Starting phenix.real_space_refine on Wed Mar 13 02:35:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opc_13015/03_2024/7opc_13015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opc_13015/03_2024/7opc_13015.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/7opc_13015/03_2024/7opc_13015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opc_13015/03_2024/7opc_13015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opc_13015/03_2024/7opc_13015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opc_13015/03_2024/7opc_13015.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 1236 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 38837 2.51 5 N 12054 2.21 5 O 12918 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 "B ASP 1057": "OD1" <-> "OD2" 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 "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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 64223 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: 7439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 7439 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 290, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1055} Chain breaks: 6 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1209 Unresolved non-hydrogen angles: 1768 Unresolved non-hydrogen dihedrals: 746 Unresolved non-hydrogen chiralities: 394 Planarities with less than four sites: {'GLN:plan1': 14, '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: 529 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 91.096 101.909 171.771 1.00 49.57 S ATOM 486 SG CYS A 74 91.328 105.508 171.634 1.00 40.65 S ATOM 533 SG CYS A 81 92.268 104.115 168.775 1.00 37.20 S ATOM 768 SG CYS A 111 135.869 95.292 185.814 1.00 99.74 S ATOM 1109 SG CYS A 154 138.084 97.228 187.500 1.00111.53 S ATOM 1132 SG CYS A 184 137.756 93.630 188.930 1.00114.62 S ATOM 19801 SG CYS B1119 103.116 113.526 180.029 1.00 38.55 S ATOM 19823 SG CYS B1122 105.366 110.857 178.756 1.00 40.72 S ATOM 19938 SG CYS B1137 102.180 109.766 179.414 1.00 48.97 S ATOM 19959 SG CYS B1140 105.102 111.393 182.033 1.00 50.74 S ATOM 20925 SG CYS C 88 59.673 118.890 113.138 1.00 53.49 S ATOM 20938 SG CYS C 90 59.392 116.190 115.243 1.00 66.25 S ATOM 20973 SG CYS C 94 58.624 116.250 112.186 1.00 45.13 S ATOM 20995 SG CYS C 97 62.443 116.239 112.512 1.00 37.92 S ATOM 28299 SG CYS I 17 167.248 63.013 138.368 1.00102.63 S ATOM 28323 SG CYS I 20 164.228 63.382 140.290 1.00102.84 S ATOM 28484 SG CYS I 39 165.618 65.751 141.677 1.00106.88 S ATOM 28509 SG CYS I 42 167.529 62.693 141.345 1.00110.61 S ATOM 28861 SG CYS I 86 159.136 83.135 99.458 1.00 62.56 S ATOM 28885 SG CYS I 89 157.987 80.824 97.270 1.00 69.99 S ATOM 29089 SG CYS I 114 155.490 81.755 98.977 1.00 51.56 S ATOM 29124 SG CYS I 119 158.282 79.352 100.174 1.00 62.37 S ATOM 29234 SG CYS J 7 90.259 110.565 99.874 1.00 19.81 S ATOM 29258 SG CYS J 10 88.430 113.078 97.998 1.00 38.23 S ATOM 29522 SG CYS J 44 92.274 112.623 97.711 1.00 18.05 S ATOM 29528 SG CYS J 45 89.835 110.598 96.017 1.00 7.87 S ATOM 30690 SG CYS L 19 77.588 74.693 121.828 1.00 42.96 S ATOM 30709 SG CYS L 22 75.219 73.258 120.113 1.00 45.49 S ATOM 30826 SG CYS L 36 74.536 72.828 123.233 1.00 57.18 S ATOM 30852 SG CYS L 39 77.836 71.112 121.439 1.00 55.62 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: 26.29, per 1000 atoms: 0.41 Number of scatterers: 64223 At special positions: 0 Unit cell: (259.35, 219.45, 309.75, 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 12918 8.00 N 12054 7.00 C 38837 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: 21.48 Conformation dependent library (CDL) restraints added in 9.3 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, 18.2% beta 40 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 18.77 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: 3.659A 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: 3.901A 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: 3.867A pdb=" N GLN b 541 " --> pdb=" O GLY b 537 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE b 542 " --> pdb=" O ARG b 538 " (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: 4.016A 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: 3.690A pdb=" N GLN e 60 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 4.062A 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: 4.645A 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: 3.557A 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: 3.667A 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: 3.565A 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: 3.855A 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: 4.182A pdb=" N VAL e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.916A 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: 3.712A 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: 4.207A 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: 3.562A 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: 4.110A pdb=" N VAL e 688 " --> pdb=" O THR e 684 " (cutoff:3.500A) removed outlier: 3.531A 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: 4.519A 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: 6.540A 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: 3.522A 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: 7.087A 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: 6.652A 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: 6.864A 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 36 through 38 removed outlier: 7.402A 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: 6.682A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.947A 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: 4.244A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) removed outlier: 3.647A 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 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 248 through 253 removed outlier: 3.612A 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: 3.512A pdb=" N THR a 328 " --> pdb=" O VAL a 318 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.202A 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: 4.410A pdb=" N PHE d1007 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU d1029 " --> pdb=" O PHE d1007 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N HIS d1009 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 7.680A 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: 4.596A pdb=" N SER d1042 " --> pdb=" O GLY d1026 " (cutoff:3.500A) removed outlier: 6.469A 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: 7.396A pdb=" N THR d1041 " --> pdb=" O VAL d 6 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL d 6 " --> pdb=" O THR d1041 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU d1043 " --> pdb=" O ASN d 4 " (cutoff:3.500A) removed outlier: 5.724A 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: 6.087A 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: 3.857A 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: 5.435A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.339A 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: 5.936A 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: 3.599A 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: 5.936A 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: 3.599A 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: 6.717A pdb=" N GLY d 274 " --> pdb=" O VAL d 259 " (cutoff:3.500A) removed outlier: 4.260A 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: 4.980A 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: 4.373A 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: 6.895A 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: 6.631A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 4.686A 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: 3.952A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) removed outlier: 24.508A pdb=" N LEU d 666 " --> pdb=" O ARG d 388 " (cutoff:3.500A) removed outlier: 18.432A pdb=" N ILE d 390 " --> pdb=" O LEU d 666 " (cutoff:3.500A) removed outlier: 13.310A pdb=" N PHE d 668 " --> pdb=" O ILE d 390 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN d 392 " --> pdb=" O PHE d 668 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN d 670 " --> pdb=" O ASN d 392 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'd' and resid 361 through 364 removed outlier: 3.952A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY d 395 " --> pdb=" O ILE d 707 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE d 707 " --> pdb=" O GLY d 395 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'd' and resid 411 through 413 Processing sheet with id=AK3, first strand: chain 'd' and resid 457 through 463 removed outlier: 3.706A pdb=" N TRP d 490 " --> pdb=" O VAL d 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 6.520A 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=AK4, 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=AK5, 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: 3.672A 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: 6.619A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'd' and resid 590 through 595 removed outlier: 4.383A 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=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: 6.344A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.573A 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: 5.291A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.693A 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: 5.291A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.693A 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: 6.400A 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: 6.651A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.539A 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: 6.884A 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: 6.770A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 4.909A 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: 3.639A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 6.675A 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: 4.085A 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: 3.921A 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) 3336 hydrogen bonds defined for protein. 9411 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: 40.33 Time building geometry restraints manager: 23.53 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: 11542 1.27 - 1.41: 16499 1.41 - 1.55: 36675 1.55 - 1.69: 252 1.69 - 1.83: 470 Bond restraints: 65438 Sorted by residual: 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 45 " pdb=" OP1 A P 45 " ideal model delta sigma weight residual 1.485 1.337 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" CD ARG M1014 " pdb=" NE ARG M1014 " ideal model delta sigma weight residual 1.458 1.359 0.099 1.40e-02 5.10e+03 5.04e+01 bond pdb=" CZ ARG M1014 " pdb=" NH2 ARG M1014 " ideal model delta sigma weight residual 1.330 1.240 0.090 1.30e-02 5.92e+03 4.76e+01 bond pdb=" CG1 ILE G 59 " pdb=" CD1 ILE G 59 " ideal model delta sigma weight residual 1.513 1.246 0.267 3.90e-02 6.57e+02 4.69e+01 ... (remaining 65433 not shown) Histogram of bond angle deviations from ideal: 91.38 - 100.56: 99 100.56 - 109.75: 10319 109.75 - 118.93: 40703 118.93 - 128.12: 35918 128.12 - 137.30: 655 Bond angle restraints: 87694 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 114.39 103.33 11.06 1.45e+00 4.76e-01 5.82e+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 110.80 122.91 -12.11 2.13e+00 2.20e-01 3.23e+01 ... (remaining 87689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 34857 35.68 - 71.36: 739 71.36 - 107.04: 49 107.04 - 142.73: 1 142.73 - 178.41: 4 Dihedral angle restraints: 35650 sinusoidal: 14361 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 a 174 " pdb=" C LYS a 174 " pdb=" N SER a 175 " pdb=" CA SER a 175 " ideal model delta harmonic sigma weight residual -180.00 -144.30 -35.70 0 5.00e+00 4.00e-02 5.10e+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 -145.43 -34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 35647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 7018 0.100 - 0.201: 1021 0.201 - 0.301: 159 0.301 - 0.401: 44 0.401 - 0.502: 14 Chirality restraints: 8256 Sorted by residual: 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 chirality pdb=" C3' DC T 22 " pdb=" C4' DC T 22 " pdb=" O3' DC T 22 " pdb=" C2' DC T 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.16 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" C1' DT T 23 " pdb=" O4' DT T 23 " pdb=" C2' DT T 23 " pdb=" N1 DT T 23 " both_signs ideal model delta sigma weight residual False 2.47 1.98 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 8253 not shown) Planarity restraints: 11939 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 4.08e-02 3.33e+01 pdb=" CG TYR b 882 " -0.099 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 11936 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 409 2.50 - 3.10: 49273 3.10 - 3.70: 97521 3.70 - 4.30: 145241 4.30 - 4.90: 235358 Nonbonded interactions: 527802 Sorted by model distance: 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 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 1.925 2.170 ... (remaining 527797 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.040 Extract box with map and model: 16.890 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 177.300 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.230 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.017 0.289 65438 Z= 1.102 Angle : 1.027 16.622 87694 Z= 0.588 Chirality : 0.077 0.502 8256 Planarity : 0.007 0.105 11939 Dihedral : 14.539 178.407 23670 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.57 % Cbeta Deviations : 0.02 % 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: -2.03 (0.08), residues: 8992 helix: -0.80 (0.08), residues: 3389 sheet: -1.49 (0.13), residues: 1476 loop : -1.67 (0.09), residues: 4127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP M 752 HIS 0.025 0.003 HIS D 93 PHE 0.064 0.004 PHE M 686 TYR 0.099 0.004 TYR b 882 ARG 0.116 0.003 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 1446 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1443 time to evaluate : 5.433 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 REVERT: A 274 ASP cc_start: 0.7334 (t70) cc_final: 0.6795 (t70) REVERT: A 285 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7749 (mtmt) REVERT: A 408 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8156 (mtp180) REVERT: A 495 ASP cc_start: 0.7610 (p0) cc_final: 0.7145 (p0) REVERT: A 497 ASP cc_start: 0.8505 (p0) cc_final: 0.8229 (p0) REVERT: A 499 ASP cc_start: 0.8009 (m-30) cc_final: 0.7547 (m-30) REVERT: A 524 MET cc_start: 0.8667 (mmp) cc_final: 0.8318 (mmm) REVERT: A 559 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 659 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 746 ASN cc_start: 0.8651 (m-40) cc_final: 0.8433 (m-40) REVERT: A 758 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8236 (mtmt) REVERT: A 1090 LEU cc_start: 0.8549 (tt) cc_final: 0.8343 (tp) REVERT: A 1168 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8307 (mmmm) REVERT: A 1286 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7932 (mmm-85) REVERT: A 1376 LYS cc_start: 0.8513 (tppt) cc_final: 0.8181 (tptp) REVERT: A 1386 ILE cc_start: 0.8874 (mt) cc_final: 0.8674 (mp) REVERT: A 1441 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 1459 MET cc_start: 0.8423 (mtp) cc_final: 0.8208 (mtp) REVERT: B 35 ASP cc_start: 0.7728 (m-30) cc_final: 0.7388 (m-30) REVERT: B 298 MET cc_start: 0.7933 (mmt) cc_final: 0.7616 (mmt) REVERT: B 600 GLU cc_start: 0.7858 (pt0) cc_final: 0.7538 (pt0) REVERT: B 764 MET cc_start: 0.8610 (mtt) cc_final: 0.8348 (mtt) REVERT: B 953 ASP cc_start: 0.8163 (m-30) cc_final: 0.7879 (m-30) REVERT: C 18 ASN cc_start: 0.9185 (p0) cc_final: 0.8894 (p0) REVERT: C 247 SER cc_start: 0.9139 (t) cc_final: 0.8904 (m) REVERT: C 253 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8372 (ttmt) REVERT: D 67 TYR cc_start: 0.8057 (t80) cc_final: 0.7852 (t80) REVERT: D 115 ILE cc_start: 0.8784 (mt) cc_final: 0.8520 (mm) REVERT: D 128 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7714 (tp40) REVERT: E 57 ASP cc_start: 0.7729 (m-30) cc_final: 0.7468 (m-30) REVERT: E 98 ASN cc_start: 0.8114 (t0) cc_final: 0.7763 (t0) REVERT: F 80 MET cc_start: 0.8586 (mmt) cc_final: 0.8289 (mmt) REVERT: G 84 VAL cc_start: 0.8410 (m) cc_final: 0.7779 (m) REVERT: G 93 ASN cc_start: 0.7671 (m110) cc_final: 0.6979 (m-40) REVERT: G 166 ASP cc_start: 0.8451 (m-30) cc_final: 0.8026 (m-30) REVERT: H 20 LYS cc_start: 0.8925 (tptm) cc_final: 0.8437 (tptm) REVERT: H 67 ASP cc_start: 0.8387 (p0) cc_final: 0.8183 (p0) REVERT: H 110 THR cc_start: 0.8845 (p) cc_final: 0.8644 (p) REVERT: H 138 ASP cc_start: 0.7142 (m-30) cc_final: 0.6874 (m-30) REVERT: H 140 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7839 (mmt180) REVERT: I 51 SER cc_start: 0.8632 (p) cc_final: 0.7946 (t) REVERT: I 75 ASP cc_start: 0.8556 (t0) cc_final: 0.8318 (t0) REVERT: I 88 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7921 (tttm) REVERT: J 48 MET cc_start: 0.9222 (mmm) cc_final: 0.8716 (mmm) REVERT: J 57 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8116 (mm-30) REVERT: J 58 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8177 (mmtp) REVERT: K 47 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8718 (tttp) REVERT: K 110 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7954 (ttpp) REVERT: L 24 THR cc_start: 0.8796 (m) cc_final: 0.8546 (m) REVERT: M 711 MET cc_start: 0.8087 (ptm) cc_final: 0.7845 (ptp) REVERT: a 33 ASN cc_start: 0.7405 (t0) cc_final: 0.7170 (t0) REVERT: a 100 TYR cc_start: 0.8210 (m-80) cc_final: 0.8008 (m-80) REVERT: a 172 ASP cc_start: 0.7994 (t0) cc_final: 0.7663 (t0) REVERT: a 177 SER cc_start: 0.8365 (t) cc_final: 0.8153 (p) REVERT: a 218 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7241 (mtm110) REVERT: a 220 SER cc_start: 0.8419 (p) cc_final: 0.8036 (p) REVERT: a 275 SER cc_start: 0.8692 (t) cc_final: 0.8289 (p) REVERT: b 605 HIS cc_start: 0.7341 (m90) cc_final: 0.7039 (m-70) REVERT: b 637 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7899 (ttm110) REVERT: b 704 MET cc_start: 0.9096 (mmp) cc_final: 0.8438 (mmt) REVERT: b 723 GLN cc_start: 0.8554 (mt0) cc_final: 0.8304 (mt0) REVERT: b 729 LYS cc_start: 0.8912 (tmmt) cc_final: 0.8705 (tttm) REVERT: b 885 MET cc_start: 0.7108 (tpt) cc_final: 0.6398 (tpt) REVERT: d 150 LYS cc_start: 0.7126 (tmtt) cc_final: 0.6792 (ttmt) REVERT: d 165 ILE cc_start: 0.8854 (mm) cc_final: 0.8635 (mm) REVERT: d 246 LEU cc_start: 0.7888 (mm) cc_final: 0.7616 (mt) REVERT: d 256 SER cc_start: 0.8521 (m) cc_final: 0.7942 (p) REVERT: d 867 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7277 (mmtp) REVERT: d 872 SER cc_start: 0.8970 (t) cc_final: 0.8678 (m) REVERT: d 950 ASN cc_start: 0.7927 (m110) cc_final: 0.7674 (m-40) outliers start: 3 outliers final: 4 residues processed: 1445 average time/residue: 1.4870 time to fit residues: 2735.8093 Evaluate side-chains 1082 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1078 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain a residue 128 ASP Chi-restraints excluded: chain b residue 539 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 772 optimal weight: 40.0000 chunk 693 optimal weight: 0.5980 chunk 384 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 467 optimal weight: 40.0000 chunk 370 optimal weight: 4.9990 chunk 717 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 436 optimal weight: 0.9980 chunk 533 optimal weight: 5.9990 chunk 830 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 278 HIS A 531 ASN A 861 GLN A1077 ASN A1078 GLN A1129 ASN A1420 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN B1003 ASN B1049 GLN B1145 GLN D 47 GLN D 66 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN G 4 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN K 69 HIS M 405 GLN M 421 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 719 GLN M 895 ASN ** M1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1151 ASN M1264 HIS a 79 GLN a 183 GLN a 187 GLN a 228 GLN a 326 GLN a 343 GLN b 616 HIS b 669 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 255 GLN d1056 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 65438 Z= 0.248 Angle : 0.600 12.724 87694 Z= 0.317 Chirality : 0.046 0.352 8256 Planarity : 0.004 0.066 11939 Dihedral : 11.519 177.580 10911 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.03 % Allowed : 12.04 % Favored : 85.93 % 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: -0.82 (0.09), residues: 8992 helix: 0.57 (0.09), residues: 3456 sheet: -1.10 (0.13), residues: 1491 loop : -1.25 (0.09), residues: 4045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 207 HIS 0.007 0.001 HIS b 616 PHE 0.021 0.002 PHE G 107 TYR 0.022 0.002 TYR I 54 ARG 0.011 0.001 ARG b 975 *********************** 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 1283 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1169 time to evaluate : 5.460 Fit side-chains 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: A 42 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8011 (ptpt) REVERT: A 274 ASP cc_start: 0.7312 (t70) cc_final: 0.7008 (t70) REVERT: A 285 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7879 (mttt) REVERT: A 317 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7424 (ttt) REVERT: A 408 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8169 (mtp180) REVERT: A 428 ASP cc_start: 0.8212 (t0) cc_final: 0.7977 (t0) REVERT: A 495 ASP cc_start: 0.7925 (p0) cc_final: 0.7715 (p0) REVERT: A 499 ASP cc_start: 0.8339 (m-30) cc_final: 0.7923 (m-30) REVERT: A 757 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: A 1168 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8232 (mmmm) REVERT: A 1325 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7082 (p0) REVERT: A 1327 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 1334 TRP cc_start: 0.8904 (m100) cc_final: 0.8603 (m100) REVERT: A 1350 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8227 (mtpp) REVERT: B 95 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8210 (mmtm) REVERT: B 222 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7723 (mtp85) REVERT: B 358 GLU cc_start: 0.7528 (pm20) cc_final: 0.7192 (pm20) REVERT: B 379 ARG cc_start: 0.8283 (mmt90) cc_final: 0.8043 (mtt90) REVERT: B 771 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 953 ASP cc_start: 0.8360 (m-30) cc_final: 0.8089 (m-30) REVERT: C 51 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: D 110 GLU cc_start: 0.7843 (tt0) cc_final: 0.7614 (tt0) REVERT: D 115 ILE cc_start: 0.8579 (mt) cc_final: 0.8356 (mm) REVERT: E 57 ASP cc_start: 0.7750 (m-30) cc_final: 0.7488 (m-30) REVERT: E 98 ASN cc_start: 0.8059 (t0) cc_final: 0.7635 (t0) REVERT: E 132 GLN cc_start: 0.8227 (pt0) cc_final: 0.7832 (tt0) REVERT: F 80 MET cc_start: 0.8651 (mmt) cc_final: 0.8348 (mmp) REVERT: G 84 VAL cc_start: 0.8339 (m) cc_final: 0.7961 (m) REVERT: G 93 ASN cc_start: 0.7501 (m110) cc_final: 0.6710 (m-40) REVERT: G 131 MET cc_start: 0.7255 (ppp) cc_final: 0.6972 (ppp) REVERT: G 135 ILE cc_start: 0.8875 (pt) cc_final: 0.8652 (pp) REVERT: G 141 ASP cc_start: 0.7600 (m-30) cc_final: 0.7366 (m-30) REVERT: G 166 ASP cc_start: 0.8080 (m-30) cc_final: 0.7610 (m-30) REVERT: H 20 LYS cc_start: 0.8888 (tptm) cc_final: 0.8608 (tptm) REVERT: H 36 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7917 (mmmt) REVERT: H 103 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: H 138 ASP cc_start: 0.7201 (m-30) cc_final: 0.6899 (m-30) REVERT: I 14 ILE cc_start: 0.9055 (tt) cc_final: 0.8766 (tp) REVERT: I 27 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7749 (ttpp) REVERT: I 51 SER cc_start: 0.8317 (p) cc_final: 0.7929 (t) REVERT: I 56 ASN cc_start: 0.8208 (t0) cc_final: 0.7826 (t0) REVERT: K 47 LYS cc_start: 0.9026 (tmmt) cc_final: 0.8758 (tttp) REVERT: K 110 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7860 (ttpp) REVERT: L 42 ARG cc_start: 0.8284 (mmt180) cc_final: 0.8081 (mmm160) REVERT: M 383 TYR cc_start: 0.8009 (m-80) cc_final: 0.7228 (m-80) REVERT: M 601 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8493 (tm) REVERT: M 714 GLU cc_start: 0.7986 (tt0) cc_final: 0.7689 (tp30) REVERT: M 800 ASN cc_start: 0.8042 (t0) cc_final: 0.7819 (t0) REVERT: M 861 ILE cc_start: 0.8292 (pt) cc_final: 0.8084 (pp) REVERT: M 892 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8542 (tp) REVERT: M 929 GLN cc_start: 0.7544 (tm-30) cc_final: 0.6994 (tp-100) REVERT: M 1067 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: a 33 ASN cc_start: 0.7419 (t0) cc_final: 0.7080 (t0) REVERT: a 172 ASP cc_start: 0.8227 (t0) cc_final: 0.7971 (t70) REVERT: a 177 SER cc_start: 0.8391 (t) cc_final: 0.8188 (p) REVERT: a 273 ASN cc_start: 0.8771 (t0) cc_final: 0.8293 (t0) REVERT: a 275 SER cc_start: 0.8542 (t) cc_final: 0.8104 (p) REVERT: b 520 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: b 588 TRP cc_start: 0.7863 (OUTLIER) cc_final: 0.6940 (m-90) REVERT: b 605 HIS cc_start: 0.7196 (m90) cc_final: 0.6868 (m-70) REVERT: b 637 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7769 (ttm110) REVERT: b 729 LYS cc_start: 0.8877 (tmmt) cc_final: 0.8536 (tttm) REVERT: b 752 MET cc_start: 0.5321 (mmm) cc_final: 0.5015 (mpp) REVERT: b 770 ASP cc_start: 0.6811 (t0) cc_final: 0.6599 (m-30) REVERT: b 885 MET cc_start: 0.6971 (tpt) cc_final: 0.6485 (tpt) REVERT: b 946 GLU cc_start: 0.7969 (tt0) cc_final: 0.7585 (tt0) REVERT: d 100 ILE cc_start: 0.8207 (mm) cc_final: 0.7880 (mm) REVERT: d 165 ILE cc_start: 0.9116 (mm) cc_final: 0.8912 (mm) REVERT: d 191 LYS cc_start: 0.8016 (tttt) cc_final: 0.7618 (tttp) REVERT: d 755 SER cc_start: 0.8379 (m) cc_final: 0.7911 (p) REVERT: d 797 HIS cc_start: 0.8071 (m-70) cc_final: 0.7695 (m-70) REVERT: d 844 LYS cc_start: 0.8589 (mptt) cc_final: 0.8159 (ptpt) REVERT: d 867 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7370 (mmtp) REVERT: d 910 MET cc_start: 0.8009 (ttm) cc_final: 0.7703 (ttm) REVERT: d 948 ASP cc_start: 0.7831 (t0) cc_final: 0.7519 (t0) REVERT: d 950 ASN cc_start: 0.8060 (m110) cc_final: 0.7768 (m-40) REVERT: d 1134 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7392 (mm-30) outliers start: 114 outliers final: 31 residues processed: 1226 average time/residue: 1.4563 time to fit residues: 2295.5128 Evaluate side-chains 1088 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1046 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1166 SER Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 739 GLU Chi-restraints excluded: chain M residue 892 LEU Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 119 SER Chi-restraints excluded: chain b residue 520 GLU Chi-restraints excluded: chain b residue 588 TRP Chi-restraints excluded: chain b residue 746 MET Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 244 LYS Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 1099 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 461 optimal weight: 0.2980 chunk 257 optimal weight: 0.5980 chunk 691 optimal weight: 0.8980 chunk 565 optimal weight: 8.9990 chunk 229 optimal weight: 0.0010 chunk 832 optimal weight: 6.9990 chunk 899 optimal weight: 50.0000 chunk 741 optimal weight: 2.9990 chunk 825 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 667 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 531 ASN A 861 GLN A1078 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B1003 ASN B1101 GLN C 108 ASN C 262 GLN E 65 ASN H 87 GLN I 74 GLN K 2 ASN K 55 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 842 ASN M 895 ASN M1264 HIS a 79 GLN a 110 HIS a 228 GLN b 616 HIS ** d 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1056 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 65438 Z= 0.196 Angle : 0.541 11.783 87694 Z= 0.283 Chirality : 0.043 0.200 8256 Planarity : 0.004 0.054 11939 Dihedral : 11.297 179.684 10908 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.47 % Allowed : 15.24 % Favored : 82.28 % 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: 1.28 (0.09), residues: 3431 sheet: -0.84 (0.13), residues: 1493 loop : -1.09 (0.09), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 207 HIS 0.005 0.001 HIS D 93 PHE 0.023 0.002 PHE G 158 TYR 0.024 0.001 TYR B 916 ARG 0.013 0.001 ARG a 92 *********************** 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 1268 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1129 time to evaluate : 5.405 Fit side-chains 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: A 42 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8081 (ptpt) REVERT: A 274 ASP cc_start: 0.7309 (t70) cc_final: 0.7000 (t70) REVERT: A 285 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7963 (mtmt) REVERT: A 408 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8191 (mtp180) REVERT: A 556 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: A 559 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 682 ILE cc_start: 0.8741 (mt) cc_final: 0.8336 (mt) REVERT: A 693 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 712 ASP cc_start: 0.7508 (m-30) cc_final: 0.7276 (m-30) REVERT: A 757 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: A 811 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8726 (pt) REVERT: A 1168 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8088 (mtpp) REVERT: A 1325 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7147 (p0) REVERT: A 1327 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 1334 TRP cc_start: 0.8906 (m100) cc_final: 0.8614 (m100) REVERT: A 1350 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8256 (mtpp) REVERT: A 1423 ASP cc_start: 0.7442 (t0) cc_final: 0.7079 (t0) REVERT: B 90 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: B 95 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8222 (mmtm) REVERT: B 200 MET cc_start: 0.7755 (tpp) cc_final: 0.7482 (tpp) REVERT: B 222 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7727 (mtp85) REVERT: B 312 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: B 344 GLN cc_start: 0.7723 (tt0) cc_final: 0.7336 (tm-30) REVERT: B 358 GLU cc_start: 0.7617 (pm20) cc_final: 0.7258 (pm20) REVERT: B 403 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8780 (mp) REVERT: B 497 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7828 (tmtt) REVERT: B 683 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7761 (mt0) REVERT: B 771 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7853 (mt-10) REVERT: B 953 ASP cc_start: 0.8391 (m-30) cc_final: 0.8104 (m-30) REVERT: B 1143 LYS cc_start: 0.8240 (pttt) cc_final: 0.7890 (mtmt) REVERT: C 51 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 83 GLN cc_start: 0.7958 (mm110) cc_final: 0.7736 (mm-40) REVERT: D 39 MET cc_start: 0.8130 (ppp) cc_final: 0.7856 (ppp) REVERT: D 73 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7479 (mpt180) REVERT: E 57 ASP cc_start: 0.7754 (m-30) cc_final: 0.7501 (m-30) REVERT: E 132 GLN cc_start: 0.8090 (pt0) cc_final: 0.7763 (tt0) REVERT: F 75 MET cc_start: 0.8769 (mtp) cc_final: 0.8543 (mtm) REVERT: G 80 PHE cc_start: 0.8443 (m-80) cc_final: 0.8166 (m-80) REVERT: G 84 VAL cc_start: 0.8277 (m) cc_final: 0.7814 (m) REVERT: G 93 ASN cc_start: 0.7292 (m110) cc_final: 0.6715 (m-40) REVERT: G 129 LYS cc_start: 0.8444 (ptmt) cc_final: 0.8002 (ptpp) REVERT: G 166 ASP cc_start: 0.8116 (m-30) cc_final: 0.7554 (m-30) REVERT: H 20 LYS cc_start: 0.8897 (tptm) cc_final: 0.8650 (tptm) REVERT: H 138 ASP cc_start: 0.7189 (m-30) cc_final: 0.6871 (m-30) REVERT: I 51 SER cc_start: 0.8251 (p) cc_final: 0.7849 (t) REVERT: I 56 ASN cc_start: 0.8378 (t0) cc_final: 0.7975 (t0) REVERT: K 47 LYS cc_start: 0.8990 (tmmt) cc_final: 0.8752 (tttp) REVERT: K 68 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: K 110 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7852 (ttpp) REVERT: L 26 ASN cc_start: 0.8248 (p0) cc_final: 0.8013 (p0) REVERT: M 383 TYR cc_start: 0.8059 (m-80) cc_final: 0.7334 (m-80) REVERT: M 585 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8607 (mm) REVERT: M 601 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8493 (tm) REVERT: M 731 ASN cc_start: 0.8540 (m-40) cc_final: 0.8335 (m-40) REVERT: M 792 HIS cc_start: 0.6792 (t-90) cc_final: 0.6509 (t-170) REVERT: M 892 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8265 (tp) REVERT: M 894 MET cc_start: 0.7319 (ttp) cc_final: 0.7092 (mtp) REVERT: M 1142 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7270 (tmm-80) REVERT: a 16 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7458 (mt) REVERT: a 33 ASN cc_start: 0.7360 (t0) cc_final: 0.7002 (t0) REVERT: a 172 ASP cc_start: 0.8253 (t0) cc_final: 0.8020 (t70) REVERT: a 273 ASN cc_start: 0.8795 (t0) cc_final: 0.8312 (t0) REVERT: a 275 SER cc_start: 0.8570 (t) cc_final: 0.8118 (p) REVERT: b 588 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.6709 (m-90) REVERT: b 605 HIS cc_start: 0.7142 (m90) cc_final: 0.6801 (m-70) REVERT: b 616 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6283 (t-90) REVERT: b 690 ASP cc_start: 0.8376 (t70) cc_final: 0.7957 (t70) REVERT: b 729 LYS cc_start: 0.8900 (tmmt) cc_final: 0.8593 (tttm) REVERT: b 752 MET cc_start: 0.5420 (mmm) cc_final: 0.5145 (mpp) REVERT: b 885 MET cc_start: 0.7022 (tpt) cc_final: 0.6776 (tpt) REVERT: b 894 ARG cc_start: 0.7258 (mtt90) cc_final: 0.7051 (mmt90) REVERT: b 936 TRP cc_start: 0.8819 (m100) cc_final: 0.8596 (m100) REVERT: b 946 GLU cc_start: 0.7943 (tt0) cc_final: 0.7486 (tt0) REVERT: d 100 ILE cc_start: 0.8290 (mm) cc_final: 0.7944 (mm) REVERT: d 191 LYS cc_start: 0.8059 (tttt) cc_final: 0.7802 (tttm) REVERT: d 201 GLU cc_start: 0.7630 (tp30) cc_final: 0.7395 (tp30) REVERT: d 366 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6496 (t0) REVERT: d 797 HIS cc_start: 0.8097 (m-70) cc_final: 0.7650 (m-70) REVERT: d 867 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7298 (mmtp) REVERT: d 948 ASP cc_start: 0.7683 (t0) cc_final: 0.7305 (t0) REVERT: d 950 ASN cc_start: 0.8056 (m110) cc_final: 0.7740 (m110) REVERT: d 1059 ASN cc_start: 0.8590 (m-40) cc_final: 0.8375 (m-40) REVERT: d 1063 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7419 (mttt) REVERT: d 1134 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7308 (mm-30) outliers start: 139 outliers final: 46 residues processed: 1195 average time/residue: 1.4333 time to fit residues: 2204.9153 Evaluate side-chains 1113 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1047 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1166 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 739 GLU Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 892 LEU Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1142 ARG Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1167 ILE Chi-restraints excluded: chain M residue 1276 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain b residue 588 TRP Chi-restraints excluded: chain b residue 616 HIS Chi-restraints excluded: chain b residue 684 GLU Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain b residue 746 MET Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 366 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 822 optimal weight: 6.9990 chunk 625 optimal weight: 40.0000 chunk 432 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 397 optimal weight: 2.9990 chunk 558 optimal weight: 30.0000 chunk 835 optimal weight: 4.9990 chunk 884 optimal weight: 8.9990 chunk 436 optimal weight: 2.9990 chunk 791 optimal weight: 50.0000 chunk 238 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 673 GLN A 861 GLN A1078 GLN B 145 GLN B 593 GLN B1003 ASN B1071 ASN B1094 GLN B1101 GLN C 260 GLN C 262 GLN E 65 ASN E 129 GLN E 133 GLN G 24 ASN H 87 GLN H 133 HIS I 45 GLN I 74 GLN M 405 GLN M 421 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 895 ASN ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 47 ASN a 79 GLN a 169 GLN a 228 GLN b 616 HIS ** b 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS d 964 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 65438 Z= 0.418 Angle : 0.619 11.931 87694 Z= 0.320 Chirality : 0.048 0.215 8256 Planarity : 0.004 0.064 11939 Dihedral : 11.328 179.767 10908 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.36 % Allowed : 16.76 % Favored : 79.88 % 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: -0.06 (0.09), residues: 8992 helix: 1.44 (0.09), residues: 3448 sheet: -0.71 (0.13), residues: 1494 loop : -1.06 (0.09), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.009 0.001 HIS b 616 PHE 0.028 0.002 PHE A 112 TYR 0.038 0.002 TYR B 916 ARG 0.015 0.001 ARG M 589 *********************** 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 1302 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1113 time to evaluate : 5.509 Fit side-chains 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: A 16 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7790 (mmm-85) REVERT: A 220 ARG cc_start: 0.8214 (tpt-90) cc_final: 0.7974 (tpt-90) REVERT: A 223 GLU cc_start: 0.7840 (tp30) cc_final: 0.7260 (tp30) REVERT: A 274 ASP cc_start: 0.7412 (t70) cc_final: 0.7034 (t70) REVERT: A 285 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8079 (mtmt) REVERT: A 382 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7501 (ttm110) REVERT: A 408 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8368 (mtp180) REVERT: A 434 LYS cc_start: 0.7443 (ptpt) cc_final: 0.7235 (ptpp) REVERT: A 556 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: A 682 ILE cc_start: 0.8807 (mt) cc_final: 0.8434 (mt) REVERT: A 743 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7212 (ttp-110) REVERT: A 757 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: A 1168 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8137 (mtpp) REVERT: A 1228 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7472 (mpt) REVERT: A 1287 CYS cc_start: 0.7871 (m) cc_final: 0.7581 (t) REVERT: A 1325 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 1337 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 1350 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8471 (mtpp) REVERT: A 1423 ASP cc_start: 0.7384 (t0) cc_final: 0.7068 (t0) REVERT: A 1455 SER cc_start: 0.8886 (m) cc_final: 0.8641 (m) REVERT: A 1459 MET cc_start: 0.8508 (mtp) cc_final: 0.8230 (mtm) REVERT: B 95 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8433 (mmtm) REVERT: B 222 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8126 (mtp85) REVERT: B 312 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: B 340 LYS cc_start: 0.7603 (tttp) cc_final: 0.7306 (tttt) REVERT: B 358 GLU cc_start: 0.7598 (pm20) cc_final: 0.7262 (pm20) REVERT: B 388 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 394 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (t0) REVERT: B 403 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 407 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8170 (mtp) REVERT: B 1071 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8244 (p0) REVERT: B 1081 ASP cc_start: 0.7862 (t0) cc_final: 0.7511 (t0) REVERT: C 94 CYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7663 (p) REVERT: D 39 MET cc_start: 0.8180 (ppp) cc_final: 0.7948 (ppp) REVERT: D 62 MET cc_start: 0.8085 (mmp) cc_final: 0.7877 (mmp) REVERT: D 73 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7529 (mpt180) REVERT: E 46 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7706 (p0) REVERT: E 57 ASP cc_start: 0.7860 (m-30) cc_final: 0.7610 (m-30) REVERT: E 132 GLN cc_start: 0.8363 (pt0) cc_final: 0.8003 (tt0) REVERT: E 166 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7584 (mtm-85) REVERT: F 80 MET cc_start: 0.8617 (mmt) cc_final: 0.8406 (mmp) REVERT: G 67 LEU cc_start: 0.8926 (tp) cc_final: 0.8723 (tp) REVERT: G 80 PHE cc_start: 0.8504 (m-80) cc_final: 0.8192 (m-80) REVERT: G 93 ASN cc_start: 0.7487 (m110) cc_final: 0.6926 (m-40) REVERT: G 166 ASP cc_start: 0.8122 (m-30) cc_final: 0.7344 (m-30) REVERT: H 20 LYS cc_start: 0.8955 (tptm) cc_final: 0.8634 (tptm) REVERT: H 103 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: H 138 ASP cc_start: 0.7350 (m-30) cc_final: 0.7069 (m-30) REVERT: H 146 LYS cc_start: 0.8713 (tttt) cc_final: 0.8381 (ttpt) REVERT: I 56 ASN cc_start: 0.8556 (t0) cc_final: 0.8090 (t0) REVERT: K 47 LYS cc_start: 0.9106 (tmmt) cc_final: 0.8826 (tttp) REVERT: K 68 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: K 110 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7873 (ttpp) REVERT: M 383 TYR cc_start: 0.8116 (m-80) cc_final: 0.7502 (m-80) REVERT: M 585 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8687 (mm) REVERT: M 601 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8573 (tm) REVERT: M 714 GLU cc_start: 0.7956 (tt0) cc_final: 0.7613 (tp30) REVERT: M 724 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: M 792 HIS cc_start: 0.6855 (t-90) cc_final: 0.6574 (t-170) REVERT: M 898 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: M 941 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8010 (mmtm) REVERT: M 1167 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8358 (pp) REVERT: a 16 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7100 (mt) REVERT: a 33 ASN cc_start: 0.7486 (t0) cc_final: 0.7030 (t0) REVERT: a 100 TYR cc_start: 0.8388 (m-80) cc_final: 0.8003 (m-80) REVERT: a 172 ASP cc_start: 0.8364 (t0) cc_final: 0.8113 (t70) REVERT: a 198 TYR cc_start: 0.8557 (m-80) cc_final: 0.8307 (m-80) REVERT: a 273 ASN cc_start: 0.8852 (t0) cc_final: 0.8625 (t0) REVERT: a 275 SER cc_start: 0.8595 (t) cc_final: 0.8308 (p) REVERT: b 520 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: b 605 HIS cc_start: 0.7143 (m90) cc_final: 0.6826 (m-70) REVERT: b 630 LEU cc_start: 0.8817 (mt) cc_final: 0.8600 (mt) REVERT: b 729 LYS cc_start: 0.9026 (tmmt) cc_final: 0.8681 (tttm) REVERT: b 752 MET cc_start: 0.5321 (mmm) cc_final: 0.5110 (mpp) REVERT: b 885 MET cc_start: 0.6914 (tpt) cc_final: 0.6617 (tpt) REVERT: b 936 TRP cc_start: 0.8849 (m100) cc_final: 0.8630 (m100) REVERT: b 946 GLU cc_start: 0.7991 (tt0) cc_final: 0.7778 (tt0) REVERT: d 151 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6974 (mm-30) REVERT: d 191 LYS cc_start: 0.8140 (tttt) cc_final: 0.7611 (tttp) REVERT: d 201 GLU cc_start: 0.7617 (tp30) cc_final: 0.7387 (tp30) REVERT: d 366 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6731 (t0) REVERT: d 797 HIS cc_start: 0.8175 (m-70) cc_final: 0.7693 (m-70) REVERT: d 867 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7259 (mmtp) REVERT: d 950 ASN cc_start: 0.8156 (m110) cc_final: 0.7866 (m-40) REVERT: d 1063 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7435 (mttt) REVERT: d 1134 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7296 (mm-30) outliers start: 189 outliers final: 70 residues processed: 1208 average time/residue: 1.5057 time to fit residues: 2372.2519 Evaluate side-chains 1140 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1046 time to evaluate : 5.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 799 VAL Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 849 THR Chi-restraints excluded: chain M residue 898 LYS Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 930 VAL Chi-restraints excluded: chain M residue 941 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1167 ILE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain M residue 1245 LEU Chi-restraints excluded: chain M residue 1276 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 520 GLU Chi-restraints excluded: chain b residue 684 GLU Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 718 ASN Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 350 MET Chi-restraints excluded: chain d residue 366 ASP Chi-restraints excluded: chain d residue 823 LYS Chi-restraints excluded: chain d residue 833 THR Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 903 CYS Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 969 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 736 optimal weight: 4.9990 chunk 502 optimal weight: 30.0000 chunk 12 optimal weight: 0.0970 chunk 658 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 754 optimal weight: 7.9990 chunk 611 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 451 optimal weight: 0.8980 chunk 793 optimal weight: 50.0000 chunk 223 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 459 ASN A1129 ASN A1332 GLN B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B1071 ASN C 262 GLN I 45 GLN I 74 GLN M 405 GLN M 421 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 842 ASN ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 79 GLN a 187 GLN a 228 GLN b 616 HIS d 240 HIS ** d1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 65438 Z= 0.212 Angle : 0.539 12.903 87694 Z= 0.279 Chirality : 0.044 0.186 8256 Planarity : 0.004 0.054 11939 Dihedral : 11.218 179.655 10908 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.99 % Allowed : 18.78 % Favored : 78.23 % 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: 0.20 (0.09), residues: 8992 helix: 1.73 (0.09), residues: 3440 sheet: -0.57 (0.13), residues: 1491 loop : -0.99 (0.10), residues: 4061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 214 HIS 0.006 0.001 HIS M1120 PHE 0.027 0.002 PHE B 320 TYR 0.028 0.001 TYR B 916 ARG 0.011 0.000 ARG a 92 *********************** 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 1250 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1082 time to evaluate : 5.508 Fit side-chains 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: A 112 PHE cc_start: 0.8715 (t80) cc_final: 0.8493 (t80) REVERT: A 220 ARG cc_start: 0.8130 (tpt-90) cc_final: 0.7910 (tpt-90) REVERT: A 223 GLU cc_start: 0.7809 (tp30) cc_final: 0.7229 (tp30) REVERT: A 274 ASP cc_start: 0.7375 (t70) cc_final: 0.7002 (t70) REVERT: A 285 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8050 (mtmt) REVERT: A 382 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7302 (ttm110) REVERT: A 408 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8332 (mtp180) REVERT: A 446 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8615 (m) REVERT: A 556 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 682 ILE cc_start: 0.8775 (mt) cc_final: 0.8407 (mt) REVERT: A 743 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7157 (ttp-110) REVERT: A 757 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: A 863 ARG cc_start: 0.9075 (mtp180) cc_final: 0.8864 (mtp180) REVERT: A 1168 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8098 (mtpp) REVERT: A 1228 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7391 (mpt) REVERT: A 1259 ILE cc_start: 0.8324 (mp) cc_final: 0.8018 (mm) REVERT: A 1286 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7793 (mmm-85) REVERT: A 1287 CYS cc_start: 0.7877 (m) cc_final: 0.7609 (t) REVERT: A 1325 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7224 (p0) REVERT: A 1350 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8431 (mtpp) REVERT: A 1423 ASP cc_start: 0.7283 (t0) cc_final: 0.7001 (t0) REVERT: B 95 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8404 (mmtm) REVERT: B 222 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8053 (mtp85) REVERT: B 340 LYS cc_start: 0.7593 (tttp) cc_final: 0.7338 (tttt) REVERT: B 358 GLU cc_start: 0.7631 (pm20) cc_final: 0.7274 (pm20) REVERT: B 359 THR cc_start: 0.8858 (m) cc_final: 0.8654 (t) REVERT: B 388 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (t80) REVERT: B 394 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 403 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8766 (mp) REVERT: B 613 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8143 (mtt-85) REVERT: B 683 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7844 (mt0) REVERT: B 1081 ASP cc_start: 0.7771 (t0) cc_final: 0.7510 (t0) REVERT: B 1101 GLN cc_start: 0.8394 (mt0) cc_final: 0.8150 (mt0) REVERT: B 1143 LYS cc_start: 0.8265 (pttt) cc_final: 0.7903 (mtmt) REVERT: C 27 ASP cc_start: 0.8017 (m-30) cc_final: 0.7524 (t70) REVERT: C 94 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 39 MET cc_start: 0.8101 (ppp) cc_final: 0.7810 (ppp) REVERT: D 62 MET cc_start: 0.8076 (mmp) cc_final: 0.7854 (mmp) REVERT: D 73 ARG cc_start: 0.7917 (mpt180) cc_final: 0.7452 (mpt180) REVERT: E 57 ASP cc_start: 0.7849 (m-30) cc_final: 0.7605 (m-30) REVERT: E 132 GLN cc_start: 0.8309 (pt0) cc_final: 0.7985 (tt0) REVERT: E 166 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7540 (mtm-85) REVERT: F 91 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9054 (mt) REVERT: G 44 PHE cc_start: 0.8050 (m-80) cc_final: 0.7839 (m-80) REVERT: G 75 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7665 (mp) REVERT: G 80 PHE cc_start: 0.8451 (m-80) cc_final: 0.8182 (m-80) REVERT: G 93 ASN cc_start: 0.7477 (m110) cc_final: 0.6895 (m-40) REVERT: G 129 LYS cc_start: 0.8620 (ptmt) cc_final: 0.7950 (ptpp) REVERT: G 166 ASP cc_start: 0.8033 (m-30) cc_final: 0.7295 (m-30) REVERT: H 20 LYS cc_start: 0.8933 (tptm) cc_final: 0.8617 (tptm) REVERT: H 107 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7484 (mm-30) REVERT: H 138 ASP cc_start: 0.7254 (m-30) cc_final: 0.6967 (m-30) REVERT: H 146 LYS cc_start: 0.8563 (tttt) cc_final: 0.8253 (ttpt) REVERT: I 56 ASN cc_start: 0.8534 (t0) cc_final: 0.8100 (t0) REVERT: K 47 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8789 (tttp) REVERT: K 68 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: K 110 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7854 (ttpp) REVERT: M 383 TYR cc_start: 0.8077 (m-80) cc_final: 0.7472 (m-80) REVERT: M 523 MET cc_start: 0.7045 (ptm) cc_final: 0.6824 (ppp) REVERT: M 585 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8704 (mm) REVERT: M 601 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8505 (tm) REVERT: M 623 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7808 (tmmm) REVERT: M 724 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: M 731 ASN cc_start: 0.8542 (m-40) cc_final: 0.8292 (m-40) REVERT: M 792 HIS cc_start: 0.6809 (t-90) cc_final: 0.6537 (t-170) REVERT: M 894 MET cc_start: 0.7394 (ttp) cc_final: 0.7162 (mtm) REVERT: M 941 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7979 (mmtm) REVERT: M 956 ASN cc_start: 0.7897 (t0) cc_final: 0.7534 (t0) REVERT: M 1167 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8362 (pp) REVERT: a 6 SER cc_start: 0.8488 (p) cc_final: 0.8194 (m) REVERT: a 12 LEU cc_start: 0.9114 (mt) cc_final: 0.8887 (mt) REVERT: a 16 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7194 (mt) REVERT: a 33 ASN cc_start: 0.7523 (t0) cc_final: 0.7171 (t0) REVERT: a 55 GLU cc_start: 0.7983 (pt0) cc_final: 0.7755 (pt0) REVERT: a 79 GLN cc_start: 0.8174 (mp10) cc_final: 0.7925 (mp10) REVERT: a 172 ASP cc_start: 0.8348 (t0) cc_final: 0.8071 (t70) REVERT: a 198 TYR cc_start: 0.8492 (m-80) cc_final: 0.8240 (m-80) REVERT: a 273 ASN cc_start: 0.8832 (t0) cc_final: 0.8392 (t0) REVERT: a 275 SER cc_start: 0.8564 (t) cc_final: 0.8097 (p) REVERT: b 605 HIS cc_start: 0.6975 (m90) cc_final: 0.6557 (m-70) REVERT: b 630 LEU cc_start: 0.8756 (mt) cc_final: 0.8541 (mt) REVERT: b 729 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8665 (tttm) REVERT: b 936 TRP cc_start: 0.8805 (m100) cc_final: 0.8586 (m100) REVERT: b 946 GLU cc_start: 0.8011 (tt0) cc_final: 0.7762 (tt0) REVERT: d 151 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6936 (mm-30) REVERT: d 191 LYS cc_start: 0.8117 (tttt) cc_final: 0.7881 (tttp) REVERT: d 366 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6825 (t0) REVERT: d 797 HIS cc_start: 0.8118 (m-70) cc_final: 0.7635 (m-70) REVERT: d 867 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7470 (mtmm) REVERT: d 950 ASN cc_start: 0.8062 (m110) cc_final: 0.7763 (m-40) REVERT: d 1063 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7434 (mttt) REVERT: d 1134 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7166 (mm-30) outliers start: 168 outliers final: 67 residues processed: 1175 average time/residue: 1.4387 time to fit residues: 2176.7054 Evaluate side-chains 1119 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1031 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 623 LYS Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 941 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1167 ILE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain M residue 1245 LEU Chi-restraints excluded: chain M residue 1276 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain b residue 684 GLU Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 366 ASP Chi-restraints excluded: chain d residue 833 THR Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 930 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 297 optimal weight: 0.9980 chunk 796 optimal weight: 40.0000 chunk 174 optimal weight: 2.9990 chunk 519 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 885 optimal weight: 50.0000 chunk 734 optimal weight: 5.9990 chunk 409 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 292 optimal weight: 6.9990 chunk 464 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 735 GLN A 861 GLN A1129 ASN A1332 GLN B 460 HIS B 593 GLN B1003 ASN B1145 GLN C 262 GLN I 45 GLN I 74 GLN M 398 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 228 GLN b 616 HIS d 240 HIS d 255 GLN d1056 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 65438 Z= 0.346 Angle : 0.580 12.682 87694 Z= 0.299 Chirality : 0.046 0.200 8256 Planarity : 0.004 0.064 11939 Dihedral : 11.228 179.253 10908 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.36 % Allowed : 19.19 % Favored : 77.45 % 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: 0.26 (0.09), residues: 8992 helix: 1.79 (0.09), residues: 3460 sheet: -0.49 (0.13), residues: 1489 loop : -1.00 (0.10), residues: 4043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 835 HIS 0.006 0.001 HIS C 194 PHE 0.024 0.002 PHE B 320 TYR 0.028 0.002 TYR B 916 ARG 0.009 0.001 ARG H 24 *********************** 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: 189 poor density : 1059 time to evaluate : 5.499 Fit side-chains 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: A 89 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: A 112 PHE cc_start: 0.8712 (t80) cc_final: 0.8499 (t80) REVERT: A 220 ARG cc_start: 0.8188 (tpt-90) cc_final: 0.7982 (tpt-90) REVERT: A 223 GLU cc_start: 0.7832 (tp30) cc_final: 0.7225 (tp30) REVERT: A 274 ASP cc_start: 0.7400 (t70) cc_final: 0.6950 (t70) REVERT: A 285 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8161 (mtmt) REVERT: A 382 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7271 (ttm110) REVERT: A 408 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8343 (mtp180) REVERT: A 556 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: A 682 ILE cc_start: 0.8795 (mt) cc_final: 0.8425 (mt) REVERT: A 743 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.7094 (ttp-110) REVERT: A 757 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: A 1168 LYS cc_start: 0.8516 (mmmm) cc_final: 0.7961 (mtpp) REVERT: A 1224 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7317 (mtt-85) REVERT: A 1259 ILE cc_start: 0.8345 (mp) cc_final: 0.8044 (mm) REVERT: A 1287 CYS cc_start: 0.7918 (m) cc_final: 0.7679 (t) REVERT: A 1325 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7194 (p0) REVERT: A 1350 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8468 (mtpp) REVERT: A 1423 ASP cc_start: 0.7378 (t0) cc_final: 0.7151 (t0) REVERT: B 95 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8448 (mmtm) REVERT: B 222 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7834 (mtp85) REVERT: B 340 LYS cc_start: 0.7575 (tttp) cc_final: 0.7310 (tttt) REVERT: B 358 GLU cc_start: 0.7649 (pm20) cc_final: 0.7361 (pm20) REVERT: B 394 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 403 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8682 (mp) REVERT: B 407 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: B 683 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7871 (mt0) REVERT: B 916 TYR cc_start: 0.7994 (m-80) cc_final: 0.7746 (m-80) REVERT: B 1081 ASP cc_start: 0.7820 (t0) cc_final: 0.7505 (t0) REVERT: B 1101 GLN cc_start: 0.8506 (mt0) cc_final: 0.8185 (mt0) REVERT: C 27 ASP cc_start: 0.8028 (m-30) cc_final: 0.7507 (t70) REVERT: C 94 CYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7602 (p) REVERT: D 39 MET cc_start: 0.8084 (ppp) cc_final: 0.7806 (ppp) REVERT: D 73 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7396 (mpt180) REVERT: E 57 ASP cc_start: 0.7827 (m-30) cc_final: 0.7597 (m-30) REVERT: E 132 GLN cc_start: 0.8403 (pt0) cc_final: 0.8045 (tt0) REVERT: F 91 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9062 (mt) REVERT: G 80 PHE cc_start: 0.8458 (m-80) cc_final: 0.8187 (m-80) REVERT: G 93 ASN cc_start: 0.7504 (m110) cc_final: 0.6965 (m-40) REVERT: G 100 GLU cc_start: 0.7048 (mp0) cc_final: 0.6634 (mp0) REVERT: G 166 ASP cc_start: 0.7979 (m-30) cc_final: 0.7532 (m-30) REVERT: H 20 LYS cc_start: 0.8950 (tptm) cc_final: 0.8624 (tptm) REVERT: H 107 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7528 (mm-30) REVERT: H 138 ASP cc_start: 0.7300 (m-30) cc_final: 0.7008 (m-30) REVERT: H 146 LYS cc_start: 0.8669 (tttt) cc_final: 0.8348 (ttpt) REVERT: I 32 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7869 (p0) REVERT: I 56 ASN cc_start: 0.8560 (t0) cc_final: 0.8046 (t0) REVERT: J 1 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: K 47 LYS cc_start: 0.9104 (tmmt) cc_final: 0.8824 (tttp) REVERT: K 68 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: K 110 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7846 (ttpp) REVERT: M 383 TYR cc_start: 0.8077 (m-80) cc_final: 0.7487 (m-80) REVERT: M 585 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8704 (mm) REVERT: M 601 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8536 (tm) REVERT: M 623 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7798 (tmmm) REVERT: M 714 GLU cc_start: 0.7893 (tt0) cc_final: 0.7648 (tp30) REVERT: M 724 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: M 731 ASN cc_start: 0.8541 (m-40) cc_final: 0.8310 (m-40) REVERT: M 792 HIS cc_start: 0.6893 (t-90) cc_final: 0.6626 (t-170) REVERT: M 894 MET cc_start: 0.7380 (ttp) cc_final: 0.6967 (mtm) REVERT: M 941 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8010 (mmtm) REVERT: M 1134 TYR cc_start: 0.8122 (m-80) cc_final: 0.7585 (m-80) REVERT: a 6 SER cc_start: 0.8483 (p) cc_final: 0.8193 (m) REVERT: a 16 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7115 (mt) REVERT: a 20 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7388 (mtp85) REVERT: a 33 ASN cc_start: 0.7443 (t0) cc_final: 0.7148 (t0) REVERT: a 99 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7369 (mmp80) REVERT: a 172 ASP cc_start: 0.8399 (t0) cc_final: 0.8107 (t70) REVERT: a 273 ASN cc_start: 0.8819 (t0) cc_final: 0.8602 (t0) REVERT: a 275 SER cc_start: 0.8571 (t) cc_final: 0.8266 (p) REVERT: b 605 HIS cc_start: 0.6985 (m90) cc_final: 0.6574 (m-70) REVERT: b 630 LEU cc_start: 0.8770 (mt) cc_final: 0.8566 (mt) REVERT: b 631 MET cc_start: 0.7238 (mtt) cc_final: 0.6930 (mtm) REVERT: b 729 LYS cc_start: 0.9055 (tmmt) cc_final: 0.8684 (tttm) REVERT: b 946 GLU cc_start: 0.8090 (tt0) cc_final: 0.7824 (tt0) REVERT: d 151 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: d 191 LYS cc_start: 0.8103 (tttt) cc_final: 0.7864 (tttp) REVERT: d 797 HIS cc_start: 0.8155 (m-70) cc_final: 0.7640 (m-70) REVERT: d 867 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7533 (mtmm) REVERT: d 950 ASN cc_start: 0.8134 (m110) cc_final: 0.7850 (m-40) REVERT: d 1063 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7426 (mttt) REVERT: d 1134 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7426 (mm-30) outliers start: 189 outliers final: 90 residues processed: 1168 average time/residue: 1.4302 time to fit residues: 2153.8732 Evaluate side-chains 1140 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1028 time to evaluate : 5.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 474 ASP Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 623 LYS Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 800 ASN Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 941 LYS Chi-restraints excluded: chain M residue 951 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain M residue 1276 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain b residue 616 HIS Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 718 ASN Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 151 GLU Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 720 SER Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 1006 VAL Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain d residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 853 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 504 optimal weight: 5.9990 chunk 646 optimal weight: 0.6980 chunk 500 optimal weight: 30.0000 chunk 745 optimal weight: 1.9990 chunk 494 optimal weight: 9.9990 chunk 881 optimal weight: 40.0000 chunk 551 optimal weight: 9.9990 chunk 537 optimal weight: 40.0000 chunk 407 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 735 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B1115 GLN C 262 GLN I 45 GLN I 74 GLN M 405 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 180 HIS a 183 GLN a 228 GLN b 616 HIS b 618 HIS b 655 ASN d 240 HIS d 255 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 65438 Z= 0.394 Angle : 0.602 13.748 87694 Z= 0.310 Chirality : 0.047 0.253 8256 Planarity : 0.004 0.119 11939 Dihedral : 11.240 179.135 10908 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.59 % Allowed : 19.44 % Favored : 76.97 % 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: 0.26 (0.09), residues: 8992 helix: 1.78 (0.09), residues: 3474 sheet: -0.49 (0.13), residues: 1519 loop : -1.00 (0.10), residues: 3999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 835 HIS 0.011 0.001 HIS b 616 PHE 0.027 0.002 PHE G 158 TYR 0.029 0.002 TYR G 167 ARG 0.009 0.001 ARG J 47 *********************** 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 1258 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1056 time to evaluate : 5.514 Fit side-chains 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: A 89 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: A 223 GLU cc_start: 0.7744 (tp30) cc_final: 0.7463 (mm-30) REVERT: A 274 ASP cc_start: 0.7523 (t70) cc_final: 0.7032 (t70) REVERT: A 285 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8150 (mtmt) REVERT: A 382 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7528 (ttm110) REVERT: A 408 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8330 (mtp180) REVERT: A 556 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: A 682 ILE cc_start: 0.8814 (mt) cc_final: 0.8459 (mt) REVERT: A 743 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.7072 (ttp-110) REVERT: A 757 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: A 1168 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8006 (mtpp) REVERT: A 1224 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7306 (mtt-85) REVERT: A 1228 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7323 (mpt) REVERT: A 1259 ILE cc_start: 0.8333 (mp) cc_final: 0.8035 (mm) REVERT: A 1287 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7695 (t) REVERT: A 1325 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7297 (p0) REVERT: A 1350 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8458 (mtpp) REVERT: B 90 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 95 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8468 (mmtm) REVERT: B 222 ARG cc_start: 0.8387 (mtp85) cc_final: 0.7821 (mtp85) REVERT: B 340 LYS cc_start: 0.7577 (tttp) cc_final: 0.7323 (tttt) REVERT: B 358 GLU cc_start: 0.7614 (pm20) cc_final: 0.7313 (pm20) REVERT: B 388 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 394 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7590 (t0) REVERT: B 403 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 407 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: B 471 ASN cc_start: 0.8935 (t0) cc_final: 0.8677 (t0) REVERT: B 613 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8117 (mtt-85) REVERT: B 683 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7868 (mt0) REVERT: B 916 TYR cc_start: 0.8035 (m-80) cc_final: 0.7811 (m-80) REVERT: B 1080 ARG cc_start: 0.7765 (mpp80) cc_final: 0.7402 (mtp180) REVERT: B 1081 ASP cc_start: 0.7866 (t0) cc_final: 0.7547 (t0) REVERT: B 1101 GLN cc_start: 0.8577 (mt0) cc_final: 0.8289 (mt0) REVERT: C 27 ASP cc_start: 0.8018 (m-30) cc_final: 0.7509 (t70) REVERT: C 94 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7612 (p) REVERT: D 39 MET cc_start: 0.8067 (ppp) cc_final: 0.7786 (ppp) REVERT: D 73 ARG cc_start: 0.7898 (mpt180) cc_final: 0.7515 (mpt180) REVERT: E 46 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7714 (p0) REVERT: E 57 ASP cc_start: 0.7802 (m-30) cc_final: 0.7580 (m-30) REVERT: F 91 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9042 (mt) REVERT: G 80 PHE cc_start: 0.8446 (m-80) cc_final: 0.8181 (m-80) REVERT: G 93 ASN cc_start: 0.7507 (m110) cc_final: 0.6989 (m-40) REVERT: G 100 GLU cc_start: 0.7099 (mp0) cc_final: 0.6714 (mp0) REVERT: G 129 LYS cc_start: 0.8517 (ptpt) cc_final: 0.7969 (ptpp) REVERT: G 166 ASP cc_start: 0.8152 (m-30) cc_final: 0.7260 (m-30) REVERT: H 20 LYS cc_start: 0.8976 (tptm) cc_final: 0.8638 (tptm) REVERT: H 107 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7539 (mm-30) REVERT: H 138 ASP cc_start: 0.7352 (m-30) cc_final: 0.7045 (m-30) REVERT: H 146 LYS cc_start: 0.8667 (tttt) cc_final: 0.8348 (ttpt) REVERT: I 56 ASN cc_start: 0.8537 (t0) cc_final: 0.8052 (t0) REVERT: J 1 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.6943 (mtp) REVERT: K 8 GLU cc_start: 0.8178 (tt0) cc_final: 0.7806 (tt0) REVERT: K 47 LYS cc_start: 0.9115 (tmmt) cc_final: 0.8828 (tttp) REVERT: K 68 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: K 110 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7846 (ttpp) REVERT: M 585 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8684 (mm) REVERT: M 601 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8576 (tm) REVERT: M 622 LYS cc_start: 0.8398 (tttt) cc_final: 0.8046 (ttpt) REVERT: M 623 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7674 (tmmm) REVERT: M 714 GLU cc_start: 0.7891 (tt0) cc_final: 0.7642 (tp30) REVERT: M 724 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: M 731 ASN cc_start: 0.8543 (m-40) cc_final: 0.8315 (m-40) REVERT: M 792 HIS cc_start: 0.6915 (t-90) cc_final: 0.6670 (t-170) REVERT: M 894 MET cc_start: 0.7400 (ttp) cc_final: 0.6984 (mtm) REVERT: M 941 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8023 (mmtm) REVERT: M 1134 TYR cc_start: 0.8022 (m-80) cc_final: 0.7264 (m-80) REVERT: a 6 SER cc_start: 0.8479 (p) cc_final: 0.8218 (m) REVERT: a 12 LEU cc_start: 0.9156 (mt) cc_final: 0.8881 (mt) REVERT: a 16 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7133 (mt) REVERT: a 33 ASN cc_start: 0.7328 (t0) cc_final: 0.7088 (t0) REVERT: a 99 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7406 (mmp80) REVERT: a 172 ASP cc_start: 0.8446 (t0) cc_final: 0.8159 (t70) REVERT: b 555 ARG cc_start: 0.5883 (tpp-160) cc_final: 0.5682 (tpp-160) REVERT: b 605 HIS cc_start: 0.6995 (m90) cc_final: 0.6586 (m-70) REVERT: b 729 LYS cc_start: 0.9052 (tmmt) cc_final: 0.8678 (tttm) REVERT: b 851 TRP cc_start: 0.7795 (m-10) cc_final: 0.7585 (m-10) REVERT: b 946 GLU cc_start: 0.8122 (tt0) cc_final: 0.7841 (tt0) REVERT: d 151 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: d 191 LYS cc_start: 0.8127 (tttt) cc_final: 0.7858 (tttp) REVERT: d 797 HIS cc_start: 0.8167 (m-70) cc_final: 0.7667 (m-70) REVERT: d 950 ASN cc_start: 0.8149 (m110) cc_final: 0.7883 (m-40) REVERT: d 1063 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7427 (mttt) REVERT: d 1134 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7404 (mm-30) outliers start: 202 outliers final: 104 residues processed: 1170 average time/residue: 1.4167 time to fit residues: 2140.9106 Evaluate side-chains 1149 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1019 time to evaluate : 5.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 601 LEU Chi-restraints excluded: chain M residue 623 LYS Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 799 VAL Chi-restraints excluded: chain M residue 800 ASN Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 849 THR Chi-restraints excluded: chain M residue 854 ASN Chi-restraints excluded: chain M residue 905 ASP Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 941 LYS Chi-restraints excluded: chain M residue 951 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1157 THR Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain M residue 1276 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 718 ASN Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 151 GLU Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 350 MET Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 720 SER Chi-restraints excluded: chain d residue 833 THR Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain d residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 545 optimal weight: 30.0000 chunk 352 optimal weight: 20.0000 chunk 526 optimal weight: 8.9990 chunk 265 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 560 optimal weight: 50.0000 chunk 600 optimal weight: 30.0000 chunk 436 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 693 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 576 GLN A 735 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B 930 GLN B1115 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN I 45 GLN I 74 GLN ** K 69 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 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 79 GLN a 183 GLN a 343 GLN b 616 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS d 255 GLN d 261 HIS d 343 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.143 65438 Z= 0.704 Angle : 0.739 14.869 87694 Z= 0.381 Chirality : 0.055 0.269 8256 Planarity : 0.005 0.091 11939 Dihedral : 11.430 178.858 10908 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.79 % Favored : 95.20 % Rotamer: Outliers : 3.86 % Allowed : 19.58 % Favored : 76.56 % 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: -0.04 (0.09), residues: 8992 helix: 1.49 (0.09), residues: 3495 sheet: -0.61 (0.13), residues: 1533 loop : -1.16 (0.09), residues: 3964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP b 835 HIS 0.009 0.002 HIS D 38 PHE 0.027 0.003 PHE A 548 TYR 0.031 0.003 TYR B 916 ARG 0.015 0.001 ARG J 47 *********************** 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 1263 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1046 time to evaluate : 5.436 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: A 89 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 225 PHE cc_start: 0.9116 (m-10) cc_final: 0.8828 (m-10) REVERT: A 285 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8203 (mtmt) REVERT: A 317 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7595 (ttt) REVERT: A 382 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7545 (ttm110) REVERT: A 556 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: A 743 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7160 (ttp-110) REVERT: A 757 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: A 1085 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: A 1168 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8114 (mtpp) REVERT: A 1224 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7328 (mtt-85) REVERT: A 1228 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7329 (mpt) REVERT: A 1259 ILE cc_start: 0.8424 (mp) cc_final: 0.8137 (mm) REVERT: A 1287 CYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7850 (t) REVERT: A 1325 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7377 (p0) REVERT: A 1350 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8439 (mtpp) REVERT: A 1386 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 1455 SER cc_start: 0.8938 (m) cc_final: 0.8655 (m) REVERT: B 90 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 95 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8506 (mmtm) REVERT: B 222 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8280 (mtp85) REVERT: B 340 LYS cc_start: 0.7700 (tttp) cc_final: 0.7403 (tttt) REVERT: B 342 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 358 GLU cc_start: 0.7593 (pm20) cc_final: 0.7333 (pm20) REVERT: B 388 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 394 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7659 (t0) REVERT: B 403 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 407 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: B 550 MET cc_start: 0.9185 (ttp) cc_final: 0.8762 (ttp) REVERT: B 582 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: B 610 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7228 (mtt180) REVERT: B 613 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8118 (mtt-85) REVERT: B 916 TYR cc_start: 0.8100 (m-80) cc_final: 0.7864 (m-80) REVERT: B 1080 ARG cc_start: 0.7797 (mpp80) cc_final: 0.7431 (mtp180) REVERT: B 1081 ASP cc_start: 0.7957 (t0) cc_final: 0.7544 (t0) REVERT: C 94 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 228 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8139 (ttm-80) REVERT: D 39 MET cc_start: 0.8074 (ppp) cc_final: 0.7756 (ppp) REVERT: D 70 ARG cc_start: 0.8555 (mtp180) cc_final: 0.8338 (mtp85) REVERT: D 73 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7346 (mpt180) REVERT: D 132 ASP cc_start: 0.8148 (m-30) cc_final: 0.7929 (m-30) REVERT: D 138 ARG cc_start: 0.7674 (tmm-80) cc_final: 0.7241 (ttm170) REVERT: E 46 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7777 (p0) REVERT: E 57 ASP cc_start: 0.7802 (m-30) cc_final: 0.7575 (m-30) REVERT: E 67 ASP cc_start: 0.7540 (t0) cc_final: 0.7117 (t0) REVERT: G 75 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7722 (mp) REVERT: G 80 PHE cc_start: 0.8454 (m-80) cc_final: 0.8068 (m-80) REVERT: G 93 ASN cc_start: 0.7569 (m110) cc_final: 0.7091 (m-40) REVERT: G 100 GLU cc_start: 0.7135 (mp0) cc_final: 0.6736 (mp0) REVERT: G 129 LYS cc_start: 0.8519 (ptpt) cc_final: 0.7954 (ptpp) REVERT: G 142 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7906 (mt-10) REVERT: H 20 LYS cc_start: 0.8965 (tptm) cc_final: 0.8501 (tptm) REVERT: H 103 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: H 107 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7611 (mm-30) REVERT: H 138 ASP cc_start: 0.7546 (m-30) cc_final: 0.7271 (m-30) REVERT: H 146 LYS cc_start: 0.8751 (tttt) cc_final: 0.8435 (ttpt) REVERT: I 56 ASN cc_start: 0.8612 (t0) cc_final: 0.8049 (t0) REVERT: I 88 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8177 (tttm) REVERT: J 1 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.6892 (mpp) REVERT: K 1 MET cc_start: 0.7083 (ttt) cc_final: 0.6878 (ttm) REVERT: K 8 GLU cc_start: 0.8322 (tt0) cc_final: 0.7972 (tt0) REVERT: K 110 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7829 (ttpp) REVERT: M 622 LYS cc_start: 0.8559 (tttt) cc_final: 0.8196 (ttpt) REVERT: M 623 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7661 (tmmm) REVERT: M 711 MET cc_start: 0.7845 (ptm) cc_final: 0.7611 (ptt) REVERT: M 724 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: M 731 ASN cc_start: 0.8579 (m-40) cc_final: 0.8363 (m-40) REVERT: M 894 MET cc_start: 0.7541 (ttp) cc_final: 0.7163 (mtm) REVERT: M 941 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8044 (mmtm) REVERT: M 1134 TYR cc_start: 0.8123 (m-80) cc_final: 0.7182 (m-80) REVERT: M 1165 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8415 (ptpp) REVERT: M 1261 MET cc_start: -0.1993 (ppp) cc_final: -0.2290 (ptp) REVERT: a 13 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: a 16 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7422 (mt) REVERT: a 88 CYS cc_start: 0.7578 (m) cc_final: 0.7254 (m) REVERT: a 99 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7482 (mmp80) REVERT: a 172 ASP cc_start: 0.8499 (t0) cc_final: 0.8207 (t70) REVERT: b 520 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: b 605 HIS cc_start: 0.7147 (m90) cc_final: 0.6695 (m-70) REVERT: b 631 MET cc_start: 0.7399 (mtt) cc_final: 0.7127 (mtm) REVERT: b 713 MET cc_start: 0.7392 (mmt) cc_final: 0.7172 (mmp) REVERT: b 729 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8701 (tttm) REVERT: b 946 GLU cc_start: 0.8167 (tt0) cc_final: 0.7847 (tt0) REVERT: d 151 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6921 (mm-30) REVERT: d 218 MET cc_start: 0.8005 (mtp) cc_final: 0.7723 (ttm) REVERT: d 875 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: d 950 ASN cc_start: 0.8160 (m110) cc_final: 0.7935 (m-40) REVERT: d 1063 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7434 (mttt) REVERT: d 1134 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7462 (mm-30) outliers start: 217 outliers final: 101 residues processed: 1185 average time/residue: 1.4350 time to fit residues: 2201.6740 Evaluate side-chains 1155 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1022 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 306 LYS Chi-restraints excluded: chain M residue 457 MET Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 623 LYS Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 799 VAL Chi-restraints excluded: chain M residue 800 ASN Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 849 THR Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 941 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1157 THR Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1165 LYS Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain a residue 2 LEU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 224 ILE Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain b residue 520 GLU Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 718 ASN Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 720 SER Chi-restraints excluded: chain d residue 823 LYS Chi-restraints excluded: chain d residue 875 GLU Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1006 VAL Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain d residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 802 optimal weight: 20.0000 chunk 844 optimal weight: 50.0000 chunk 770 optimal weight: 0.9990 chunk 821 optimal weight: 2.9990 chunk 494 optimal weight: 50.0000 chunk 358 optimal weight: 1.9990 chunk 645 optimal weight: 0.9990 chunk 252 optimal weight: 0.6980 chunk 742 optimal weight: 8.9990 chunk 777 optimal weight: 40.0000 chunk 818 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 289 GLN A 341 GLN A 576 GLN A 731 ASN A 735 GLN A 861 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 262 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 74 GLN M 405 GLN M 421 GLN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 183 GLN a 228 GLN b 616 HIS b 866 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 65438 Z= 0.263 Angle : 0.585 15.122 87694 Z= 0.300 Chirality : 0.045 0.270 8256 Planarity : 0.004 0.054 11939 Dihedral : 11.264 178.998 10908 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.63 % Allowed : 21.11 % Favored : 76.25 % 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: 0.27 (0.09), residues: 8992 helix: 1.82 (0.09), residues: 3474 sheet: -0.44 (0.13), residues: 1476 loop : -1.04 (0.09), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 835 HIS 0.010 0.001 HIS M 792 PHE 0.030 0.002 PHE G 158 TYR 0.032 0.001 TYR G 167 ARG 0.019 0.001 ARG A 220 *********************** 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 1203 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1055 time to evaluate : 5.523 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: A 225 PHE cc_start: 0.9062 (m-10) cc_final: 0.8848 (m-10) REVERT: A 285 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8229 (mtmt) REVERT: A 382 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7266 (ttm110) REVERT: A 446 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8672 (m) REVERT: A 556 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: A 682 ILE cc_start: 0.8823 (mt) cc_final: 0.8481 (mt) REVERT: A 743 ARG cc_start: 0.7316 (ttm-80) cc_final: 0.7115 (ttp-110) REVERT: A 757 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: A 1085 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: A 1168 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8206 (mtpp) REVERT: A 1228 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: A 1259 ILE cc_start: 0.8401 (mp) cc_final: 0.8149 (mm) REVERT: A 1325 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7485 (p0) REVERT: A 1350 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8414 (mtpp) REVERT: B 90 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 95 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8492 (mmtm) REVERT: B 222 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7814 (mtp85) REVERT: B 340 LYS cc_start: 0.7747 (tttp) cc_final: 0.7470 (tttt) REVERT: B 344 GLN cc_start: 0.7800 (tt0) cc_final: 0.7469 (tm-30) REVERT: B 358 GLU cc_start: 0.7589 (pm20) cc_final: 0.7315 (pm20) REVERT: B 359 THR cc_start: 0.9015 (m) cc_final: 0.8750 (t) REVERT: B 388 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8314 (t80) REVERT: B 394 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7578 (t0) REVERT: B 403 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8750 (mp) REVERT: B 582 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 610 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7252 (mtt180) REVERT: B 613 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8128 (mtt-85) REVERT: B 638 ARG cc_start: 0.8004 (ptt-90) cc_final: 0.7717 (ptt-90) REVERT: B 683 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7791 (mt0) REVERT: B 840 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7602 (mmm) REVERT: B 916 TYR cc_start: 0.8055 (m-80) cc_final: 0.7822 (m-80) REVERT: B 1080 ARG cc_start: 0.7735 (mpp80) cc_final: 0.7386 (mtp180) REVERT: B 1081 ASP cc_start: 0.7758 (t0) cc_final: 0.7377 (t0) REVERT: B 1101 GLN cc_start: 0.8577 (mt0) cc_final: 0.8275 (mt0) REVERT: C 94 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7586 (p) REVERT: D 39 MET cc_start: 0.7944 (ppp) cc_final: 0.7634 (ppp) REVERT: D 73 ARG cc_start: 0.7823 (mpt180) cc_final: 0.7417 (mpt180) REVERT: D 132 ASP cc_start: 0.8101 (m-30) cc_final: 0.7873 (m-30) REVERT: D 138 ARG cc_start: 0.7471 (tmm-80) cc_final: 0.7102 (ttm170) REVERT: E 57 ASP cc_start: 0.7789 (m-30) cc_final: 0.7577 (m-30) REVERT: E 67 ASP cc_start: 0.7547 (t0) cc_final: 0.7131 (t0) REVERT: E 91 CYS cc_start: 0.8872 (t) cc_final: 0.8463 (m) REVERT: E 127 LEU cc_start: 0.9243 (pt) cc_final: 0.9011 (pp) REVERT: G 80 PHE cc_start: 0.8446 (m-80) cc_final: 0.8129 (m-80) REVERT: G 93 ASN cc_start: 0.7510 (m110) cc_final: 0.7149 (m-40) REVERT: G 100 GLU cc_start: 0.7202 (mp0) cc_final: 0.6775 (mp0) REVERT: G 129 LYS cc_start: 0.8533 (ptpt) cc_final: 0.7967 (ptpp) REVERT: G 166 ASP cc_start: 0.7912 (m-30) cc_final: 0.7307 (m-30) REVERT: H 20 LYS cc_start: 0.8978 (tptm) cc_final: 0.8614 (tptm) REVERT: H 103 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: H 107 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7571 (mm-30) REVERT: H 138 ASP cc_start: 0.7313 (m-30) cc_final: 0.7009 (m-30) REVERT: H 146 LYS cc_start: 0.8587 (tttt) cc_final: 0.8275 (ttpt) REVERT: I 56 ASN cc_start: 0.8584 (t0) cc_final: 0.8020 (t0) REVERT: K 8 GLU cc_start: 0.8284 (tt0) cc_final: 0.8009 (tt0) REVERT: K 47 LYS cc_start: 0.9082 (tmmt) cc_final: 0.8808 (tttp) REVERT: K 110 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7841 (ttpp) REVERT: M 585 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8656 (mm) REVERT: M 622 LYS cc_start: 0.8325 (tttt) cc_final: 0.7964 (ttpt) REVERT: M 623 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7762 (tmmm) REVERT: M 711 MET cc_start: 0.7705 (ptm) cc_final: 0.7422 (ptt) REVERT: M 714 GLU cc_start: 0.7854 (tt0) cc_final: 0.7643 (tp30) REVERT: M 724 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: M 731 ASN cc_start: 0.8540 (m-40) cc_final: 0.8336 (m-40) REVERT: M 810 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7132 (ttt-90) REVERT: M 894 MET cc_start: 0.7459 (ttp) cc_final: 0.7028 (mtm) REVERT: M 926 GLU cc_start: 0.7679 (tp30) cc_final: 0.7387 (tp30) REVERT: M 1134 TYR cc_start: 0.8023 (m-80) cc_final: 0.7283 (m-80) REVERT: M 1261 MET cc_start: -0.1863 (ppp) cc_final: -0.2214 (ptp) REVERT: a 13 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: a 16 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7452 (mt) REVERT: a 33 ASN cc_start: 0.7691 (t0) cc_final: 0.7213 (t0) REVERT: a 99 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7423 (mmp80) REVERT: a 172 ASP cc_start: 0.8524 (t0) cc_final: 0.8232 (t70) REVERT: a 292 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8036 (mmtp) REVERT: b 605 HIS cc_start: 0.7018 (m90) cc_final: 0.6569 (m-70) REVERT: b 631 MET cc_start: 0.7349 (mtt) cc_final: 0.7098 (mtm) REVERT: b 713 MET cc_start: 0.7287 (mmt) cc_final: 0.7087 (mmp) REVERT: b 729 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8677 (tttm) REVERT: b 946 GLU cc_start: 0.8180 (tt0) cc_final: 0.7856 (tt0) REVERT: d 151 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6890 (mm-30) REVERT: d 191 LYS cc_start: 0.8126 (tttt) cc_final: 0.7856 (tttp) REVERT: d 797 HIS cc_start: 0.8192 (m-70) cc_final: 0.7776 (m-70) REVERT: d 875 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: d 950 ASN cc_start: 0.8022 (m110) cc_final: 0.7783 (m-40) REVERT: d 1063 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7386 (mttt) REVERT: d 1134 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7436 (mm-30) outliers start: 148 outliers final: 75 residues processed: 1148 average time/residue: 1.4617 time to fit residues: 2157.3867 Evaluate side-chains 1117 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1020 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 623 LYS Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 951 LYS Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1163 ILE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 157 CYS Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain b residue 616 HIS Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain b residue 785 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 720 SER Chi-restraints excluded: chain d residue 875 GLU Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 1006 VAL 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: 30.0000 chunk 530 optimal weight: 30.0000 chunk 412 optimal weight: 1.9990 chunk 604 optimal weight: 30.0000 chunk 911 optimal weight: 20.0000 chunk 839 optimal weight: 0.9980 chunk 725 optimal weight: 50.0000 chunk 75 optimal weight: 0.2980 chunk 560 optimal weight: 50.0000 chunk 445 optimal weight: 1.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 289 GLN A 341 GLN A 576 GLN A 735 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B1115 GLN C 262 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 GLN M 421 GLN M 561 GLN ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1120 HIS M1264 HIS a 79 GLN a 169 GLN a 183 GLN a 228 GLN b 616 HIS b 664 GLN b 866 GLN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 904 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.163 65438 Z= 0.873 Angle : 0.813 14.981 87694 Z= 0.419 Chirality : 0.060 0.321 8256 Planarity : 0.006 0.104 11939 Dihedral : 11.497 178.663 10908 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.06 % Favored : 94.93 % Rotamer: Outliers : 2.56 % Allowed : 21.72 % Favored : 75.72 % 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: -0.16 (0.09), residues: 8992 helix: 1.37 (0.09), residues: 3493 sheet: -0.59 (0.13), residues: 1465 loop : -1.25 (0.09), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP b 835 HIS 0.014 0.002 HIS b 616 PHE 0.042 0.003 PHE A 112 TYR 0.038 0.003 TYR G 167 ARG 0.018 0.001 ARG J 47 ********************** 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 1176 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1032 time to evaluate : 5.635 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: A 193 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8586 (ttp80) REVERT: A 223 GLU cc_start: 0.7592 (tp30) cc_final: 0.7029 (tp30) REVERT: A 225 PHE cc_start: 0.9136 (m-10) cc_final: 0.8871 (m-10) REVERT: A 285 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8238 (mtmt) REVERT: A 319 ASP cc_start: 0.8385 (t70) cc_final: 0.8113 (t0) REVERT: A 382 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: A 439 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: A 556 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: A 757 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: A 893 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: A 1085 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: A 1168 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8287 (mtpp) REVERT: A 1228 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7328 (mpt) REVERT: A 1259 ILE cc_start: 0.8443 (mp) cc_final: 0.8155 (mm) REVERT: A 1325 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7470 (p0) REVERT: A 1350 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8435 (mtpp) REVERT: A 1455 SER cc_start: 0.8887 (m) cc_final: 0.8482 (m) REVERT: B 90 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: B 95 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8507 (mmtm) REVERT: B 336 ILE cc_start: 0.7831 (mt) cc_final: 0.7621 (mp) REVERT: B 340 LYS cc_start: 0.7815 (tttp) cc_final: 0.7523 (tttt) REVERT: B 344 GLN cc_start: 0.7943 (tt0) cc_final: 0.7531 (tm-30) REVERT: B 358 GLU cc_start: 0.7589 (pm20) cc_final: 0.7335 (pm20) REVERT: B 388 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 394 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 403 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8979 (mp) REVERT: B 610 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7370 (mtt180) REVERT: B 916 TYR cc_start: 0.8139 (m-80) cc_final: 0.7860 (m-80) REVERT: B 1080 ARG cc_start: 0.7801 (mpp80) cc_final: 0.7423 (mtp180) REVERT: B 1081 ASP cc_start: 0.8005 (t0) cc_final: 0.7650 (t0) REVERT: D 39 MET cc_start: 0.7996 (ppp) cc_final: 0.7710 (ppp) REVERT: D 70 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8217 (mtp180) REVERT: D 73 ARG cc_start: 0.7918 (mpt180) cc_final: 0.7320 (mpt180) REVERT: D 132 ASP cc_start: 0.8150 (m-30) cc_final: 0.7904 (m-30) REVERT: D 138 ARG cc_start: 0.7660 (tmm-80) cc_final: 0.7285 (ttm170) REVERT: E 57 ASP cc_start: 0.7801 (m-30) cc_final: 0.7585 (m-30) REVERT: E 67 ASP cc_start: 0.7608 (t0) cc_final: 0.7151 (t0) REVERT: E 132 GLN cc_start: 0.8605 (pt0) cc_final: 0.8292 (tt0) REVERT: G 75 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7560 (mp) REVERT: G 80 PHE cc_start: 0.8453 (m-80) cc_final: 0.8096 (m-80) REVERT: G 93 ASN cc_start: 0.7606 (m110) cc_final: 0.7227 (m-40) REVERT: G 129 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8008 (ptpp) REVERT: G 142 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7691 (mt-10) REVERT: G 166 ASP cc_start: 0.8099 (m-30) cc_final: 0.7561 (m-30) REVERT: H 20 LYS cc_start: 0.8964 (tptm) cc_final: 0.8647 (tptm) REVERT: H 103 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: H 107 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7653 (mm-30) REVERT: H 138 ASP cc_start: 0.7558 (m-30) cc_final: 0.7269 (m-30) REVERT: H 146 LYS cc_start: 0.8790 (tttt) cc_final: 0.8475 (ttpt) REVERT: I 56 ASN cc_start: 0.8658 (t0) cc_final: 0.8156 (t0) REVERT: I 88 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8265 (tttm) REVERT: J 1 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7101 (mtp) REVERT: K 8 GLU cc_start: 0.8336 (tt0) cc_final: 0.7975 (tt0) REVERT: K 110 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7844 (ttpp) REVERT: M 522 ASP cc_start: 0.7447 (p0) cc_final: 0.7115 (p0) REVERT: M 569 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8326 (tp) REVERT: M 622 LYS cc_start: 0.8574 (tttt) cc_final: 0.8108 (ttpt) REVERT: M 711 MET cc_start: 0.7843 (ptm) cc_final: 0.7611 (ptt) REVERT: M 714 GLU cc_start: 0.8002 (tt0) cc_final: 0.7766 (tp30) REVERT: M 724 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: M 792 HIS cc_start: 0.7074 (t-90) cc_final: 0.6571 (t-170) REVERT: M 894 MET cc_start: 0.7568 (ttp) cc_final: 0.7179 (mtm) REVERT: M 1134 TYR cc_start: 0.8153 (m-80) cc_final: 0.7300 (m-80) REVERT: a 16 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7442 (mt) REVERT: a 88 CYS cc_start: 0.7654 (m) cc_final: 0.7303 (m) REVERT: a 99 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7496 (mmp80) REVERT: a 172 ASP cc_start: 0.8490 (t0) cc_final: 0.8229 (t0) REVERT: b 534 MET cc_start: 0.4386 (tpt) cc_final: 0.4181 (tpt) REVERT: b 605 HIS cc_start: 0.7192 (m90) cc_final: 0.6736 (m-70) REVERT: b 713 MET cc_start: 0.7416 (mmt) cc_final: 0.7198 (mmp) REVERT: b 729 LYS cc_start: 0.9083 (tmmt) cc_final: 0.8723 (tttm) REVERT: b 946 GLU cc_start: 0.8077 (tt0) cc_final: 0.7735 (tt0) REVERT: b 1393 MET cc_start: 0.8747 (mtt) cc_final: 0.8250 (mtt) REVERT: d 151 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6990 (mm-30) REVERT: d 218 MET cc_start: 0.8042 (mtp) cc_final: 0.7698 (ttm) REVERT: d 875 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: d 950 ASN cc_start: 0.8144 (m110) cc_final: 0.7898 (m-40) REVERT: d 1063 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7420 (mttt) REVERT: d 1134 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7503 (mm-30) outliers start: 144 outliers final: 87 residues processed: 1130 average time/residue: 1.4732 time to fit residues: 2134.2953 Evaluate side-chains 1117 residues out of total 8056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1010 time to evaluate : 5.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 306 LYS Chi-restraints excluded: chain M residue 457 MET Chi-restraints excluded: chain M residue 474 ASP Chi-restraints excluded: chain M residue 569 LEU Chi-restraints excluded: chain M residue 572 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 672 ASP Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 732 LYS Chi-restraints excluded: chain M residue 799 VAL Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 929 GLN Chi-restraints excluded: chain M residue 1008 ASN Chi-restraints excluded: chain M residue 1067 ARG Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1143 SER Chi-restraints excluded: chain M residue 1145 ASN Chi-restraints excluded: chain M residue 1157 THR Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1234 ASN Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 255 SER Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 722 VAL Chi-restraints excluded: chain b residue 785 VAL Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 366 ASP Chi-restraints excluded: chain d residue 720 SER Chi-restraints excluded: chain d residue 875 GLU Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 916 THR Chi-restraints excluded: chain d residue 1006 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 915 random chunks: chunk 576 optimal weight: 0.8980 chunk 773 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 669 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 727 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 746 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 341 GLN A 576 GLN A 861 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 98 GLN M 405 GLN M 421 GLN M 561 GLN ** M 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS a 79 GLN a 183 GLN a 228 GLN a 343 GLN b 616 HIS b 866 GLN d 797 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.204872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.139434 restraints weight = 76991.099| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.89 r_work: 0.3016 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 65438 Z= 0.256 Angle : 0.597 15.470 87694 Z= 0.306 Chirality : 0.045 0.253 8256 Planarity : 0.004 0.055 11939 Dihedral : 11.286 179.203 10908 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.08 % Allowed : 22.11 % Favored : 75.81 % 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: 0.25 (0.09), residues: 8992 helix: 1.79 (0.09), residues: 3493 sheet: -0.44 (0.13), residues: 1485 loop : -1.07 (0.10), residues: 4014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 851 HIS 0.010 0.001 HIS M1120 PHE 0.028 0.002 PHE G 158 TYR 0.030 0.001 TYR G 167 ARG 0.013 0.001 ARG A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30196.70 seconds wall clock time: 520 minutes 31.09 seconds (31231.09 seconds total)