Starting phenix.real_space_refine on Wed Feb 14 22:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oop_13010/02_2024/7oop_13010.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 314 5.16 5 C 38267 2.51 5 N 11407 2.21 5 O 12341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1258": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 106": "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 312": "OE1" <-> "OE2" Residue "M GLU 372": "OE1" <-> "OE2" Residue "M GLU 385": "OE1" <-> "OE2" Residue "M ARG 409": "NH1" <-> "NH2" 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 560": "OE1" <-> "OE2" Residue "M GLU 630": "OE1" <-> "OE2" Residue "M GLU 662": "OE1" <-> "OE2" Residue "M ARG 707": "NH1" <-> "NH2" Residue "M GLU 714": "OE1" <-> "OE2" Residue "M ARG 759": "NH1" <-> "NH2" Residue "M GLU 824": "OE1" <-> "OE2" Residue "M GLU 834": "OE1" <-> "OE2" Residue "M GLU 853": "OE1" <-> "OE2" Residue "M ARG 855": "NH1" <-> "NH2" Residue "M ARG 918": "NH1" <-> "NH2" Residue "M GLU 926": "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 1112": "OE1" <-> "OE2" Residue "M GLU 1273": "OE1" <-> "OE2" Residue "a GLU 13": "OE1" <-> "OE2" Residue "a GLU 22": "OE1" <-> "OE2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "a GLU 141": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "b ARG 516": "NH1" <-> "NH2" Residue "b ARG 562": "NH1" <-> "NH2" Residue "b GLU 564": "OE1" <-> "OE2" Residue "b GLU 584": "OE1" <-> "OE2" Residue "b ARG 593": "NH1" <-> "NH2" Residue "b ARG 637": "NH1" <-> "NH2" Residue "b ARG 652": "NH1" <-> "NH2" Residue "b ARG 666": "NH1" <-> "NH2" Residue "b ARG 767": "NH1" <-> "NH2" 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 GLU 969": "OE1" <-> "OE2" Residue "b ARG 985": "NH1" <-> "NH2" Residue "b ARG 993": "NH1" <-> "NH2" Residue "b GLU 1003": "OE1" <-> "OE2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d GLU 210": "OE1" <-> "OE2" Residue "d GLU 277": "OE1" <-> "OE2" Residue "d GLU 728": "OE1" <-> "OE2" Residue "d GLU 865": "OE1" <-> "OE2" Residue "d GLU 898": "OE1" <-> "OE2" Residue "d GLU 943": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62441 Number of models: 1 Model: "" Number of chains: 32 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: 4356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4356 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 21, 'TRANS': 512} 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: 8491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8491 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 40, 'TRANS': 1055} Chain breaks: 6 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 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 87.702 115.096 166.840 1.00 48.17 S ATOM 486 SG CYS A 74 87.874 118.695 166.622 1.00 41.36 S ATOM 533 SG CYS A 81 88.867 117.253 163.805 1.00 35.27 S ATOM 768 SG CYS A 111 132.433 109.578 181.477 1.00 91.82 S ATOM 1109 SG CYS A 154 134.598 111.589 183.140 1.00109.34 S ATOM 1132 SG CYS A 184 134.317 108.021 184.649 1.00108.62 S ATOM 19801 SG CYS B1119 99.438 127.106 174.945 1.00 36.20 S ATOM 19823 SG CYS B1122 101.746 124.448 173.756 1.00 36.20 S ATOM 19938 SG CYS B1137 98.571 123.317 174.409 1.00 45.73 S ATOM 19959 SG CYS B1140 101.438 125.055 177.017 1.00 50.22 S ATOM 20925 SG CYS C 88 56.602 130.176 107.518 1.00 29.26 S ATOM 20938 SG CYS C 90 56.345 127.520 109.683 1.00 40.74 S ATOM 20973 SG CYS C 94 55.607 127.498 106.619 1.00 24.46 S ATOM 20995 SG CYS C 97 59.422 127.558 106.983 1.00 19.44 S ATOM 28299 SG CYS I 17 164.843 76.757 135.108 1.00 82.37 S ATOM 28323 SG CYS I 20 161.798 77.117 136.993 1.00 84.97 S ATOM 28484 SG CYS I 39 163.133 79.542 138.338 1.00 88.77 S ATOM 28509 SG CYS I 42 165.098 76.509 138.096 1.00 91.84 S ATOM 28861 SG CYS I 86 156.794 95.831 95.663 1.00 49.99 S ATOM 28885 SG CYS I 89 155.706 93.449 93.517 1.00 47.96 S ATOM 29089 SG CYS I 114 153.176 94.377 95.179 1.00 39.99 S ATOM 29124 SG CYS I 119 155.996 92.051 96.458 1.00 52.59 S ATOM 29234 SG CYS J 7 87.460 122.073 94.757 1.00 21.20 S ATOM 29258 SG CYS J 10 85.608 124.510 92.805 1.00 13.53 S ATOM 29522 SG CYS J 44 89.462 124.116 92.566 1.00 10.85 S ATOM 29528 SG CYS J 45 87.075 122.011 90.895 1.00 13.16 S ATOM 30690 SG CYS L 19 75.174 86.506 117.413 1.00 42.92 S ATOM 30709 SG CYS L 22 72.847 84.991 115.708 1.00 47.73 S ATOM 30826 SG CYS L 36 72.138 84.622 118.831 1.00 54.46 S ATOM 30852 SG CYS L 39 75.486 82.922 117.110 1.00 52.44 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: 26.35, per 1000 atoms: 0.42 Number of scatterers: 62441 At special positions: 0 Unit cell: (199.5, 228.9, 304.5, 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 314 16.00 P 103 15.00 Mg 1 11.99 O 12341 8.00 N 11407 7.00 C 38267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.54 Conformation dependent library (CDL) restraints added in 8.2 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 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " 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 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12586 Finding SS restraints... Secondary structure from input PDB file: 287 helices and 105 sheets defined 40.1% alpha, 19.5% beta 40 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 16.89 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.840A 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: 3.741A 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: 3.987A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.717A 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: 3.819A 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: 3.753A 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: 3.990A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.662A 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: 4.171A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.167A 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: 3.839A 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: 3.844A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.719A 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: 3.588A 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: 4.095A 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: 3.720A 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: 4.255A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.551A 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: 3.677A 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: 3.818A 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: 3.560A 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: 3.529A 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: 4.107A 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 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 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: 3.728A 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 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.216A 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: 3.552A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.040A 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 301 removed outlier: 3.696A pdb=" N GLN M 299 " --> pdb=" O PRO M 295 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG M 301 " --> pdb=" O ARG M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 325 Processing helix chain 'M' and resid 356 through 368 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: 3.636A pdb=" N GLU M 401 " --> pdb=" O TRP M 397 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS M 402 " --> pdb=" O GLN M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 450 Processing helix chain 'M' and resid 456 through 471 WARNING: missing atoms! removed outlier: 3.636A pdb=" N TYR M 470 " --> pdb=" O HIS M 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 530 removed outlier: 3.915A pdb=" N CYS M 527 " --> pdb=" O MET M 523 " (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: 3.763A pdb=" N LEU M 569 " --> pdb=" O GLU M 565 " (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 627 removed outlier: 4.826A pdb=" N LYS M 626 " --> pdb=" O LYS M 622 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP M 627 " --> pdb=" O LYS M 623 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 636 removed outlier: 4.257A pdb=" N SER M 636 " --> pdb=" O TYR M 633 " (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 663 Processing helix chain 'M' and resid 685 through 693 removed outlier: 3.989A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR M 693 " --> pdb=" O ILE M 689 " (cutoff:3.500A) Processing helix chain 'M' and resid 701 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 870 removed outlier: 3.789A pdb=" N MET M 859 " --> pdb=" O ARG M 855 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 870 " --> pdb=" O ARG M 866 " (cutoff:3.500A) Processing helix chain 'M' and resid 888 through 896 Processing helix chain 'M' and resid 896 through 903 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 Processing helix chain 'M' and resid 943 through 948 removed outlier: 4.428A pdb=" N GLU M 947 " --> pdb=" O PRO M 944 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 Processing helix chain 'M' and resid 973 through 979 Processing helix chain 'M' and resid 980 through 982 No H-bonds generated for 'chain 'M' and resid 980 through 982' Processing helix chain 'M' and resid 983 through 988 removed outlier: 4.356A pdb=" N GLN M 987 " --> pdb=" O GLN M 983 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR M 988 " --> pdb=" O ALA M 984 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 983 through 988' 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 1032 Processing helix chain 'M' and resid 1051 through 1055 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 Processing helix chain 'M' and resid 1086 through 1095 Processing helix chain 'M' and resid 1098 through 1102 removed outlier: 3.989A pdb=" N LEU M1102 " --> pdb=" O LEU M1099 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1114 removed outlier: 4.027A pdb=" N ARG M1113 " --> pdb=" O GLU M1109 " (cutoff:3.500A) Processing helix chain 'M' and resid 1119 through 1132 Processing helix chain 'M' and resid 1145 through 1155 Processing helix chain 'M' and resid 1241 through 1246 Processing helix chain 'M' and resid 1252 through 1256 removed outlier: 4.330A 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 14 through 40 Processing helix chain 'S' and resid 26 through 36 removed outlier: 3.538A pdb=" N VAL S 30 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 54 removed outlier: 4.155A pdb=" N TRP S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 67 removed outlier: 3.969A 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: 3.667A pdb=" N ALA S 66 " --> pdb=" O LYS S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 99 removed outlier: 4.568A pdb=" N VAL S 94 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG S 98 " --> pdb=" O VAL S 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS S 99 " --> pdb=" O GLN S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 124 removed outlier: 5.280A pdb=" N GLN S 112 " --> pdb=" O ASP S 108 " (cutoff:3.500A) removed outlier: 4.287A 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: 3.586A pdb=" N LEU S 139 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 3.810A 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: 4.175A 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: 3.927A 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: 3.835A pdb=" N THR S 192 " --> pdb=" O LYS S 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 210 removed outlier: 3.892A 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: 4.608A pdb=" N LEU S 235 " --> pdb=" O CYS S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 255 removed outlier: 3.855A 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: 3.931A pdb=" N ALA S 336 " --> pdb=" O ALA S 332 " (cutoff:3.500A) Processing helix chain 'S' and resid 341 through 353 removed outlier: 3.544A 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: 3.879A pdb=" N ALA S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN S 362 " --> pdb=" O GLU S 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS S 366 " --> pdb=" O GLN S 362 " (cutoff:3.500A) removed outlier: 3.899A 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: 3.878A pdb=" N LYS S 379 " --> pdb=" O TYR S 375 " (cutoff:3.500A) removed outlier: 4.160A 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: 3.503A pdb=" N ALA S 397 " --> pdb=" O LYS S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 413 through 423 removed outlier: 3.941A 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: 3.667A pdb=" N LEU S 441 " --> pdb=" O ALA S 437 " (cutoff:3.500A) removed outlier: 4.329A 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: 3.738A 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: 3.651A pdb=" N GLY S 572 " --> pdb=" O TRP S 568 " (cutoff:3.500A) Processing helix chain 'S' and resid 584 through 589 removed outlier: 3.706A 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: 3.667A pdb=" N VAL S 673 " --> pdb=" O VAL S 669 " (cutoff:3.500A) Processing helix chain 'S' and resid 680 through 694 removed outlier: 3.934A pdb=" N TRP S 684 " --> pdb=" O ILE S 680 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU S 685 " --> pdb=" O SER S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 696 through 708 removed outlier: 5.523A 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: 3.664A 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: 3.510A pdb=" N VAL S 779 " --> pdb=" O ASN S 775 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS S 784 " --> pdb=" O LEU S 780 " (cutoff:3.500A) removed outlier: 3.544A 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: 4.052A 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: 4.116A 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: 3.894A pdb=" N ASN S 887 " --> pdb=" O GLU S 883 " (cutoff:3.500A) removed outlier: 3.937A 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: 3.602A 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: 3.761A 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: 3.538A pdb=" N THR V 192 " --> pdb=" O ALA V 188 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE V 193 " --> pdb=" O ILE V 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 228 removed outlier: 4.062A 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: 3.856A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 500 through 505 Processing helix chain 'b' and resid 508 through 525 Processing helix chain 'b' and resid 538 through 552 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 617 Processing helix chain 'b' and resid 624 through 631 Processing helix chain 'b' and resid 648 through 652 Processing helix chain 'b' and resid 656 through 663 Processing helix chain 'b' and resid 681 through 693 removed outlier: 4.196A 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 750 through 754 Processing helix chain 'b' and resid 769 through 782 Processing helix chain 'b' and resid 782 through 790 removed outlier: 3.715A pdb=" N TYR b 786 " --> pdb=" O SER b 782 " (cutoff:3.500A) Processing helix chain 'b' and resid 794 through 808 removed outlier: 4.340A pdb=" N GLY b 798 " --> pdb=" O GLN b 794 " (cutoff:3.500A) Processing helix chain 'b' and resid 808 through 814 removed outlier: 3.957A pdb=" N PHE b 812 " --> pdb=" O HIS b 808 " (cutoff:3.500A) Processing helix chain 'b' and resid 834 through 837 Processing helix chain 'b' and resid 838 through 855 Processing helix chain 'b' and resid 864 through 878 Processing helix chain 'b' and resid 890 through 892 No H-bonds generated for 'chain 'b' and resid 890 through 892' Processing helix chain 'b' and resid 893 through 904 removed outlier: 3.875A pdb=" N LEU b 897 " --> pdb=" O SER b 893 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP b 904 " --> pdb=" O ARG b 900 " (cutoff:3.500A) Processing helix chain 'b' and resid 937 through 949 removed outlier: 3.823A pdb=" N ASP b 941 " --> pdb=" O ASN b 937 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA b 948 " --> pdb=" O ALA b 944 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP b 949 " --> pdb=" O ARG b 945 " (cutoff:3.500A) Processing helix chain 'b' and resid 967 through 988 removed outlier: 3.565A pdb=" N LYS b 971 " --> pdb=" O THR b 967 " (cutoff:3.500A) Processing helix chain 'b' and resid 997 through 1003 Processing helix chain 'b' and resid 1016 through 1022 Processing helix chain 'b' and resid 1387 through 1399 removed outlier: 3.509A pdb=" N LEU b1399 " --> pdb=" O ALA b1395 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 14 removed outlier: 3.513A 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: 3.532A pdb=" N SER c 40 " --> pdb=" O GLU c 36 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.703A pdb=" N ASP c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 124 removed outlier: 4.131A 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: 3.944A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 756 through 760 removed outlier: 3.837A pdb=" N ALA d 760 " --> pdb=" O SER d 757 " (cutoff:3.500A) Processing helix chain 'd' and resid 986 through 991 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1074 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: 3.692A pdb=" N LEU d1129 " --> pdb=" O THR d1125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.522A 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: 6.851A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.010A 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: 4.388A 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: 3.717A 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: 6.062A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.596A 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: 3.993A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.899A 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: 5.660A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.430A 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: 4.430A 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: 5.335A 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: 3.811A 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: 3.512A 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: 4.621A 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: 4.466A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.830A 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 'A' and resid 1471 through 1475 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC7, 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: 7.091A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.649A 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: 6.555A 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: 5.107A 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: 5.885A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.014A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD2, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.657A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.769A 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: 6.586A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.672A 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: 3.580A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 531 through 532 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 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: 3.574A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.765A 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=AD6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.693A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.433A 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: 4.504A 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=AD7, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.693A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.433A 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: 4.504A 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: 5.308A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD9, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.367A 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: 6.705A 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=AE1, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE2, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.904A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AE4, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE5, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.631A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.717A 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: 6.143A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.966A 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: 7.043A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE8, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.037A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.037A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.094A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF3, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.639A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF5, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AF6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.624A 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: 6.788A 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: 6.340A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 640 through 644 removed outlier: 5.516A pdb=" N LYS M 641 " --> pdb=" O ILE M 618 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE M 618 " --> pdb=" O LYS M 641 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 805 through 811 removed outlier: 6.974A pdb=" N LEU M 798 " --> pdb=" O THR M 806 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE M 808 " --> pdb=" O CYS M 796 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS M 796 " --> pdb=" O PHE M 808 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG M 810 " --> pdb=" O VAL M 794 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL M 794 " --> pdb=" O ARG M 810 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU M 782 " --> pdb=" O THR M 849 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 971 through 972 removed outlier: 6.270A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 3.645A pdb=" N VAL M1228 " --> pdb=" O ILE M1240 " (cutoff:3.500A) Processing sheet with id=AG3, 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: 3.866A pdb=" N LEU S 19 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE S 17 " --> pdb=" O ILE S 8 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.687A 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: 3.667A pdb=" N PHE V 315 " --> pdb=" O LEU V 326 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 456 through 459 removed outlier: 3.783A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE U 440 " --> pdb=" O VAL V 214 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL V 214 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS U 442 " --> pdb=" O VAL V 212 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 461 through 463 Processing sheet with id=AG7, first strand: chain 'U' and resid 472 through 475 removed outlier: 3.561A 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=AG8, first strand: chain 'V' and resid 231 through 232 Processing sheet with id=AG9, first strand: chain 'V' and resid 260 through 261 removed outlier: 4.265A pdb=" N GLN V 260 " --> pdb=" O VAL V 271 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 9 through 11 Processing sheet with id=AH2, first strand: chain 'Y' and resid 19 through 24 removed outlier: 5.804A pdb=" N VAL Y 44 " --> pdb=" O SER Y 59 " (cutoff:3.500A) removed outlier: 4.080A 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=AH3, 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: 5.522A pdb=" N ASP Y 92 " --> pdb=" O GLN Y 98 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN Y 98 " --> pdb=" O ASP Y 92 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 112 through 114 removed outlier: 3.505A pdb=" N ALA Y 113 " --> pdb=" O ALA Y 122 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA Y 122 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 3.755A 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: 6.762A pdb=" N LYS Y 140 " --> pdb=" O GLY Y 134 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 151 through 156 removed outlier: 5.780A 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: 6.226A pdb=" N ILE Y 174 " --> pdb=" O LEU Y 183 " (cutoff:3.500A) Processing sheet with id=AH6, 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: 3.571A pdb=" N THR Y 197 " --> pdb=" O VAL Y 206 " (cutoff:3.500A) removed outlier: 3.800A 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: 5.807A pdb=" N LEU Y 224 " --> pdb=" O ASP Y 218 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 235 through 240 removed outlier: 6.272A 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: 6.503A pdb=" N VAL Y 248 " --> pdb=" O VAL Y 238 " (cutoff:3.500A) removed outlier: 4.796A 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: 6.637A 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=AH8, first strand: chain 'Y' and resid 277 through 282 removed outlier: 4.197A pdb=" N GLY Y 279 " --> pdb=" O VAL Y 292 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.516A pdb=" N CYS a 339 " --> pdb=" O GLY a 352 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 36 through 38 removed outlier: 7.359A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.350A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.594A pdb=" N THR a 104 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN a 133 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'a' and resid 144 through 149 Processing sheet with id=AI5, first strand: chain 'a' and resid 189 through 194 Processing sheet with id=AI6, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.676A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'a' and resid 298 through 299 removed outlier: 6.476A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN a 326 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'b' and resid 594 through 596 removed outlier: 6.236A pdb=" N THR b 569 " --> pdb=" O LEU b 621 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR b 623 " --> pdb=" O THR b 569 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE b 571 " --> pdb=" O THR b 623 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE b 529 " --> pdb=" O LEU b 743 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'b' and resid 759 through 765 removed outlier: 6.842A pdb=" N ASN b 760 " --> pdb=" O VAL b 959 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ARG b 961 " --> pdb=" O ASN b 760 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN b 762 " --> pdb=" O ARG b 961 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU b 963 " --> pdb=" O GLN b 762 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU b 764 " --> pdb=" O LEU b 963 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL b 929 " --> pdb=" O TYR b 960 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU b 962 " --> pdb=" O VAL b 929 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE b 931 " --> pdb=" O LEU b 962 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU b 859 " --> pdb=" O VAL b 930 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU b 883 " --> pdb=" O LEU b 911 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 1004 through 1009 removed outlier: 6.803A pdb=" N GLY d1031 " --> pdb=" O ASN d1005 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE d1007 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU d1029 " --> pdb=" O PHE d1007 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS d1009 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER d1027 " --> pdb=" O HIS d1009 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER d1027 " --> pdb=" O VAL d1040 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL d1040 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU d1029 " --> pdb=" O GLY d1038 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY d1038 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU d1039 " --> pdb=" O THR d 8 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR d 8 " --> pdb=" O LEU d1039 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR d1041 " --> pdb=" O VAL d 6 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL d 6 " --> pdb=" O THR d1041 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 15 through 21 removed outlier: 5.885A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 61 through 67 removed outlier: 3.963A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA d 86 " --> pdb=" O HIS d 105 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS d 105 " --> pdb=" O ALA d 86 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE d 88 " --> pdb=" O ARG d 103 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 121 through 124 Processing sheet with id=AJ5, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.635A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.635A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'd' and resid 218 through 221 Processing sheet with id=AJ8, first strand: chain 'd' and resid 258 through 263 removed outlier: 4.256A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 313 through 318 removed outlier: 6.660A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS d 335 " --> pdb=" O ALA d 349 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA d 349 " --> pdb=" O LYS d 335 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'd' and resid 361 through 365 removed outlier: 3.875A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'd' and resid 398 through 400 removed outlier: 3.739A pdb=" N ALA d 400 " --> pdb=" O ILE d 701 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'd' and resid 410 through 413 Processing sheet with id=AK4, first strand: chain 'd' and resid 457 through 463 removed outlier: 3.576A pdb=" N GLN d 467 " --> pdb=" O VAL d 463 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER d 475 " --> pdb=" O THR d 472 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'd' and resid 507 through 512 removed outlier: 3.985A pdb=" N SER d 530 " --> pdb=" O TYR d 518 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN d 520 " --> pdb=" O GLN d 528 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN d 528 " --> pdb=" O GLN d 520 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N HIS d 522 " --> pdb=" O LEU d 526 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU d 526 " --> pdb=" O HIS d 522 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.446A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU d 560 " --> pdb=" O SER d 565 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU d 580 " --> pdb=" O ALA d 566 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'd' and resid 588 through 595 removed outlier: 4.002A pdb=" N HIS d 600 " --> pdb=" O LEU d 616 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS d 627 " --> pdb=" O TYR d 613 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY d 615 " --> pdb=" O ASP d 625 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP d 625 " --> pdb=" O GLY d 615 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'd' and resid 637 through 642 removed outlier: 3.705A pdb=" N PHE d 641 " --> pdb=" O ASN d 648 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR d 660 " --> pdb=" O VAL d 667 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.258A pdb=" N SER d 738 " --> pdb=" O PRO d 721 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS d 723 " --> pdb=" O LEU d 736 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.342A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.342A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'd' and resid 872 through 876 removed outlier: 3.870A pdb=" N SER d 872 " --> pdb=" O SER d 883 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL d 888 " --> pdb=" O ASN d 904 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN d 904 " --> pdb=" O VAL d 888 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'd' and resid 911 through 917 removed outlier: 4.713A pdb=" N VAL d 930 " --> pdb=" O ASP d 948 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP d 948 " --> pdb=" O VAL d 930 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS d 936 " --> pdb=" O PHE d 942 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE d 942 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'd' and resid 954 through 961 removed outlier: 6.529A pdb=" N ALA d 968 " --> pdb=" O SER d 955 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL d 957 " --> pdb=" O LEU d 966 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE d 959 " --> pdb=" O ASN d 964 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN d 964 " --> pdb=" O ILE d 959 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'd' and resid 1076 through 1078 2998 hydrogen bonds defined for protein. 8424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 32.51 Time building geometry restraints manager: 22.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 10865 1.31 - 1.43: 16737 1.43 - 1.56: 35403 1.56 - 1.69: 213 1.69 - 1.82: 488 Bond restraints: 63706 Sorted by residual: bond pdb=" CA ILE M 475 " pdb=" CB ILE M 475 " ideal model delta sigma weight residual 1.534 1.584 -0.050 6.80e-03 2.16e+04 5.39e+01 bond pdb=" C1' U P 26 " pdb=" N1 U P 26 " ideal model delta sigma weight residual 1.470 1.561 -0.091 1.50e-02 4.44e+03 3.72e+01 bond pdb=" C1' U P 30 " pdb=" N1 U P 30 " ideal model delta sigma weight residual 1.470 1.558 -0.088 1.50e-02 4.44e+03 3.47e+01 bond pdb=" C1' C P 32 " pdb=" N1 C P 32 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" C1' A P 25 " pdb=" N9 A P 25 " ideal model delta sigma weight residual 1.475 1.392 0.083 1.50e-02 4.44e+03 3.04e+01 ... (remaining 63701 not shown) Histogram of bond angle deviations from ideal: 70.65 - 83.58: 3 83.58 - 96.52: 6 96.52 - 109.45: 7973 109.45 - 122.39: 67503 122.39 - 135.32: 10338 Bond angle restraints: 85823 Sorted by residual: angle pdb=" OP1 A P 36 " pdb=" P A P 36 " pdb=" OP2 A P 36 " ideal model delta sigma weight residual 119.60 82.08 37.52 3.00e+00 1.11e-01 1.56e+02 angle pdb=" OP2 A P 36 " pdb=" P A P 36 " pdb=" O5' A P 36 " ideal model delta sigma weight residual 108.00 70.65 37.35 3.00e+00 1.11e-01 1.55e+02 angle pdb=" OP1 A P 36 " pdb=" P A P 36 " pdb=" O5' A P 36 " ideal model delta sigma weight residual 108.00 135.32 -27.32 3.00e+00 1.11e-01 8.29e+01 angle pdb=" O3' A P 35 " pdb=" P A P 36 " pdb=" OP1 A P 36 " ideal model delta sigma weight residual 108.00 81.36 26.64 3.00e+00 1.11e-01 7.88e+01 angle pdb=" O3' A P 35 " pdb=" P A P 36 " pdb=" OP2 A P 36 " ideal model delta sigma weight residual 108.00 133.83 -25.83 3.00e+00 1.11e-01 7.41e+01 ... (remaining 85818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 35188 35.42 - 70.85: 801 70.85 - 106.27: 56 106.27 - 141.69: 1 141.69 - 177.12: 4 Dihedral angle restraints: 36050 sinusoidal: 14864 harmonic: 21186 Sorted by residual: dihedral pdb=" CA PHE b 995 " pdb=" C PHE b 995 " pdb=" N PHE b 996 " pdb=" CA PHE b 996 " ideal model delta harmonic sigma weight residual 180.00 135.78 44.22 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA LEU b 912 " pdb=" C LEU b 912 " pdb=" N THR b 913 " pdb=" CA THR b 913 " ideal model delta harmonic sigma weight residual 180.00 147.37 32.63 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 -148.11 -31.89 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 36047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 8650 0.381 - 0.762: 1 0.762 - 1.143: 0 1.143 - 1.524: 2 1.524 - 1.906: 14 Chirality restraints: 8667 Sorted by residual: chirality pdb=" CG LEU M 924 " pdb=" CB LEU M 924 " pdb=" CD1 LEU M 924 " pdb=" CD2 LEU M 924 " both_signs ideal model delta sigma weight residual False -2.59 -0.68 -1.91 2.00e-01 2.50e+01 9.08e+01 chirality pdb=" CG LEU M 836 " pdb=" CB LEU M 836 " pdb=" CD1 LEU M 836 " pdb=" CD2 LEU M 836 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.65e+01 chirality pdb=" CG LEU M 889 " pdb=" CB LEU M 889 " pdb=" CD1 LEU M 889 " pdb=" CD2 LEU M 889 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.58e+01 ... (remaining 8664 not shown) Planarity restraints: 11326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 113 " -0.088 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO G 114 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO G 114 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO G 114 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 84 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C ARG D 84 " -0.083 2.00e-02 2.50e+03 pdb=" O ARG D 84 " 0.031 2.00e-02 2.50e+03 pdb=" N SER D 85 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 91 " 0.023 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" CD GLN G 91 " -0.082 2.00e-02 2.50e+03 pdb=" OE1 GLN G 91 " 0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN G 91 " 0.028 2.00e-02 2.50e+03 ... (remaining 11323 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 125 2.36 - 2.99: 33649 2.99 - 3.63: 94519 3.63 - 4.26: 147683 4.26 - 4.90: 242924 Nonbonded interactions: 518900 Sorted by model distance: nonbonded pdb=" O ASP b 532 " pdb=" NH1 ARG b 538 " model vdw 1.721 2.520 nonbonded pdb=" OG1 THR G 130 " pdb=" OD1 ASP G 132 " model vdw 1.877 2.440 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.918 2.170 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 1.924 2.170 ... (remaining 518895 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 14.840 Check model and map are aligned: 0.720 Set scattering table: 0.430 Process input model: 160.300 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.220 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.007 0.143 63706 Z= 0.492 Angle : 0.916 37.522 85823 Z= 0.490 Chirality : 0.088 1.906 8667 Planarity : 0.005 0.128 11326 Dihedral : 14.644 177.117 23464 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.09), residues: 8278 helix: -0.40 (0.09), residues: 2985 sheet: -1.28 (0.13), residues: 1467 loop : -1.39 (0.10), residues: 3826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP b 517 HIS 0.023 0.002 HIS b 808 PHE 0.052 0.003 PHE G 107 TYR 0.064 0.003 TYR M 722 ARG 0.054 0.001 ARG b 876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 6.749 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: A 1440 MET cc_start: 0.8142 (tpp) cc_final: 0.7938 (tpp) REVERT: A 1451 MET cc_start: 0.8260 (mmm) cc_final: 0.7803 (mmm) REVERT: B 312 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6457 (tm-30) REVERT: B 550 MET cc_start: 0.8535 (ttp) cc_final: 0.8309 (ttm) REVERT: D 39 MET cc_start: 0.7077 (tpp) cc_final: 0.6673 (tpt) REVERT: E 113 SER cc_start: 0.9167 (m) cc_final: 0.8960 (p) REVERT: G 9 HIS cc_start: 0.8241 (t70) cc_final: 0.7948 (t70) REVERT: G 166 ASP cc_start: 0.7239 (p0) cc_final: 0.6771 (p0) REVERT: H 37 MET cc_start: 0.7410 (mtp) cc_final: 0.7168 (mtp) REVERT: H 130 ASN cc_start: 0.7566 (m-40) cc_final: 0.7143 (m-40) REVERT: J 58 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8213 (mmtm) REVERT: K 110 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7803 (tptp) REVERT: M 1137 LEU cc_start: 0.7962 (mt) cc_final: 0.7612 (tm) REVERT: b 664 GLN cc_start: 0.7948 (mt0) cc_final: 0.7329 (mt0) REVERT: b 752 MET cc_start: 0.4370 (ppp) cc_final: 0.3984 (ttp) REVERT: b 867 MET cc_start: 0.6352 (tmm) cc_final: 0.5595 (ttm) REVERT: d 57 MET cc_start: 0.8138 (mmm) cc_final: 0.7858 (mmt) REVERT: d 282 MET cc_start: 0.8506 (tpt) cc_final: 0.8252 (tpp) REVERT: d 679 MET cc_start: 0.4766 (tmm) cc_final: 0.4464 (tmt) REVERT: d 1047 TRP cc_start: 0.8552 (m100) cc_final: 0.8190 (m100) outliers start: 0 outliers final: 2 residues processed: 855 average time/residue: 1.5989 time to fit residues: 1708.2997 Evaluate side-chains 529 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain b residue 977 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 711 optimal weight: 1.9990 chunk 638 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 431 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 660 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 491 optimal weight: 50.0000 chunk 765 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 562 ASN A1077 ASN A1220 HIS A1384 HIS A1445 HIS B 52 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B 992 ASN C 108 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN H 130 ASN I 56 ASN J 52 HIS K 2 ASN K 55 GLN M 943 HIS ** M 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 ASN ** b 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 807 ASN b 974 HIS d 399 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1055 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63706 Z= 0.267 Angle : 0.650 39.013 85823 Z= 0.329 Chirality : 0.046 0.548 8667 Planarity : 0.005 0.068 11326 Dihedral : 11.830 178.848 10205 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 1.60 % Allowed : 9.27 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 8278 helix: 0.75 (0.09), residues: 3016 sheet: -0.90 (0.13), residues: 1506 loop : -1.12 (0.10), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 517 HIS 0.009 0.001 HIS a 156 PHE 0.028 0.002 PHE M 786 TYR 0.018 0.002 TYR M 693 ARG 0.011 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 578 time to evaluate : 5.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8496 (mtm) cc_final: 0.8232 (mtm) REVERT: A 565 MET cc_start: 0.8738 (mmm) cc_final: 0.7675 (mmm) REVERT: A 735 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: A 1054 MET cc_start: 0.7875 (tpp) cc_final: 0.7607 (tpt) REVERT: A 1303 GLN cc_start: 0.7777 (mp10) cc_final: 0.7554 (pm20) REVERT: A 1440 MET cc_start: 0.8071 (tpp) cc_final: 0.7786 (tpp) REVERT: A 1451 MET cc_start: 0.8363 (mmm) cc_final: 0.7938 (mmm) REVERT: B 312 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6297 (tm-30) REVERT: B 497 LYS cc_start: 0.7878 (tptp) cc_final: 0.7531 (tptt) REVERT: B 1151 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7901 (ptp) REVERT: D 39 MET cc_start: 0.6915 (tpp) cc_final: 0.6638 (tpt) REVERT: E 98 ASN cc_start: 0.7685 (t0) cc_final: 0.7407 (t0) REVERT: F 96 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8107 (mt-10) REVERT: G 128 TYR cc_start: 0.6799 (m-80) cc_final: 0.6491 (m-80) REVERT: I 33 ARG cc_start: 0.6984 (mmm-85) cc_final: 0.6282 (mmp80) REVERT: M 366 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7924 (mtp) REVERT: M 623 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7447 (tptp) REVERT: M 725 MET cc_start: 0.8345 (mmp) cc_final: 0.8061 (mmp) REVERT: M 1137 LEU cc_start: 0.7966 (mt) cc_final: 0.7536 (tm) REVERT: d 57 MET cc_start: 0.8293 (mmm) cc_final: 0.7818 (mmt) REVERT: d 954 MET cc_start: 0.8266 (mmp) cc_final: 0.8061 (mmp) REVERT: d 1047 TRP cc_start: 0.8453 (m100) cc_final: 0.8221 (m100) outliers start: 94 outliers final: 30 residues processed: 626 average time/residue: 1.4756 time to fit residues: 1176.9772 Evaluate side-chains 532 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 499 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 1010 ARG Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1261 MET Chi-restraints excluded: chain b residue 742 LEU Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 885 MET Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 425 optimal weight: 20.0000 chunk 237 optimal weight: 0.9990 chunk 637 optimal weight: 4.9990 chunk 521 optimal weight: 30.0000 chunk 211 optimal weight: 3.9990 chunk 766 optimal weight: 6.9990 chunk 828 optimal weight: 5.9990 chunk 683 optimal weight: 1.9990 chunk 760 optimal weight: 9.9990 chunk 261 optimal weight: 0.0870 chunk 615 optimal weight: 20.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 278 HIS A 459 ASN A1384 HIS A1445 HIS B 117 ASN B 319 ASN B 500 GLN B 552 ASN B 749 HIS B 825 GLN B 941 GLN B1101 GLN C 111 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN K 69 HIS M 405 GLN ** M 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1264 HIS ** a 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 ASN a 289 ASN b 762 GLN d 240 HIS ** d 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 63706 Z= 0.371 Angle : 0.653 40.231 85823 Z= 0.328 Chirality : 0.046 0.558 8667 Planarity : 0.004 0.072 11326 Dihedral : 11.698 178.164 10201 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 2.43 % Allowed : 11.94 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 8278 helix: 1.18 (0.09), residues: 3029 sheet: -0.75 (0.13), residues: 1475 loop : -1.01 (0.10), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 517 HIS 0.021 0.002 HIS D 38 PHE 0.031 0.002 PHE A 112 TYR 0.042 0.002 TYR B 916 ARG 0.011 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 552 time to evaluate : 5.377 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: A 101 VAL cc_start: 0.8942 (p) cc_final: 0.8705 (t) REVERT: A 317 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7294 (ttt) REVERT: A 446 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 565 MET cc_start: 0.8776 (mmm) cc_final: 0.7736 (mmm) REVERT: A 1440 MET cc_start: 0.8056 (tpp) cc_final: 0.7801 (tpp) REVERT: A 1451 MET cc_start: 0.8424 (mmm) cc_final: 0.8176 (mmm) REVERT: B 53 MET cc_start: 0.7579 (mmm) cc_final: 0.7347 (mmm) REVERT: B 312 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7073 (tp-100) REVERT: B 340 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (ttmt) REVERT: B 497 LYS cc_start: 0.7946 (tptp) cc_final: 0.7599 (tptt) REVERT: C 212 ASP cc_start: 0.6862 (p0) cc_final: 0.6639 (p0) REVERT: D 39 MET cc_start: 0.6939 (tpp) cc_final: 0.6705 (tpt) REVERT: E 34 ASP cc_start: 0.7317 (p0) cc_final: 0.7089 (p0) REVERT: E 98 ASN cc_start: 0.7787 (t0) cc_final: 0.7512 (t0) REVERT: I 30 LYS cc_start: 0.8182 (mppt) cc_final: 0.7978 (mppt) REVERT: I 33 ARG cc_start: 0.7077 (mmm-85) cc_final: 0.6459 (mmp80) REVERT: J 1 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7315 (mtt) REVERT: M 623 LYS cc_start: 0.8017 (tmmt) cc_final: 0.7763 (tptp) REVERT: M 717 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8687 (tm) REVERT: M 725 MET cc_start: 0.8331 (mmp) cc_final: 0.8046 (mmp) REVERT: M 1137 LEU cc_start: 0.8113 (mt) cc_final: 0.7610 (tm) REVERT: b 841 MET cc_start: 0.2474 (mtp) cc_final: 0.2072 (mtp) REVERT: d 57 MET cc_start: 0.8348 (mmm) cc_final: 0.7884 (mmt) REVERT: d 954 MET cc_start: 0.8402 (mmp) cc_final: 0.8183 (mmp) REVERT: d 1134 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7692 (mp0) outliers start: 143 outliers final: 50 residues processed: 635 average time/residue: 1.4565 time to fit residues: 1182.0500 Evaluate side-chains 559 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 503 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL 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 423 ASN 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 611 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 355 THR Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 717 LEU Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 1010 ARG Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain M residue 1261 MET Chi-restraints excluded: chain b residue 732 CYS Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 977 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 757 optimal weight: 0.6980 chunk 576 optimal weight: 50.0000 chunk 398 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 366 optimal weight: 0.6980 chunk 514 optimal weight: 4.9990 chunk 769 optimal weight: 3.9990 chunk 814 optimal weight: 0.6980 chunk 402 optimal weight: 6.9990 chunk 729 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 412 GLN A 905 ASN A1077 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 430 ASN B 460 HIS B 582 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS B1101 GLN C 111 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN H 130 ASN M 800 ASN a 156 HIS a 241 ASN b 664 GLN d 240 HIS d 343 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63706 Z= 0.179 Angle : 0.578 40.236 85823 Z= 0.286 Chirality : 0.043 0.509 8667 Planarity : 0.003 0.059 11326 Dihedral : 11.530 179.123 10201 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.53 % Favored : 96.46 % Rotamer: Outliers : 2.13 % Allowed : 13.88 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.09), residues: 8278 helix: 1.59 (0.10), residues: 3033 sheet: -0.63 (0.13), residues: 1446 loop : -0.93 (0.10), residues: 3799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 517 HIS 0.007 0.001 HIS a 156 PHE 0.028 0.001 PHE A 112 TYR 0.031 0.001 TYR b 510 ARG 0.011 0.000 ARG a 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 538 time to evaluate : 5.479 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 REVERT: A 565 MET cc_start: 0.8713 (mmm) cc_final: 0.8081 (mmm) REVERT: A 1054 MET cc_start: 0.7867 (tpp) cc_final: 0.7487 (tpt) REVERT: A 1228 MET cc_start: 0.7764 (mpt) cc_final: 0.7548 (mpt) REVERT: A 1440 MET cc_start: 0.8018 (tpp) cc_final: 0.7801 (tpp) REVERT: A 1451 MET cc_start: 0.8423 (mmm) cc_final: 0.8065 (mmm) REVERT: B 53 MET cc_start: 0.7545 (mmm) cc_final: 0.7339 (mmm) REVERT: B 497 LYS cc_start: 0.7934 (tptp) cc_final: 0.7601 (tptt) REVERT: D 128 GLN cc_start: 0.6566 (tp-100) cc_final: 0.5795 (mp10) REVERT: E 34 ASP cc_start: 0.7267 (p0) cc_final: 0.7064 (p0) REVERT: H 14 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7015 (t70) REVERT: H 37 MET cc_start: 0.7524 (mmm) cc_final: 0.7285 (mmm) REVERT: H 130 ASN cc_start: 0.7736 (m110) cc_final: 0.7171 (m-40) REVERT: I 33 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6368 (mmp80) REVERT: K 114 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6054 (mp0) REVERT: M 366 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: M 623 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7650 (tppt) REVERT: M 725 MET cc_start: 0.8373 (mmp) cc_final: 0.8098 (mmp) REVERT: M 1137 LEU cc_start: 0.8071 (mt) cc_final: 0.7573 (tm) REVERT: b 732 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7990 (m) REVERT: b 780 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.6281 (m) REVERT: b 834 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5760 (t80) REVERT: b 841 MET cc_start: 0.2461 (mtp) cc_final: 0.2258 (mtp) REVERT: b 971 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7598 (tptp) REVERT: d 57 MET cc_start: 0.8396 (mmm) cc_final: 0.7953 (mmt) REVERT: d 410 LEU cc_start: 0.3102 (OUTLIER) cc_final: 0.2547 (mt) REVERT: d 1134 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7646 (mp0) outliers start: 125 outliers final: 43 residues processed: 613 average time/residue: 1.4609 time to fit residues: 1146.9132 Evaluate side-chains 542 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 491 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 935 GLU Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain b residue 732 CYS Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 834 TYR Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 678 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 606 optimal weight: 50.0000 chunk 336 optimal weight: 6.9990 chunk 695 optimal weight: 20.0000 chunk 563 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 416 optimal weight: 10.0000 chunk 731 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 372 ASN A 735 GLN A1077 ASN A1129 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 582 GLN B 683 GLN B1030 ASN C 66 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 168 ASN G 91 GLN I 22 ASN I 56 ASN K 89 ASN a 241 ASN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 904 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.134 63706 Z= 0.712 Angle : 0.783 40.723 85823 Z= 0.396 Chirality : 0.053 0.585 8667 Planarity : 0.005 0.119 11326 Dihedral : 11.763 177.632 10201 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 3.11 % Allowed : 14.66 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.09), residues: 8278 helix: 1.23 (0.10), residues: 3038 sheet: -0.76 (0.13), residues: 1462 loop : -1.07 (0.10), residues: 3778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 203 HIS 0.014 0.002 HIS C 173 PHE 0.044 0.003 PHE B 935 TYR 0.035 0.003 TYR G 17 ARG 0.011 0.001 ARG B 803 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 513 time to evaluate : 5.331 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: A 238 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8233 (mpp) REVERT: A 1017 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 1129 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7370 (p0) REVERT: A 1293 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 1440 MET cc_start: 0.8111 (tpp) cc_final: 0.7881 (tpp) REVERT: A 1451 MET cc_start: 0.8471 (mmm) cc_final: 0.8135 (mmm) REVERT: B 340 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: B 497 LYS cc_start: 0.7874 (tptp) cc_final: 0.7560 (tptt) REVERT: E 54 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.7118 (ttm-80) REVERT: E 98 ASN cc_start: 0.7672 (t0) cc_final: 0.7458 (t0) REVERT: F 80 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7428 (mmt) REVERT: G 1 MET cc_start: 0.5060 (tmm) cc_final: 0.4312 (ttt) REVERT: G 27 LYS cc_start: 0.6784 (mtmt) cc_final: 0.6557 (mttt) REVERT: H 14 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7178 (t70) REVERT: H 66 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: H 123 MET cc_start: 0.8563 (ttp) cc_final: 0.8307 (ttt) REVERT: H 130 ASN cc_start: 0.7721 (m110) cc_final: 0.7226 (m-40) REVERT: H 133 HIS cc_start: 0.7346 (p-80) cc_final: 0.7141 (p-80) REVERT: I 33 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6626 (mmp80) REVERT: I 42 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8269 (p) REVERT: J 1 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: K 68 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: K 114 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6083 (mp0) REVERT: M 468 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8763 (mp) REVERT: M 623 LYS cc_start: 0.8154 (tmmt) cc_final: 0.7869 (tppt) REVERT: M 725 MET cc_start: 0.8393 (mmp) cc_final: 0.8126 (mmp) REVERT: M 1137 LEU cc_start: 0.8421 (mt) cc_final: 0.7760 (tm) REVERT: a 81 TYR cc_start: 0.6601 (t80) cc_final: 0.6305 (t80) REVERT: b 732 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7942 (m) REVERT: b 773 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: b 780 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6383 (m) REVERT: b 1021 ILE cc_start: 0.7684 (mt) cc_final: 0.7280 (mt) REVERT: d 57 MET cc_start: 0.8334 (mmm) cc_final: 0.7934 (mmt) REVERT: d 230 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8895 (mm) REVERT: d 410 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2896 (mt) outliers start: 183 outliers final: 83 residues processed: 636 average time/residue: 1.4652 time to fit residues: 1193.0646 Evaluate side-chains 587 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 486 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR 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 611 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain M residue 355 THR Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 696 ASP Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 935 GLU Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1168 ILE Chi-restraints excluded: chain M residue 1172 THR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 310 VAL Chi-restraints excluded: chain b residue 732 CYS Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 773 HIS Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 977 ILE Chi-restraints excluded: chain d residue 230 ILE Chi-restraints excluded: chain d residue 253 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 364 VAL Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 274 optimal weight: 2.9990 chunk 733 optimal weight: 30.0000 chunk 161 optimal weight: 6.9990 chunk 478 optimal weight: 50.0000 chunk 201 optimal weight: 0.9990 chunk 815 optimal weight: 0.9990 chunk 677 optimal weight: 0.1980 chunk 377 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 428 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 372 ASN A 439 HIS A 735 GLN A 905 ASN A1077 ASN A1129 ASN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 319 ASN B1101 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 91 GLN I 56 ASN K 89 ASN a 289 ASN b 512 GLN d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 63706 Z= 0.199 Angle : 0.603 40.618 85823 Z= 0.299 Chirality : 0.043 0.502 8667 Planarity : 0.004 0.053 11326 Dihedral : 11.569 179.781 10201 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.52 % Favored : 96.47 % Rotamer: Outliers : 2.43 % Allowed : 16.10 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 8278 helix: 1.62 (0.10), residues: 3047 sheet: -0.63 (0.13), residues: 1479 loop : -0.93 (0.10), residues: 3752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 214 HIS 0.006 0.001 HIS D 38 PHE 0.027 0.002 PHE M 637 TYR 0.032 0.001 TYR b 510 ARG 0.011 0.000 ARG d1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 502 time to evaluate : 5.382 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 REVERT: A 104 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7788 (mtp) REVERT: A 565 MET cc_start: 0.8734 (mmm) cc_final: 0.8067 (mmm) REVERT: A 567 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 1129 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7274 (p0) REVERT: A 1199 MET cc_start: 0.4760 (ppp) cc_final: 0.4554 (pp-130) REVERT: A 1221 MET cc_start: 0.7497 (mmm) cc_final: 0.7135 (mmt) REVERT: A 1262 MET cc_start: 0.7541 (mmp) cc_final: 0.7326 (mmt) REVERT: A 1440 MET cc_start: 0.8086 (tpp) cc_final: 0.7447 (mmt) REVERT: B 463 ARG cc_start: 0.7440 (ptt180) cc_final: 0.7177 (ptt180) REVERT: B 497 LYS cc_start: 0.7885 (tptp) cc_final: 0.7553 (tptt) REVERT: B 1075 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7524 (mtt) REVERT: D 128 GLN cc_start: 0.6634 (tp-100) cc_final: 0.6063 (mp10) REVERT: E 98 ASN cc_start: 0.7598 (t0) cc_final: 0.7286 (t0) REVERT: G 65 PHE cc_start: 0.7091 (m-80) cc_final: 0.6877 (m-80) REVERT: G 146 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7771 (tmtm) REVERT: H 14 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7038 (t70) REVERT: H 52 LEU cc_start: 0.9023 (tt) cc_final: 0.8774 (tt) REVERT: H 130 ASN cc_start: 0.7805 (m110) cc_final: 0.7210 (m-40) REVERT: H 133 HIS cc_start: 0.7243 (p-80) cc_final: 0.7007 (p-80) REVERT: I 18 GLN cc_start: 0.8198 (mp10) cc_final: 0.7874 (mm-40) REVERT: I 33 ARG cc_start: 0.6904 (mmm-85) cc_final: 0.6471 (tpp-160) REVERT: I 72 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9044 (p) REVERT: K 114 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: M 623 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7791 (tmmm) REVERT: M 694 TYR cc_start: 0.7801 (t80) cc_final: 0.7596 (t80) REVERT: M 725 MET cc_start: 0.8462 (mmp) cc_final: 0.8156 (mmp) REVERT: M 1137 LEU cc_start: 0.8316 (mt) cc_final: 0.7751 (tm) REVERT: b 503 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7713 (tp) REVERT: b 705 GLU cc_start: 0.7388 (pp20) cc_final: 0.7061 (pp20) REVERT: b 732 CYS cc_start: 0.8227 (t) cc_final: 0.7978 (m) REVERT: b 780 VAL cc_start: 0.6579 (OUTLIER) cc_final: 0.6319 (m) REVERT: b 971 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7626 (tptp) REVERT: b 1021 ILE cc_start: 0.7677 (mt) cc_final: 0.7246 (mt) REVERT: d 57 MET cc_start: 0.8314 (mmm) cc_final: 0.7919 (mmt) REVERT: d 410 LEU cc_start: 0.3104 (OUTLIER) cc_final: 0.2571 (mt) REVERT: d 954 MET cc_start: 0.8209 (mmp) cc_final: 0.8002 (mmt) REVERT: d 1134 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7555 (mp0) outliers start: 143 outliers final: 66 residues processed: 598 average time/residue: 1.4476 time to fit residues: 1110.5725 Evaluate side-chains 561 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 484 time to evaluate : 5.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 548 TRP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 503 LEU Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 672 ILE Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 995 PHE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 647 THR Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 933 LEU Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 786 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 595 optimal weight: 40.0000 chunk 461 optimal weight: 20.0000 chunk 686 optimal weight: 1.9990 chunk 455 optimal weight: 0.7980 chunk 812 optimal weight: 10.0000 chunk 508 optimal weight: 50.0000 chunk 495 optimal weight: 7.9990 chunk 375 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 552 ASN B 585 ASN C 223 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 91 GLN K 89 ASN a 241 ASN a 289 ASN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS d 399 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 63706 Z= 0.491 Angle : 0.688 40.620 85823 Z= 0.345 Chirality : 0.048 0.513 8667 Planarity : 0.005 0.116 11326 Dihedral : 11.614 178.646 10201 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 2.89 % Allowed : 16.31 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.09), residues: 8278 helix: 1.55 (0.10), residues: 3044 sheet: -0.67 (0.13), residues: 1488 loop : -0.97 (0.10), residues: 3746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 479 HIS 0.022 0.002 HIS D 38 PHE 0.030 0.002 PHE B 935 TYR 0.021 0.002 TYR B 388 ARG 0.010 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 495 time to evaluate : 5.299 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 REVERT: A 565 MET cc_start: 0.8841 (mmm) cc_final: 0.7989 (mmm) REVERT: A 567 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 1199 MET cc_start: 0.4614 (ppp) cc_final: 0.4377 (pp-130) REVERT: A 1228 MET cc_start: 0.7834 (mpt) cc_final: 0.7629 (mpt) REVERT: A 1262 MET cc_start: 0.7604 (mmp) cc_final: 0.7387 (mmt) REVERT: A 1440 MET cc_start: 0.8083 (tpp) cc_final: 0.7460 (mmt) REVERT: B 298 MET cc_start: 0.7842 (mmt) cc_final: 0.7345 (mmt) REVERT: E 54 ARG cc_start: 0.7326 (ttm-80) cc_final: 0.7123 (ttm-80) REVERT: E 98 ASN cc_start: 0.7722 (t0) cc_final: 0.7454 (t0) REVERT: G 1 MET cc_start: 0.5194 (tmm) cc_final: 0.3994 (ttt) REVERT: G 117 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7219 (mpt) REVERT: G 146 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7878 (tmmm) REVERT: H 14 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7142 (t70) REVERT: H 123 MET cc_start: 0.8550 (ttp) cc_final: 0.8319 (ttt) REVERT: H 130 ASN cc_start: 0.7876 (m110) cc_final: 0.7123 (m-40) REVERT: H 133 HIS cc_start: 0.7230 (p-80) cc_final: 0.6961 (p-80) REVERT: I 14 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8184 (tt) REVERT: I 33 ARG cc_start: 0.6989 (mmm-85) cc_final: 0.6547 (tpp-160) REVERT: I 72 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9053 (p) REVERT: K 114 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: M 468 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8772 (mp) REVERT: M 725 MET cc_start: 0.8420 (mmp) cc_final: 0.8138 (mmp) REVERT: M 1137 LEU cc_start: 0.8412 (mt) cc_final: 0.7764 (tm) REVERT: b 705 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7254 (pp20) REVERT: b 732 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7981 (m) REVERT: b 780 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6398 (m) REVERT: b 923 LEU cc_start: 0.4128 (OUTLIER) cc_final: 0.3898 (mt) REVERT: d 57 MET cc_start: 0.8298 (mmm) cc_final: 0.7918 (mmt) REVERT: d 410 LEU cc_start: 0.3503 (OUTLIER) cc_final: 0.3023 (mt) outliers start: 170 outliers final: 77 residues processed: 606 average time/residue: 1.4538 time to fit residues: 1129.9300 Evaluate side-chains 566 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 477 time to evaluate : 5.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 548 TRP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 905 ASP Chi-restraints excluded: chain M residue 935 GLU Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1172 THR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain a residue 310 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 672 ILE Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 732 CYS Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 923 LEU Chi-restraints excluded: chain d residue 253 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 647 THR Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 933 LEU Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 502 optimal weight: 8.9990 chunk 324 optimal weight: 0.0010 chunk 485 optimal weight: 50.0000 chunk 244 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 516 optimal weight: 30.0000 chunk 553 optimal weight: 40.0000 chunk 401 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 638 optimal weight: 1.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 905 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 319 ASN B 683 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN K 89 ASN a 289 ASN d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 507 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 63706 Z= 0.205 Angle : 0.601 40.868 85823 Z= 0.297 Chirality : 0.043 0.491 8667 Planarity : 0.004 0.053 11326 Dihedral : 11.481 179.661 10201 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 2.21 % Allowed : 17.34 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 8278 helix: 1.80 (0.10), residues: 3047 sheet: -0.52 (0.13), residues: 1488 loop : -0.87 (0.10), residues: 3743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1192 HIS 0.010 0.001 HIS D 38 PHE 0.027 0.002 PHE d 650 TYR 0.031 0.001 TYR b 510 ARG 0.012 0.000 ARG G 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 507 time to evaluate : 5.368 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: A 446 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 532 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7382 (ptt90) REVERT: A 1221 MET cc_start: 0.7584 (mmm) cc_final: 0.7197 (mmp) REVERT: A 1228 MET cc_start: 0.7700 (mpt) cc_final: 0.7472 (mpt) REVERT: A 1262 MET cc_start: 0.7660 (mmp) cc_final: 0.7422 (mmt) REVERT: A 1440 MET cc_start: 0.8081 (tpp) cc_final: 0.7452 (mmt) REVERT: B 298 MET cc_start: 0.7589 (mmt) cc_final: 0.7299 (mmt) REVERT: B 1151 MET cc_start: 0.8109 (ptp) cc_final: 0.7907 (ptm) REVERT: D 128 GLN cc_start: 0.6924 (tp-100) cc_final: 0.6304 (mp10) REVERT: E 98 ASN cc_start: 0.7645 (t0) cc_final: 0.7344 (t0) REVERT: G 1 MET cc_start: 0.5034 (tmm) cc_final: 0.4066 (ttt) REVERT: G 146 LYS cc_start: 0.8143 (tmmt) cc_final: 0.7669 (tmtt) REVERT: H 14 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7028 (t70) REVERT: H 130 ASN cc_start: 0.7876 (m110) cc_final: 0.7133 (m-40) REVERT: H 133 HIS cc_start: 0.7107 (p-80) cc_final: 0.6818 (p-80) REVERT: I 14 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8105 (tt) REVERT: I 18 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7840 (mp10) REVERT: I 33 ARG cc_start: 0.6890 (mmm-85) cc_final: 0.6425 (tpp-160) REVERT: J 1 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.6920 (mpp) REVERT: L 29 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7876 (mmtt) REVERT: M 468 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8781 (mp) REVERT: M 623 LYS cc_start: 0.8291 (tptp) cc_final: 0.8039 (tptp) REVERT: M 627 ASP cc_start: 0.7400 (p0) cc_final: 0.7152 (p0) REVERT: M 650 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7870 (p0) REVERT: M 725 MET cc_start: 0.8441 (mmp) cc_final: 0.8179 (mmp) REVERT: M 859 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6911 (ptm) REVERT: M 1137 LEU cc_start: 0.8331 (mt) cc_final: 0.7756 (tm) REVERT: b 660 LEU cc_start: 0.8433 (mm) cc_final: 0.8097 (mp) REVERT: b 705 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: b 732 CYS cc_start: 0.8220 (t) cc_final: 0.8018 (m) REVERT: b 780 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6368 (m) REVERT: b 971 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7744 (tptp) REVERT: b 995 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: d 57 MET cc_start: 0.8269 (mmm) cc_final: 0.7911 (mmt) REVERT: d 230 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8893 (mm) REVERT: d 410 LEU cc_start: 0.3232 (OUTLIER) cc_final: 0.2667 (mt) REVERT: d 647 THR cc_start: 0.3699 (OUTLIER) cc_final: 0.3257 (p) REVERT: d 1134 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 130 outliers final: 67 residues processed: 599 average time/residue: 1.4007 time to fit residues: 1087.0392 Evaluate side-chains 565 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 484 time to evaluate : 5.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 650 ASP Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 859 MET Chi-restraints excluded: chain M residue 905 ASP Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1168 ILE Chi-restraints excluded: chain M residue 1172 THR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 310 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 995 PHE Chi-restraints excluded: chain d residue 230 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 350 MET Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 647 THR Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 739 optimal weight: 3.9990 chunk 778 optimal weight: 1.9990 chunk 710 optimal weight: 10.0000 chunk 757 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 594 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 684 optimal weight: 0.9990 chunk 716 optimal weight: 9.9990 chunk 754 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 683 GLN C 223 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 24 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN K 89 ASN L 26 ASN a 289 ASN b 664 GLN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 63706 Z= 0.361 Angle : 0.645 41.385 85823 Z= 0.321 Chirality : 0.045 0.481 8667 Planarity : 0.004 0.065 11326 Dihedral : 11.475 179.144 10201 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.13 % Favored : 95.86 % Rotamer: Outliers : 1.99 % Allowed : 17.51 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 8278 helix: 1.78 (0.10), residues: 3043 sheet: -0.55 (0.13), residues: 1505 loop : -0.85 (0.10), residues: 3730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1192 HIS 0.008 0.001 HIS G 14 PHE 0.027 0.002 PHE A 112 TYR 0.020 0.002 TYR M1124 ARG 0.013 0.001 ARG d1080 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 494 time to evaluate : 5.270 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: A 104 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7779 (mtp) REVERT: A 446 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 565 MET cc_start: 0.8746 (mmm) cc_final: 0.7788 (mmm) REVERT: A 1221 MET cc_start: 0.7562 (mmm) cc_final: 0.7230 (mmt) REVERT: A 1262 MET cc_start: 0.7650 (mmp) cc_final: 0.7437 (mmt) REVERT: A 1440 MET cc_start: 0.8102 (tpp) cc_final: 0.7486 (mmt) REVERT: B 298 MET cc_start: 0.7812 (mmt) cc_final: 0.7448 (mmt) REVERT: D 128 GLN cc_start: 0.6897 (tp-100) cc_final: 0.6230 (mp10) REVERT: E 98 ASN cc_start: 0.7681 (t0) cc_final: 0.7429 (t0) REVERT: G 1 MET cc_start: 0.5105 (tmm) cc_final: 0.4032 (ttt) REVERT: G 104 MET cc_start: 0.3329 (ptt) cc_final: 0.2611 (ptp) REVERT: G 110 ARG cc_start: 0.7494 (tpt170) cc_final: 0.7118 (tpm170) REVERT: G 144 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8238 (ttm110) REVERT: G 146 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7649 (tmtt) REVERT: H 14 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7082 (t70) REVERT: H 123 MET cc_start: 0.8548 (ttp) cc_final: 0.8296 (ttt) REVERT: H 130 ASN cc_start: 0.7897 (m110) cc_final: 0.7037 (m-40) REVERT: H 133 HIS cc_start: 0.7135 (p-80) cc_final: 0.6823 (p-80) REVERT: I 14 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8038 (tt) REVERT: I 33 ARG cc_start: 0.7010 (mmm-85) cc_final: 0.6549 (tpp-160) REVERT: J 1 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7362 (mpp) REVERT: L 26 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8349 (p0) REVERT: M 468 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8783 (mp) REVERT: M 650 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (p0) REVERT: M 725 MET cc_start: 0.8464 (mmp) cc_final: 0.8151 (mmp) REVERT: M 1137 LEU cc_start: 0.8424 (mt) cc_final: 0.7795 (tm) REVERT: b 660 LEU cc_start: 0.8447 (mm) cc_final: 0.8111 (mp) REVERT: b 705 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: b 732 CYS cc_start: 0.8223 (t) cc_final: 0.8020 (m) REVERT: b 746 MET cc_start: 0.6401 (mmm) cc_final: 0.6164 (mmm) REVERT: b 780 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6411 (m) REVERT: b 971 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7669 (tptp) REVERT: b 995 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: d 57 MET cc_start: 0.8236 (mmm) cc_final: 0.7852 (mmt) REVERT: d 230 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8895 (mm) REVERT: d 410 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.2969 (mt) REVERT: d 647 THR cc_start: 0.3844 (OUTLIER) cc_final: 0.3419 (p) REVERT: d 954 MET cc_start: 0.8800 (mmm) cc_final: 0.8505 (mmp) REVERT: d 1134 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7548 (mp0) outliers start: 117 outliers final: 75 residues processed: 578 average time/residue: 1.4235 time to fit residues: 1061.3046 Evaluate side-chains 572 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 482 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 650 ASP Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 905 ASP Chi-restraints excluded: chain M residue 935 GLU Chi-restraints excluded: chain M residue 945 LEU Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1168 ILE Chi-restraints excluded: chain M residue 1172 THR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 310 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 672 ILE Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 995 PHE Chi-restraints excluded: chain d residue 230 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 350 MET Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 647 THR Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 497 optimal weight: 50.0000 chunk 800 optimal weight: 4.9990 chunk 488 optimal weight: 0.0070 chunk 379 optimal weight: 1.9990 chunk 556 optimal weight: 50.0000 chunk 839 optimal weight: 7.9990 chunk 772 optimal weight: 7.9990 chunk 668 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 516 optimal weight: 30.0000 chunk 410 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A1129 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 319 ASN B 683 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 168 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN a 289 ASN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 578 HIS ** d1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 63706 Z= 0.405 Angle : 0.665 41.256 85823 Z= 0.331 Chirality : 0.046 0.464 8667 Planarity : 0.004 0.065 11326 Dihedral : 11.498 179.097 10201 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.24 % Favored : 95.75 % Rotamer: Outliers : 1.85 % Allowed : 18.01 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 8278 helix: 1.75 (0.10), residues: 3039 sheet: -0.57 (0.13), residues: 1495 loop : -0.89 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1192 HIS 0.011 0.001 HIS G 14 PHE 0.032 0.002 PHE A 112 TYR 0.030 0.002 TYR b 510 ARG 0.014 0.001 ARG d1080 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16556 Ramachandran restraints generated. 8278 Oldfield, 0 Emsley, 8278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 496 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7785 (mtp) REVERT: A 446 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 565 MET cc_start: 0.8764 (mmm) cc_final: 0.7769 (mmm) REVERT: A 1129 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7024 (p0) REVERT: A 1221 MET cc_start: 0.7684 (mmm) cc_final: 0.7458 (mmt) REVERT: A 1228 MET cc_start: 0.7696 (mpt) cc_final: 0.7400 (mpt) REVERT: A 1440 MET cc_start: 0.8081 (tpp) cc_final: 0.7452 (mmt) REVERT: D 128 GLN cc_start: 0.6839 (tp-100) cc_final: 0.6177 (mp10) REVERT: E 98 ASN cc_start: 0.7679 (t0) cc_final: 0.7436 (t0) REVERT: E 141 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: G 1 MET cc_start: 0.5045 (tmm) cc_final: 0.4164 (ttt) REVERT: G 104 MET cc_start: 0.3568 (ptt) cc_final: 0.2781 (ptp) REVERT: G 144 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8233 (ttm110) REVERT: G 146 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7651 (tmtt) REVERT: H 14 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7120 (t70) REVERT: H 123 MET cc_start: 0.8562 (ttp) cc_final: 0.8306 (ttt) REVERT: H 130 ASN cc_start: 0.7916 (m110) cc_final: 0.7068 (m-40) REVERT: H 133 HIS cc_start: 0.7141 (p-80) cc_final: 0.6823 (p-80) REVERT: I 33 ARG cc_start: 0.7017 (mmm-85) cc_final: 0.6555 (tpp-160) REVERT: J 1 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: M 468 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (mp) REVERT: M 725 MET cc_start: 0.8472 (mmp) cc_final: 0.8154 (mmp) REVERT: M 1137 LEU cc_start: 0.8427 (mt) cc_final: 0.7803 (tm) REVERT: a 114 MET cc_start: 0.8132 (tmm) cc_final: 0.7906 (ptt) REVERT: b 660 LEU cc_start: 0.8452 (mm) cc_final: 0.8110 (mp) REVERT: b 705 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7277 (pp20) REVERT: b 746 MET cc_start: 0.6570 (mmm) cc_final: 0.6331 (mmm) REVERT: b 780 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6458 (m) REVERT: b 971 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7678 (tptp) REVERT: b 995 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: d 57 MET cc_start: 0.8233 (mmm) cc_final: 0.7858 (mmt) REVERT: d 230 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8878 (mm) REVERT: d 410 LEU cc_start: 0.3535 (OUTLIER) cc_final: 0.2975 (mt) REVERT: d 647 THR cc_start: 0.3866 (OUTLIER) cc_final: 0.3442 (p) REVERT: d 954 MET cc_start: 0.8748 (mmm) cc_final: 0.8479 (mmp) REVERT: d 1134 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7552 (mp0) outliers start: 109 outliers final: 77 residues processed: 578 average time/residue: 1.4463 time to fit residues: 1075.3596 Evaluate side-chains 574 residues out of total 7400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 482 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain M residue 458 ASP Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 711 MET Chi-restraints excluded: chain M residue 724 GLN Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 905 ASP Chi-restraints excluded: chain M residue 935 GLU Chi-restraints excluded: chain M residue 945 LEU Chi-restraints excluded: chain M residue 1062 THR Chi-restraints excluded: chain M residue 1102 LEU Chi-restraints excluded: chain M residue 1103 ASP Chi-restraints excluded: chain M residue 1124 TYR Chi-restraints excluded: chain M residue 1168 ILE Chi-restraints excluded: chain M residue 1172 THR Chi-restraints excluded: chain M residue 1250 VAL Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain a residue 310 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 672 ILE Chi-restraints excluded: chain b residue 705 GLU Chi-restraints excluded: chain b residue 763 VAL Chi-restraints excluded: chain b residue 780 VAL Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 995 PHE Chi-restraints excluded: chain d residue 230 ILE Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 330 ASP Chi-restraints excluded: chain d residue 350 MET Chi-restraints excluded: chain d residue 382 PHE Chi-restraints excluded: chain d residue 410 LEU Chi-restraints excluded: chain d residue 534 MET Chi-restraints excluded: chain d residue 647 THR Chi-restraints excluded: chain d residue 742 VAL Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1065 VAL Chi-restraints excluded: chain d residue 1134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 843 random chunks: chunk 531 optimal weight: 50.0000 chunk 712 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 616 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 669 optimal weight: 10.0000 chunk 280 optimal weight: 50.0000 chunk 687 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS A1129 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 683 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.157736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106586 restraints weight = 111671.309| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.92 r_work: 0.3135 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 63706 Z= 0.357 Angle : 0.756 59.187 85823 Z= 0.406 Chirality : 0.046 1.019 8667 Planarity : 0.004 0.086 11326 Dihedral : 11.499 179.120 10201 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.31 % Favored : 95.68 % Rotamer: Outliers : 1.75 % Allowed : 18.18 % Favored : 80.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8278 helix: 1.78 (0.10), residues: 3039 sheet: -0.57 (0.13), residues: 1495 loop : -0.88 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1192 HIS 0.015 0.001 HIS G 4 PHE 0.027 0.002 PHE d 650 TYR 0.049 0.002 TYR M 740 ARG 0.015 0.000 ARG B 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20015.56 seconds wall clock time: 351 minutes 6.28 seconds (21066.28 seconds total)