 through 124 Processing sheet with id=AJ4, first strand: chain 'd' and resid 164 through 169 removed outlier: 5.937A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP d 166 " --> pdb=" O VAL d 181 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'd' and resid 164 through 169 removed outlier: 5.937A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP d 166 " --> pdb=" O VAL d 181 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'd' and resid 218 through 221 Processing sheet with id=AJ7, first strand: chain 'd' and resid 258 through 263 removed outlier: 6.715A pdb=" N GLY d 274 " --> pdb=" O VAL d 259 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS d 261 " --> pdb=" O LEU d 272 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU d 272 " --> pdb=" O HIS d 261 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG d 263 " --> pdb=" O ARG d 270 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG d 270 " --> pdb=" O ARG d 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'd' and resid 313 through 318 removed outlier: 6.630A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 361 through 364 removed outlier: 3.954A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'd' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'd' and resid 457 through 463 removed outlier: 3.707A pdb=" N TRP d 490 " --> pdb=" O VAL d 476 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER d 480 " --> pdb=" O LEU d 486 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU d 486 " --> pdb=" O SER d 480 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'd' and resid 507 through 512 removed outlier: 6.650A pdb=" N LEU d 516 " --> pdb=" O HIS d 531 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS d 531 " --> pdb=" O LEU d 516 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR d 518 " --> pdb=" O ILE d 529 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.213A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'd' and resid 590 through 595 removed outlier: 4.384A pdb=" N SER d 590 " --> pdb=" O ALA d 605 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS d 627 " --> pdb=" O TYR d 613 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'd' and resid 638 through 642 removed outlier: 8.537A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'd' and resid 679 through 682 Processing sheet with id=AK8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.343A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.290A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.290A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'd' and resid 872 through 876 removed outlier: 4.078A pdb=" N SER d 872 " --> pdb=" O SER d 883 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL d 888 " --> pdb=" O ASN d 904 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN d 904 " --> pdb=" O VAL d 888 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'd' and resid 911 through 917 removed outlier: 3.539A pdb=" N PHE d 920 " --> pdb=" O LYS d 917 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'd' and resid 954 through 959 removed outlier: 6.883A pdb=" N ALA d 968 " --> pdb=" O SER d 955 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL d 957 " --> pdb=" O LEU d 966 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE d 959 " --> pdb=" O ASN d 964 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN d 964 " --> pdb=" O ILE d 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'd' and resid 1076 through 1078 Processing sheet with id=AL6, first strand: chain 'e' and resid 525 through 526 Processing sheet with id=AL7, first strand: chain 'e' and resid 566 through 568 removed outlier: 4.087A pdb=" N LYS e 566 " --> pdb=" O ALA f 34 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA f 34 " --> pdb=" O LYS e 566 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN e 568 " --> pdb=" O LEU f 32 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU f 32 " --> pdb=" O GLN e 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'e' and resid 575 through 580 removed outlier: 3.920A pdb=" N LYS e 587 " --> pdb=" O ALA e 580 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'e' and resid 746 through 748 removed outlier: 4.074A pdb=" N GLN e 754 " --> pdb=" O ASP e 748 " (cutoff:3.500A) 3322 hydrogen bonds defined for protein. 9378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 34.84 Time building geometry restraints manager: 22.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 11554 1.27 - 1.41: 16605 1.41 - 1.55: 36560 1.55 - 1.69: 253 1.69 - 1.83: 470 Bond restraints: 65442 Sorted by residual: bond pdb=" CB ARG a 19 " pdb=" CG ARG a 19 " ideal model delta sigma weight residual 1.520 1.269 0.251 3.00e-02 1.11e+03 7.02e+01 bond pdb=" CA ASP a 215 " pdb=" CB ASP a 215 " ideal model delta sigma weight residual 1.525 1.421 0.104 1.29e-02 6.01e+03 6.51e+01 bond pdb=" CA TYR a 312 " pdb=" CB TYR a 312 " ideal model delta sigma weight residual 1.531 1.280 0.250 3.12e-02 1.03e+03 6.43e+01 bond pdb=" CB GLN M 912 " pdb=" CG GLN M 912 " ideal model delta sigma weight residual 1.520 1.283 0.237 3.00e-02 1.11e+03 6.24e+01 bond pdb=" P A P 50 " pdb=" OP1 A P 50 " ideal model delta sigma weight residual 1.485 1.337 0.148 2.00e-02 2.50e+03 5.51e+01 ... (remaining 65437 not shown) Histogram of bond angle deviations from ideal: 91.38 - 100.56: 97 100.56 - 109.75: 10436 109.75 - 118.93: 40639 118.93 - 128.12: 35869 128.12 - 137.30: 658 Bond angle restraints: 87699 Sorted by residual: angle pdb=" N SER e 128 " pdb=" CA SER e 128 " pdb=" C SER e 128 " ideal model delta sigma weight residual 114.39 103.27 11.12 1.45e+00 4.76e-01 5.88e+01 angle pdb=" N GLN M 724 " pdb=" CA GLN M 724 " pdb=" CB GLN M 724 " ideal model delta sigma weight residual 110.28 120.06 -9.78 1.55e+00 4.16e-01 3.98e+01 angle pdb=" NE ARG M1014 " pdb=" CZ ARG M1014 " pdb=" NH2 ARG M1014 " ideal model delta sigma weight residual 119.20 113.71 5.49 9.00e-01 1.23e+00 3.72e+01 angle pdb=" C GLU S 772 " pdb=" N LYS S 773 " pdb=" CA LYS S 773 " ideal model delta sigma weight residual 121.70 132.33 -10.63 1.80e+00 3.09e-01 3.49e+01 angle pdb=" N SER d 929 " pdb=" CA SER d 929 " pdb=" C SER d 929 " ideal model delta sigma weight residual 110.80 122.94 -12.14 2.13e+00 2.20e-01 3.25e+01 ... (remaining 87694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 34851 35.68 - 71.36: 733 71.36 - 107.04: 48 107.04 - 142.73: 1 142.73 - 178.41: 4 Dihedral angle restraints: 35637 sinusoidal: 14348 harmonic: 21289 Sorted by residual: dihedral pdb=" CA UNK R 11 " pdb=" C UNK R 11 " pdb=" N UNK R 12 " pdb=" CA UNK R 12 " ideal model delta harmonic sigma weight residual -180.00 -141.98 -38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA LYS d 35 " pdb=" C LYS d 35 " pdb=" N ASN d 36 " pdb=" CA ASN d 36 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA CYS M 575 " pdb=" C CYS M 575 " pdb=" N SER M 576 " pdb=" CA SER M 576 " ideal model delta harmonic sigma weight residual -180.00 -145.52 -34.48 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 35634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 7246 0.116 - 0.232: 818 0.232 - 0.349: 152 0.349 - 0.465: 34 0.465 - 0.581: 6 Chirality restraints: 8256 Sorted by residual: chirality pdb=" CB VAL a 105 " pdb=" CA VAL a 105 " pdb=" CG1 VAL a 105 " pdb=" CG2 VAL a 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CG LEU a 251 " pdb=" CB LEU a 251 " pdb=" CD1 LEU a 251 " pdb=" CD2 LEU a 251 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" C3' DT T 23 " pdb=" C4' DT T 23 " pdb=" O3' DT T 23 " pdb=" C2' DT T 23 " both_signs ideal model delta sigma weight residual False -2.66 -2.16 -0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 8253 not shown) Planarity restraints: 11940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 876 " 0.146 9.50e-02 1.11e+02 8.87e-02 4.74e+01 pdb=" NE ARG b 876 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG b 876 " 0.114 2.00e-02 2.50e+03 pdb=" NH1 ARG b 876 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG b 876 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 882 " 0.045 2.00e-02 2.50e+03 4.12e-02 3.39e+01 pdb=" CG TYR b 882 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TYR b 882 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR b 882 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR b 882 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR b 882 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR b 882 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR b 882 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 30 " -0.002 2.00e-02 2.50e+03 3.15e-02 2.97e+01 pdb=" N9 DG T 30 " -0.053 2.00e-02 2.50e+03 pdb=" C8 DG T 30 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG T 30 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG T 30 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG T 30 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG T 30 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG T 30 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG T 30 " -0.037 2.00e-02 2.50e+03 pdb=" N2 DG T 30 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DG T 30 " 0.084 2.00e-02 2.50e+03 pdb=" C4 DG T 30 " 0.015 2.00e-02 2.50e+03 ... (remaining 11937 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 264 2.44 - 3.05: 43956 3.05 - 3.67: 96410 3.67 - 4.28: 147149 4.28 - 4.90: 240250 Nonbonded interactions: 528029 Sorted by model distance: nonbonded pdb=" OD1 ASN d 392 " pdb=" CD2 LEU d 710 " model vdw 1.819 3.460 nonbonded pdb=" OE1 GLU M 926 " pdb=" OH TYR M 981 " model vdw 1.898 2.440 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.918 2.170 nonbonded pdb=" NH2 ARG b 975 " pdb=" OD1 ASP b1000 " model vdw 1.919 2.520 nonbonded pdb=" OG SER A 338 " pdb=" OE1 GLN A 341 " model vdw 1.920 2.440 ... (remaining 528024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.050 Extract box with map and model: 16.710 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 163.590 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.019 0.289 65442 Z= 1.280 Angle : 1.060 16.622 87699 Z= 0.605 Chirality : 0.083 0.581 8256 Planarity : 0.007 0.105 11940 Dihedral : 14.506 178.407 23657 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.05 (0.08), residues: 8992 helix: -0.81 (0.08), residues: 3390 sheet: -1.53 (0.13), residues: 1481 loop : -1.68 (0.09), residues: 4121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP M 752 HIS 0.025 0.003 HIS D 93 PHE 0.064 0.004 PHE M 686 TYR 0.100 0.004 TYR b 882 ARG 0.116 0.002 ARG b 876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1435 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 1437 average time/residue: 1.5132 time to fit residues: 2766.3803 Evaluate side-chains 1077 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1074 time to evaluate : 5.360 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.5639 time to fit residues: 8.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 772 optimal weight: 20.0000 chunk 693 optimal weight: 7.9990 chunk 384 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 467 optimal weight: 50.0000 chunk 370 optimal weight: 1.9990 chunk 717 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 436 optimal weight: 3.9990 chunk 533 optimal weight: 5.9990 chunk 830 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 439 HIS A 441 GLN A 531 ASN A 723 ASN A 764 ASN A 926 ASN A1077 ASN A1078 GLN A1129 ASN A1420 ASN A1422 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN B 552 ASN B 593 GLN B 654 GLN B 683 GLN B 749 HIS B 941 GLN B 948 GLN B1003 ASN B1049 GLN C 108 ASN D 47 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN E 65 ASN E 95 GLN E 129 GLN G 4 HIS I 22 ASN K 2 ASN K 55 GLN K 113 GLN M 405 GLN M 421 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 718 GLN M 719 GLN M 929 GLN M1008 ASN M1264 HIS a 110 HIS d 36 ASN ** d 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1034 ASN ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 65442 Z= 0.335 Angle : 0.634 12.247 87699 Z= 0.336 Chirality : 0.047 0.209 8256 Planarity : 0.005 0.063 11940 Dihedral : 11.452 177.471 10888 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.72 % Allowed : 12.68 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.92 (0.09), residues: 8992 helix: 0.46 (0.09), residues: 3473 sheet: -1.14 (0.13), residues: 1481 loop : -1.29 (0.09), residues: 4038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 27 HIS 0.012 0.001 HIS M 869 PHE 0.028 0.002 PHE C 63 TYR 0.035 0.002 TYR B 916 ARG 0.012 0.001 ARG b 876 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1172 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 48 residues processed: 1240 average time/residue: 1.4540 time to fit residues: 2329.5940 Evaluate side-chains 1094 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1046 time to evaluate : 5.420 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 26 residues processed: 23 average time/residue: 0.7309 time to fit residues: 33.6675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 461 optimal weight: 20.0000 chunk 257 optimal weight: 0.5980 chunk 691 optimal weight: 5.9990 chunk 565 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 832 optimal weight: 3.9990 chunk 899 optimal weight: 9.9990 chunk 741 optimal weight: 4.9990 chunk 825 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 667 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 439 HIS A 441 GLN A 459 ASN A 531 ASN A 723 ASN A 926 ASN A1078 GLN A1129 ASN A1299 GLN B 144 HIS B 145 GLN B 552 ASN B 582 GLN B 593 GLN B 825 GLN B 948 GLN B1003 ASN B1145 GLN C 108 ASN C 260 GLN D 66 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN F 48 ASN I 22 ASN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 718 GLN M 895 ASN M 929 GLN M 987 GLN ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 187 GLN a 326 GLN a 343 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 65442 Z= 0.490 Angle : 0.659 11.458 87699 Z= 0.344 Chirality : 0.050 0.227 8256 Planarity : 0.005 0.074 11940 Dihedral : 11.343 178.979 10888 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.48 % Favored : 95.51 % Rotamer: Outliers : 3.77 % Allowed : 16.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.47 (0.09), residues: 8992 helix: 1.00 (0.09), residues: 3463 sheet: -0.94 (0.13), residues: 1494 loop : -1.19 (0.09), residues: 4035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.008 0.002 HIS A 465 PHE 0.026 0.002 PHE G 158 TYR 0.043 0.002 TYR B 916 ARG 0.013 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1094 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 81 residues processed: 1196 average time/residue: 1.4315 time to fit residues: 2206.9118 Evaluate side-chains 1106 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1025 time to evaluate : 5.353 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 53 residues processed: 29 average time/residue: 0.8906 time to fit residues: 44.9230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 822 optimal weight: 3.9990 chunk 625 optimal weight: 50.0000 chunk 432 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 397 optimal weight: 0.9980 chunk 558 optimal weight: 50.0000 chunk 835 optimal weight: 6.9990 chunk 884 optimal weight: 50.0000 chunk 436 optimal weight: 3.9990 chunk 791 optimal weight: 9.9990 chunk 238 optimal weight: 0.5980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS A 441 GLN A 723 ASN A 926 ASN A1129 ASN B 552 ASN B 582 GLN B 593 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 718 GLN M1264 HIS a 228 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 964 ASN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 65442 Z= 0.293 Angle : 0.568 12.530 87699 Z= 0.296 Chirality : 0.045 0.215 8256 Planarity : 0.004 0.058 11940 Dihedral : 11.200 178.971 10888 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.65 % Allowed : 18.50 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.09 (0.09), residues: 8992 helix: 1.40 (0.09), residues: 3471 sheet: -0.75 (0.13), residues: 1487 loop : -1.07 (0.10), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 851 HIS 0.007 0.001 HIS D 38 PHE 0.026 0.002 PHE G 158 TYR 0.038 0.002 TYR B 916 ARG 0.010 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1085 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 205 outliers final: 85 residues processed: 1201 average time/residue: 1.4316 time to fit residues: 2223.9985 Evaluate side-chains 1119 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1034 time to evaluate : 5.433 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 56 residues processed: 31 average time/residue: 0.8926 time to fit residues: 48.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 736 optimal weight: 2.9990 chunk 502 optimal weight: 30.0000 chunk 12 optimal weight: 0.0870 chunk 658 optimal weight: 1.9990 chunk 364 optimal weight: 2.9990 chunk 754 optimal weight: 6.9990 chunk 611 optimal weight: 50.0000 chunk 1 optimal weight: 0.4980 chunk 451 optimal weight: 5.9990 chunk 793 optimal weight: 50.0000 chunk 223 optimal weight: 0.0970 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 441 GLN A 723 ASN A 757 GLN A 780 ASN A 926 ASN A1129 ASN A1384 HIS B 582 GLN B 593 GLN B1003 ASN D 34 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN G 24 ASN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 718 GLN M1234 ASN M1264 HIS a 228 GLN d 372 GLN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 65442 Z= 0.257 Angle : 0.549 12.176 87699 Z= 0.285 Chirality : 0.044 0.213 8256 Planarity : 0.004 0.058 11940 Dihedral : 11.117 179.364 10888 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.05 % Favored : 95.94 % Rotamer: Outliers : 3.63 % Allowed : 19.37 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % 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: 0.12 (0.09), residues: 8992 helix: 1.64 (0.09), residues: 3481 sheet: -0.69 (0.13), residues: 1488 loop : -0.99 (0.10), residues: 4023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 851 HIS 0.007 0.001 HIS D 38 PHE 0.032 0.002 PHE B 320 TYR 0.044 0.001 TYR B 916 ARG 0.010 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1064 time to evaluate : 6.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 95 residues processed: 1177 average time/residue: 1.4694 time to fit residues: 2239.9845 Evaluate side-chains 1120 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1025 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 63 residues processed: 32 average time/residue: 0.9004 time to fit residues: 49.6791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 297 optimal weight: 0.9990 chunk 796 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 519 optimal weight: 20.0000 chunk 218 optimal weight: 0.9990 chunk 885 optimal weight: 30.0000 chunk 734 optimal weight: 4.9990 chunk 409 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 464 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 372 ASN A 441 GLN A 723 ASN A 926 ASN A1129 ASN B 98 HIS B 582 GLN B 593 GLN B1003 ASN D 34 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 398 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 183 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN d 240 HIS ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 65442 Z= 0.330 Angle : 0.576 11.968 87699 Z= 0.299 Chirality : 0.046 0.253 8256 Planarity : 0.004 0.060 11940 Dihedral : 11.099 179.573 10888 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.27 % Favored : 95.72 % Rotamer: Outliers : 3.57 % Allowed : 20.06 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.22 (0.09), residues: 8992 helix: 1.73 (0.09), residues: 3485 sheet: -0.63 (0.13), residues: 1508 loop : -0.96 (0.10), residues: 3999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 851 HIS 0.007 0.001 HIS D 38 PHE 0.028 0.002 PHE G 158 TYR 0.048 0.002 TYR B 916 ARG 0.012 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1047 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 108 residues processed: 1165 average time/residue: 1.4593 time to fit residues: 2198.4033 Evaluate side-chains 1133 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1025 time to evaluate : 5.483 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 73 residues processed: 36 average time/residue: 0.7312 time to fit residues: 48.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 853 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 504 optimal weight: 8.9990 chunk 646 optimal weight: 5.9990 chunk 500 optimal weight: 40.0000 chunk 745 optimal weight: 4.9990 chunk 494 optimal weight: 20.0000 chunk 881 optimal weight: 50.0000 chunk 551 optimal weight: 30.0000 chunk 537 optimal weight: 40.0000 chunk 407 optimal weight: 0.8980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS A 441 GLN A 757 GLN A 926 ASN A1129 ASN B 460 HIS B 537 GLN B 582 GLN B 593 GLN B 930 GLN B1003 ASN D 34 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 183 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN d 107 ASN d 261 HIS ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 65442 Z= 0.490 Angle : 0.647 12.793 87699 Z= 0.334 Chirality : 0.049 0.264 8256 Planarity : 0.004 0.080 11940 Dihedral : 11.160 179.296 10888 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.58 % Favored : 95.41 % Rotamer: Outliers : 3.31 % Allowed : 20.91 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.15 (0.09), residues: 8992 helix: 1.64 (0.09), residues: 3491 sheet: -0.64 (0.13), residues: 1515 loop : -0.98 (0.10), residues: 3986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 851 HIS 0.009 0.001 HIS a 180 PHE 0.028 0.002 PHE G 158 TYR 0.035 0.002 TYR B 916 ARG 0.012 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1047 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 106 residues processed: 1159 average time/residue: 1.5056 time to fit residues: 2254.7433 Evaluate side-chains 1127 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1021 time to evaluate : 5.491 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 79 residues processed: 29 average time/residue: 0.7805 time to fit residues: 42.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 545 optimal weight: 8.9990 chunk 352 optimal weight: 0.0770 chunk 526 optimal weight: 30.0000 chunk 265 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 560 optimal weight: 50.0000 chunk 600 optimal weight: 50.0000 chunk 436 optimal weight: 0.1980 chunk 82 optimal weight: 0.3980 chunk 693 optimal weight: 9.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 926 ASN A1129 ASN B 537 GLN B 582 GLN B 593 GLN ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 133 GLN G 60 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 183 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65442 Z= 0.207 Angle : 0.563 14.655 87699 Z= 0.290 Chirality : 0.044 0.224 8256 Planarity : 0.004 0.061 11940 Dihedral : 11.054 179.922 10888 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 2.72 % Allowed : 22.35 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.37 (0.09), residues: 8992 helix: 1.87 (0.09), residues: 3484 sheet: -0.54 (0.13), residues: 1503 loop : -0.90 (0.10), residues: 4005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP b 851 HIS 0.007 0.001 HIS B 144 PHE 0.030 0.001 PHE G 158 TYR 0.030 0.001 TYR B 916 ARG 0.014 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1069 time to evaluate : 5.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 86 residues processed: 1169 average time/residue: 1.4927 time to fit residues: 2260.3067 Evaluate side-chains 1113 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1027 time to evaluate : 5.441 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 68 residues processed: 18 average time/residue: 0.7425 time to fit residues: 28.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 802 optimal weight: 0.4980 chunk 844 optimal weight: 30.0000 chunk 770 optimal weight: 0.9980 chunk 821 optimal weight: 3.9990 chunk 494 optimal weight: 30.0000 chunk 358 optimal weight: 2.9990 chunk 645 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 742 optimal weight: 2.9990 chunk 777 optimal weight: 30.0000 chunk 818 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN A1129 ASN A1299 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 582 GLN B 593 GLN B 749 HIS D 34 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 47 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 133 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1145 ASN M1264 HIS a 79 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN ** d 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1056 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 65442 Z= 0.288 Angle : 0.587 12.984 87699 Z= 0.302 Chirality : 0.045 0.322 8256 Planarity : 0.004 0.060 11940 Dihedral : 11.050 179.831 10888 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 22.94 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.40 (0.09), residues: 8992 helix: 1.90 (0.09), residues: 3497 sheet: -0.48 (0.13), residues: 1500 loop : -0.90 (0.10), residues: 3995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 851 HIS 0.006 0.001 HIS a 180 PHE 0.028 0.002 PHE B 320 TYR 0.033 0.002 TYR B 916 ARG 0.015 0.001 ARG A1160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1033 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 89 residues processed: 1128 average time/residue: 1.4739 time to fit residues: 2153.8612 Evaluate side-chains 1105 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1016 time to evaluate : 5.378 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 71 residues processed: 18 average time/residue: 0.7981 time to fit residues: 29.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 539 optimal weight: 50.0000 chunk 869 optimal weight: 20.0000 chunk 530 optimal weight: 30.0000 chunk 412 optimal weight: 2.9990 chunk 604 optimal weight: 50.0000 chunk 911 optimal weight: 40.0000 chunk 839 optimal weight: 4.9990 chunk 725 optimal weight: 40.0000 chunk 75 optimal weight: 0.6980 chunk 560 optimal weight: 50.0000 chunk 445 optimal weight: 0.1980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 757 GLN A 926 ASN A1129 ASN B 98 HIS B 145 GLN B 537 GLN B 582 GLN B 593 GLN C 51 GLN D 34 ASN D 43 HIS ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN H 131 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 777 GLN b 927 ASN d 904 ASN d 970 ASN ** d1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.160 65442 Z= 0.985 Angle : 0.876 14.107 87699 Z= 0.450 Chirality : 0.065 0.336 8256 Planarity : 0.006 0.123 11940 Dihedral : 11.371 178.807 10888 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.67 % Allowed : 23.03 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.21 (0.09), residues: 8992 helix: 1.29 (0.09), residues: 3508 sheet: -0.58 (0.13), residues: 1499 loop : -1.25 (0.09), residues: 3985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP b 851 HIS 0.016 0.002 HIS A 472 PHE 0.033 0.004 PHE A 592 TYR 0.053 0.003 TYR B 916 ARG 0.019 0.001 ARG B 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17984 Ramachandran restraints generated. 8992 Oldfield, 0 Emsley, 8992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1011 time to evaluate : 5.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP M 572 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 91 residues processed: 1112 average time/residue: 1.5399 time to fit residues: 2209.6491 Evaluate side-chains 1077 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 986 time to evaluate : 5.450 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 72 residues processed: 21 average time/residue: 0.9206 time to fit residues: 35.9576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 576 optimal weight: 40.0000 chunk 773 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 669 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 727 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 746 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 926 ASN A1129 ASN B 314 GLN B 537 GLN B 582 GLN B 593 GLN B 913 GLN C 5 ASN D 43 HIS ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN I 45 GLN I 91 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 183 GLN ** b 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.203948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135556 restraints weight = 76867.548| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.00 r_work: 0.2931 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 65442 Z= 0.279 Angle : 0.631 15.793 87699 Z= 0.323 Chirality : 0.046 0.298 8256 Planarity : 0.004 0.101 11940 Dihedral : 11.194 179.374 10888 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 2.06 % Allowed : 23.97 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.17 (0.09), residues: 8992 helix: 1.71 (0.09), residues: 3500 sheet: -0.55 (0.13), residues: 1512 loop : -1.07 (0.10), residues: 3980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP b 851 HIS 0.007 0.001 HIS B 144 PHE 0.030 0.002 PHE G 77 TYR 0.042 0.002 TYR B 916 ARG 0.015 0.001 ARG A 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30355.57 seconds wall clock time: 523 minutes 4.93 seconds (31384.93 seconds total)