Starting phenix.real_space_refine on Sat Apr 6 13:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cun_30473/04_2024/7cun_30473.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Se 13 7.20 5 Zn 2 6.06 5 S 291 5.16 5 C 36291 2.51 5 N 10234 2.21 5 O 10809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1623": "OE1" <-> "OE2" Residue "A ASP 1635": "OD1" <-> "OD2" Residue "A ARG 1657": "NH1" <-> "NH2" Residue "A ASP 1712": "OD1" <-> "OD2" Residue "A GLU 1722": "OE1" <-> "OE2" Residue "A ASP 1749": "OD1" <-> "OD2" Residue "A ASP 1751": "OD1" <-> "OD2" Residue "A ASP 1772": "OD1" <-> "OD2" Residue "A ASP 1792": "OD1" <-> "OD2" Residue "A GLU 1916": "OE1" <-> "OE2" Residue "A ASP 2069": "OD1" <-> "OD2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 725": "OD1" <-> "OD2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B ARG 866": "NH1" <-> "NH2" Residue "B ARG 991": "NH1" <-> "NH2" Residue "B ASP 1008": "OD1" <-> "OD2" Residue "B ARG 1112": "NH1" <-> "NH2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "B ASP 1135": "OD1" <-> "OD2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 726": "NH1" <-> "NH2" Residue "D ARG 739": "NH1" <-> "NH2" Residue "D ASP 759": "OD1" <-> "OD2" Residue "D PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 768": "OD1" <-> "OD2" Residue "D ARG 786": "NH1" <-> "NH2" Residue "D TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 891": "NH1" <-> "NH2" Residue "D GLU 905": "OE1" <-> "OE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 475": "OD1" <-> "OD2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "E ARG 495": "NH1" <-> "NH2" Residue "E ARG 573": "NH1" <-> "NH2" Residue "E ARG 654": "NH1" <-> "NH2" Residue "E ASP 823": "OD1" <-> "OD2" Residue "E ASP 844": "OD1" <-> "OD2" Residue "E ARG 849": "NH1" <-> "NH2" Residue "E ARG 850": "NH1" <-> "NH2" Residue "E ARG 968": "NH1" <-> "NH2" Residue "E ARG 971": "NH1" <-> "NH2" Residue "E PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 442": "OD1" <-> "OD2" Residue "F TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 549": "NH1" <-> "NH2" Residue "G ASP 30": "OD1" <-> "OD2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 182": "OE1" <-> "OE2" Residue "G TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 275": "OD1" <-> "OD2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 391": "OE1" <-> "OE2" Residue "G ASP 443": "OD1" <-> "OD2" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 535": "NH1" <-> "NH2" Residue "G GLU 572": "OE1" <-> "OE2" Residue "G TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 760": "OE1" <-> "OE2" Residue "G ARG 764": "NH1" <-> "NH2" Residue "G ARG 813": "NH1" <-> "NH2" Residue "G GLU 817": "OE1" <-> "OE2" Residue "G GLU 882": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H ARG 359": "NH1" <-> "NH2" Residue "H ARG 391": "NH1" <-> "NH2" Residue "H ASP 392": "OD1" <-> "OD2" Residue "H ARG 487": "NH1" <-> "NH2" Residue "H GLU 513": "OE1" <-> "OE2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H ARG 539": "NH1" <-> "NH2" Residue "H ARG 567": "NH1" <-> "NH2" Residue "H ASP 637": "OD1" <-> "OD2" Residue "H ARG 643": "NH1" <-> "NH2" Residue "H ARG 712": "NH1" <-> "NH2" Residue "H ARG 738": "NH1" <-> "NH2" Residue "H GLU 766": "OE1" <-> "OE2" Residue "H TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 865": "OD1" <-> "OD2" Residue "H ASP 878": "OD1" <-> "OD2" Residue "H ARG 883": "NH1" <-> "NH2" Residue "H TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 926": "OD1" <-> "OD2" Residue "H ASP 930": "OD1" <-> "OD2" Residue "H ARG 954": "NH1" <-> "NH2" Residue "H ARG 981": "NH1" <-> "NH2" Residue "H TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 31": "OD1" <-> "OD2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 97": "OD1" <-> "OD2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I ASP 307": "OD1" <-> "OD2" Residue "I PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 449": "OD1" <-> "OD2" Residue "I PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 500": "NH1" <-> "NH2" Residue "I ASP 605": "OD1" <-> "OD2" Residue "I GLU 609": "OE1" <-> "OE2" Residue "I ASP 610": "OD1" <-> "OD2" Residue "I GLU 621": "OE1" <-> "OE2" Residue "I GLU 629": "OE1" <-> "OE2" Residue "I ASP 638": "OD1" <-> "OD2" Residue "I ASP 640": "OD1" <-> "OD2" Residue "I PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 177": "OE1" <-> "OE2" Residue "K ASP 199": "OD1" <-> "OD2" Residue "K ARG 217": "NH1" <-> "NH2" Residue "K ASP 218": "OD1" <-> "OD2" Residue "K GLU 224": "OE1" <-> "OE2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "K GLU 263": "OE1" <-> "OE2" Residue "K ARG 264": "NH1" <-> "NH2" Residue "K TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 512": "OE1" <-> "OE2" Residue "K GLU 531": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 100": "OE1" <-> "OE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P ARG 105": "NH1" <-> "NH2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P ASP 177": "OD1" <-> "OD2" Residue "P GLU 226": "OE1" <-> "OE2" Residue "P GLU 238": "OE1" <-> "OE2" Residue "P ASP 316": "OD1" <-> "OD2" Residue "P GLU 393": "OE1" <-> "OE2" Residue "P GLU 437": "OE1" <-> "OE2" Residue "P PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 565": "OE1" <-> "OE2" Residue "P PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 2": "OD1" <-> "OD2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 204": "OD1" <-> "OD2" Residue "Q TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 253": "OD1" <-> "OD2" Residue "Q TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 57642 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 4653 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 317} Link IDs: {'PTRANS': 39, 'TRANS': 690} Chain breaks: 3 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1115 Unresolved non-hydrogen angles: 1424 Unresolved non-hydrogen dihedrals: 919 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 14, 'PHE:plan': 18, 'GLU:plan': 19, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 597 Chain: "B" Number of atoms: 7541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 7541 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1005} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 986 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 397 Chain: "D" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 5942 Classifications: {'peptide': 827} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 39, 'TRANS': 787} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 796 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 302 Chain: "E" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 5288 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 227} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 733} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 735 Unresolved non-hydrogen angles: 948 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 12, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 349 Chain: "F" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 3822 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 489} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 225 Chain: "G" Number of atoms: 6826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6826 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 31, 'TRANS': 863} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 6657 Classifications: {'peptide': 912} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PTRANS': 40, 'TRANS': 871} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 677 Unresolved non-hydrogen angles: 862 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 340 Chain: "I" Number of atoms: 4701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4701 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 46, 'TRANS': 577} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "K" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 3792 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 26, 'TRANS': 561} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 913 Unresolved non-hydrogen angles: 1154 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 13, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 467 Chain: "P" Number of atoms: 4535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4535 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 555} Chain: "Q" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2366 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 281} Chain: "U" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 1515 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 303} Link IDs: {'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 303 Planarities with less than four sites: {'UNK:plan-1': 303} Unresolved non-hydrogen planarities: 303 Chain: "K" 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: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.97, per 1000 atoms: 0.40 Number of scatterers: 57642 At special positions: 0 Unit cell: (189.9, 223.66, 282.74, 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) Se 13 33.99 Zn 2 29.99 Mn 2 24.99 S 291 16.00 O 10809 8.00 N 10234 7.00 C 36291 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: 17.52 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" NE2 HIS K 79 " pdb=" ZN K 702 " pdb="ZN ZN K 702 " - pdb=" NE2 HIS K 163 " pdb="ZN ZN K 702 " - pdb=" NE2 HIS K 74 " pdb="ZN ZN K 702 " - pdb=" NE2 HIS K 76 " 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15502 Finding SS restraints... Secondary structure from input PDB file: 394 helices and 25 sheets defined 62.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 1393 through 1403 Proline residue: A1399 - end of helix Processing helix chain 'A' and resid 1406 through 1425 removed outlier: 4.311A pdb=" N ALA A1410 " --> pdb=" O LEU A1406 " (cutoff:3.500A) Proline residue: A1416 - end of helix Processing helix chain 'A' and resid 1431 through 1445 Processing helix chain 'A' and resid 1447 through 1456 Processing helix chain 'A' and resid 1457 through 1475 removed outlier: 3.791A pdb=" N LEU A1461 " --> pdb=" O LEU A1457 " (cutoff:3.500A) Proline residue: A1470 - end of helix Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 4.226A pdb=" N ARG A1498 " --> pdb=" O LEU A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1519 removed outlier: 4.549A pdb=" N ARG A1511 " --> pdb=" O ALA A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1537 Processing helix chain 'A' and resid 1542 through 1558 Proline residue: A1554 - end of helix Processing helix chain 'A' and resid 1567 through 1572 Processing helix chain 'A' and resid 1572 through 1578 Processing helix chain 'A' and resid 1582 through 1592 Processing helix chain 'A' and resid 1597 through 1609 removed outlier: 3.620A pdb=" N ALA A1601 " --> pdb=" O GLY A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1625 removed outlier: 3.919A pdb=" N LEU A1625 " --> pdb=" O TRP A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1642 removed outlier: 3.567A pdb=" N GLN A1637 " --> pdb=" O CYS A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1668 removed outlier: 3.666A pdb=" N SER A1668 " --> pdb=" O PHE A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1681 Processing helix chain 'A' and resid 1690 through 1703 removed outlier: 4.215A pdb=" N ASP A1696 " --> pdb=" O SER A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1743 Processing helix chain 'A' and resid 1751 through 1770 Proline residue: A1763 - end of helix removed outlier: 3.949A pdb=" N CYS A1769 " --> pdb=" O LEU A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1780 Processing helix chain 'A' and resid 1791 through 1797 Processing helix chain 'A' and resid 1798 through 1801 Processing helix chain 'A' and resid 1805 through 1815 Proline residue: A1811 - end of helix Processing helix chain 'A' and resid 1825 through 1843 Processing helix chain 'A' and resid 1859 through 1864 removed outlier: 4.028A pdb=" N SER A1863 " --> pdb=" O GLY A1859 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1859 through 1864' Processing helix chain 'A' and resid 1864 through 1873 removed outlier: 3.581A pdb=" N LYS A1868 " --> pdb=" O MET A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1886 removed outlier: 3.854A pdb=" N LEU A1877 " --> pdb=" O HIS A1873 " (cutoff:3.500A) Proline residue: A1882 - end of helix removed outlier: 3.567A pdb=" N ALA A1886 " --> pdb=" O PRO A1882 " (cutoff:3.500A) Processing helix chain 'A' and resid 1905 through 1917 Processing helix chain 'A' and resid 1918 through 1923 removed outlier: 3.947A pdb=" N PHE A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1945 removed outlier: 3.881A pdb=" N CYS A1934 " --> pdb=" O ALA A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1969 Processing helix chain 'A' and resid 1970 through 1981 removed outlier: 5.026A pdb=" N LEU A1978 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN A1979 " --> pdb=" O ILE A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1986 Processing helix chain 'A' and resid 2044 through 2046 No H-bonds generated for 'chain 'A' and resid 2044 through 2046' Processing helix chain 'A' and resid 2047 through 2057 Processing helix chain 'A' and resid 2059 through 2074 Processing helix chain 'A' and resid 2077 through 2083 removed outlier: 3.894A pdb=" N ILE A2080 " --> pdb=" O ARG A2077 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2093 removed outlier: 4.256A pdb=" N SER A2093 " --> pdb=" O GLN A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2114 Processing helix chain 'A' and resid 2115 through 2120 removed outlier: 3.947A pdb=" N ALA A2119 " --> pdb=" O SER A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2121 through 2130 removed outlier: 3.606A pdb=" N CYS A2128 " --> pdb=" O THR A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 removed outlier: 3.758A pdb=" N THR A2139 " --> pdb=" O GLU A2135 " (cutoff:3.500A) Proline residue: A2145 - end of helix Processing helix chain 'A' and resid 2154 through 2169 Processing helix chain 'A' and resid 2173 through 2185 removed outlier: 3.778A pdb=" N ILE A2177 " --> pdb=" O PRO A2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.825A pdb=" N LEU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.535A pdb=" N TRP B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 89 Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 153 through 162 removed outlier: 5.968A pdb=" N GLU B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 186 removed outlier: 3.578A pdb=" N GLU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 171 - end of helix removed outlier: 3.812A pdb=" N ALA B 186 " --> pdb=" O CYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 229 through 238 removed outlier: 3.549A pdb=" N GLY B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 264 through 280 removed outlier: 4.175A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Proline residue: B 275 - end of helix Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.669A pdb=" N VAL B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.432A pdb=" N GLU B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 366 removed outlier: 3.974A pdb=" N VAL B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.699A pdb=" N VAL B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.746A pdb=" N ALA B 385 " --> pdb=" O HIS B 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 removed outlier: 4.467A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 445 through 470 removed outlier: 3.544A pdb=" N GLU B 449 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TYR B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.893A pdb=" N MET B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.526A pdb=" N THR B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 521 " --> pdb=" O MET B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 552 through 564 removed outlier: 4.124A pdb=" N CYS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 615 through 622 Processing helix chain 'B' and resid 644 through 665 removed outlier: 3.742A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 703 through 718 removed outlier: 3.879A pdb=" N HIS B 707 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 708 " --> pdb=" O GLY B 704 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 753 through 762 removed outlier: 3.566A pdb=" N LEU B 757 " --> pdb=" O SER B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 778 removed outlier: 3.775A pdb=" N GLN B 773 " --> pdb=" O THR B 769 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 794 removed outlier: 4.228A pdb=" N GLU B 791 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 792 " --> pdb=" O PRO B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 removed outlier: 3.850A pdb=" N LEU B 801 " --> pdb=" O MET B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 820 removed outlier: 4.255A pdb=" N LEU B 810 " --> pdb=" O PRO B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 836 Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.657A pdb=" N MET B 854 " --> pdb=" O GLN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 862 removed outlier: 3.583A pdb=" N ILE B 859 " --> pdb=" O ASP B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 869 removed outlier: 3.607A pdb=" N ARG B 869 " --> pdb=" O ARG B 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 866 through 869' Processing helix chain 'B' and resid 870 through 896 Processing helix chain 'B' and resid 923 through 946 removed outlier: 3.530A pdb=" N CYS B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1008 removed outlier: 3.604A pdb=" N GLU B 992 " --> pdb=" O CYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1019 removed outlier: 4.439A pdb=" N ALA B1012 " --> pdb=" O ASP B1008 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B1013 " --> pdb=" O PRO B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1023 No H-bonds generated for 'chain 'B' and resid 1021 through 1023' Processing helix chain 'B' and resid 1024 through 1030 removed outlier: 3.773A pdb=" N ALA B1030 " --> pdb=" O PRO B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1040 removed outlier: 4.478A pdb=" N HIS B1036 " --> pdb=" O PRO B1033 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B1037 " --> pdb=" O SER B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1047 Processing helix chain 'B' and resid 1050 through 1068 Processing helix chain 'B' and resid 1070 through 1087 Processing helix chain 'B' and resid 1092 through 1101 removed outlier: 3.718A pdb=" N ALA B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1114 Processing helix chain 'B' and resid 1117 through 1137 removed outlier: 3.947A pdb=" N ALA B1137 " --> pdb=" O ALA B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1151 removed outlier: 3.858A pdb=" N LEU B1150 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1202 Processing helix chain 'D' and resid 34 through 45 removed outlier: 3.672A pdb=" N ALA D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.760A pdb=" N LEU D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.768A pdb=" N TYR D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.817A pdb=" N LEU D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.194A pdb=" N GLN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.965A pdb=" N ARG D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 213 " --> pdb=" O PRO D 209 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 240 removed outlier: 3.862A pdb=" N LYS D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 removed outlier: 4.085A pdb=" N GLN D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.715A pdb=" N ARG D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 314 through 325 removed outlier: 3.908A pdb=" N LYS D 323 " --> pdb=" O GLN D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 387 through 405 removed outlier: 4.122A pdb=" N ARG D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 418 Processing helix chain 'D' and resid 424 through 437 removed outlier: 3.521A pdb=" N ARG D 428 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 453 removed outlier: 3.761A pdb=" N LEU D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 478 through 496 removed outlier: 3.892A pdb=" N ILE D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 514 removed outlier: 3.547A pdb=" N HIS D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.662A pdb=" N VAL D 518 " --> pdb=" O PRO D 515 " (cutoff:3.500A) Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.885A pdb=" N LEU D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 555 removed outlier: 4.245A pdb=" N VAL D 547 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 580 removed outlier: 4.404A pdb=" N ARG D 571 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 624 Processing helix chain 'D' and resid 628 through 650 Processing helix chain 'D' and resid 653 through 675 removed outlier: 3.658A pdb=" N ALA D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 710 removed outlier: 3.928A pdb=" N GLN D 699 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 741 removed outlier: 3.628A pdb=" N THR D 740 " --> pdb=" O VAL D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 765 removed outlier: 3.991A pdb=" N LEU D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 748 " --> pdb=" O LEU D 744 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 788 Proline residue: D 785 - end of helix removed outlier: 3.616A pdb=" N MET D 788 " --> pdb=" O MET D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 804 Processing helix chain 'E' and resid 186 through 204 Processing helix chain 'E' and resid 210 through 224 removed outlier: 3.561A pdb=" N ASP E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Proline residue: E 221 - end of helix Processing helix chain 'E' and resid 225 through 240 Proline residue: E 235 - end of helix removed outlier: 4.292A pdb=" N ILE E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.617A pdb=" N CYS E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 Proline residue: E 271 - end of helix removed outlier: 3.619A pdb=" N ASP E 274 " --> pdb=" O THR E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 283 through 288 Processing helix chain 'E' and resid 289 through 292 removed outlier: 3.723A pdb=" N ALA E 292 " --> pdb=" O PRO E 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 289 through 292' Processing helix chain 'E' and resid 293 through 315 Processing helix chain 'E' and resid 318 through 331 Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.544A pdb=" N LEU E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET E 347 " --> pdb=" O GLN E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 369 Proline residue: E 365 - end of helix Processing helix chain 'E' and resid 383 through 393 removed outlier: 3.761A pdb=" N MET E 387 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 403 through 413 removed outlier: 3.642A pdb=" N THR E 413 " --> pdb=" O PHE E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 431 removed outlier: 3.579A pdb=" N THR E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) Proline residue: E 428 - end of helix Processing helix chain 'E' and resid 439 through 459 Proline residue: E 457 - end of helix Processing helix chain 'E' and resid 471 through 478 Processing helix chain 'E' and resid 480 through 489 Processing helix chain 'E' and resid 494 through 510 Processing helix chain 'E' and resid 514 through 525 removed outlier: 4.060A pdb=" N ARG E 525 " --> pdb=" O HIS E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 removed outlier: 3.699A pdb=" N LEU E 532 " --> pdb=" O SER E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 563 Processing helix chain 'E' and resid 567 through 587 Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.699A pdb=" N LEU E 595 " --> pdb=" O GLY E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 604 Processing helix chain 'E' and resid 606 through 611 Processing helix chain 'E' and resid 612 through 616 removed outlier: 3.645A pdb=" N LEU E 615 " --> pdb=" O PRO E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 630 Processing helix chain 'E' and resid 640 through 662 Processing helix chain 'E' and resid 663 through 666 Processing helix chain 'E' and resid 667 through 679 removed outlier: 3.709A pdb=" N GLN E 679 " --> pdb=" O THR E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 696 Processing helix chain 'E' and resid 732 through 738 removed outlier: 3.783A pdb=" N ALA E 738 " --> pdb=" O ARG E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 788 removed outlier: 3.530A pdb=" N THR E 776 " --> pdb=" O VAL E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 821 Processing helix chain 'E' and resid 834 through 839 Processing helix chain 'E' and resid 840 through 854 Processing helix chain 'E' and resid 855 through 865 removed outlier: 3.619A pdb=" N GLU E 859 " --> pdb=" O PRO E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 871 removed outlier: 3.800A pdb=" N LEU E 871 " --> pdb=" O PRO E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 891 removed outlier: 4.226A pdb=" N LEU E 878 " --> pdb=" O CYS E 874 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 891 " --> pdb=" O GLY E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 899 removed outlier: 3.696A pdb=" N HIS E 899 " --> pdb=" O ASP E 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 896 through 899' Processing helix chain 'E' and resid 900 through 917 Processing helix chain 'E' and resid 921 through 931 removed outlier: 3.731A pdb=" N GLY E 925 " --> pdb=" O PRO E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 932 through 934 No H-bonds generated for 'chain 'E' and resid 932 through 934' Processing helix chain 'E' and resid 935 through 953 Processing helix chain 'E' and resid 981 through 995 removed outlier: 3.575A pdb=" N ASN E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1000 Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.633A pdb=" N ASN F 15 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN F 16 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 40 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 195 through 204 removed outlier: 4.327A pdb=" N MET F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 203 " --> pdb=" O MET F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 224 Processing helix chain 'F' and resid 334 through 339 Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.980A pdb=" N LEU F 389 " --> pdb=" O ASN F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.962A pdb=" N LEU F 427 " --> pdb=" O TYR F 423 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 429 " --> pdb=" O GLY F 425 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 430 " --> pdb=" O PRO F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 470 removed outlier: 3.514A pdb=" N VAL F 470 " --> pdb=" O GLU F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 583 through 590 removed outlier: 3.603A pdb=" N MET F 587 " --> pdb=" O PRO F 583 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR F 590 " --> pdb=" O GLN F 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 4.113A pdb=" N SER G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 Proline residue: G 49 - end of helix Processing helix chain 'G' and resid 57 through 74 removed outlier: 3.691A pdb=" N VAL G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 100 through 109 Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 152 through 168 removed outlier: 3.682A pdb=" N GLU G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 186 removed outlier: 4.846A pdb=" N ASN G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS G 179 " --> pdb=" O GLY G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 199 through 204 removed outlier: 3.573A pdb=" N MET G 204 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 225 Processing helix chain 'G' and resid 227 through 245 Processing helix chain 'G' and resid 248 through 263 Processing helix chain 'G' and resid 265 through 283 removed outlier: 3.878A pdb=" N LYS G 269 " --> pdb=" O ARG G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 301 Processing helix chain 'G' and resid 305 through 320 Processing helix chain 'G' and resid 322 through 328 removed outlier: 3.758A pdb=" N PHE G 328 " --> pdb=" O ILE G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 351 Processing helix chain 'G' and resid 352 through 354 No H-bonds generated for 'chain 'G' and resid 352 through 354' Processing helix chain 'G' and resid 356 through 374 removed outlier: 3.745A pdb=" N ALA G 360 " --> pdb=" O ASN G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 393 removed outlier: 3.837A pdb=" N LEU G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN G 384 " --> pdb=" O LEU G 380 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 423 removed outlier: 3.954A pdb=" N THR G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 426 No H-bonds generated for 'chain 'G' and resid 424 through 426' Processing helix chain 'G' and resid 427 through 438 removed outlier: 3.531A pdb=" N VAL G 431 " --> pdb=" O SER G 427 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR G 433 " --> pdb=" O SER G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 457 Processing helix chain 'G' and resid 460 through 478 removed outlier: 4.353A pdb=" N GLY G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY G 469 " --> pdb=" O ASP G 465 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP G 470 " --> pdb=" O GLY G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 501 Processing helix chain 'G' and resid 506 through 518 removed outlier: 4.206A pdb=" N LYS G 510 " --> pdb=" O SER G 506 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU G 518 " --> pdb=" O LYS G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 537 Processing helix chain 'G' and resid 539 through 551 removed outlier: 4.167A pdb=" N THR G 551 " --> pdb=" O GLN G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 576 Processing helix chain 'G' and resid 583 through 606 removed outlier: 4.294A pdb=" N LEU G 587 " --> pdb=" O TYR G 583 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 588 " --> pdb=" O SER G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 615 through 641 Processing helix chain 'G' and resid 645 through 650 removed outlier: 4.216A pdb=" N ILE G 649 " --> pdb=" O PRO G 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 650 " --> pdb=" O PRO G 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 645 through 650' Processing helix chain 'G' and resid 666 through 693 removed outlier: 4.026A pdb=" N GLN G 670 " --> pdb=" O ARG G 666 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER G 692 " --> pdb=" O LEU G 688 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE G 693 " --> pdb=" O TYR G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 696 through 720 Processing helix chain 'G' and resid 742 through 760 Processing helix chain 'G' and resid 772 through 785 Processing helix chain 'G' and resid 792 through 796 Processing helix chain 'G' and resid 840 through 844 removed outlier: 3.791A pdb=" N LEU G 843 " --> pdb=" O LYS G 840 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE G 844 " --> pdb=" O PRO G 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 840 through 844' Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 82 through 97 removed outlier: 4.016A pdb=" N LYS H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 96 " --> pdb=" O LEU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 119 Processing helix chain 'H' and resid 136 through 157 Processing helix chain 'H' and resid 170 through 192 removed outlier: 3.641A pdb=" N LYS H 192 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 207 removed outlier: 4.044A pdb=" N SER H 198 " --> pdb=" O GLN H 194 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE H 199 " --> pdb=" O ALA H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 233 Proline residue: H 227 - end of helix removed outlier: 3.594A pdb=" N GLU H 233 " --> pdb=" O MET H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 259 removed outlier: 3.742A pdb=" N THR H 245 " --> pdb=" O LEU H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 283 removed outlier: 4.171A pdb=" N GLU H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 337 removed outlier: 3.884A pdb=" N ILE H 331 " --> pdb=" O SER H 327 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS H 332 " --> pdb=" O GLN H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 348 Processing helix chain 'H' and resid 355 through 372 Processing helix chain 'H' and resid 377 through 396 Processing helix chain 'H' and resid 400 through 408 removed outlier: 4.089A pdb=" N ASN H 404 " --> pdb=" O SER H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 423 Processing helix chain 'H' and resid 434 through 446 removed outlier: 3.783A pdb=" N ASN H 438 " --> pdb=" O SER H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 449 No H-bonds generated for 'chain 'H' and resid 447 through 449' Processing helix chain 'H' and resid 452 through 460 removed outlier: 3.827A pdb=" N VAL H 456 " --> pdb=" O ASP H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 465 Processing helix chain 'H' and resid 466 through 470 removed outlier: 3.798A pdb=" N LEU H 469 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS H 470 " --> pdb=" O THR H 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 466 through 470' Processing helix chain 'H' and resid 473 through 485 removed outlier: 4.045A pdb=" N LEU H 477 " --> pdb=" O GLU H 473 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER H 485 " --> pdb=" O MET H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 518 Processing helix chain 'H' and resid 521 through 536 Processing helix chain 'H' and resid 551 through 559 removed outlier: 3.976A pdb=" N GLY H 556 " --> pdb=" O SER H 552 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL H 557 " --> pdb=" O VAL H 553 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 559 " --> pdb=" O SER H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 583 removed outlier: 3.531A pdb=" N ARG H 567 " --> pdb=" O ASP H 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 601 removed outlier: 4.152A pdb=" N GLN H 591 " --> pdb=" O SER H 587 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 626 removed outlier: 3.563A pdb=" N ARG H 608 " --> pdb=" O SER H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 649 removed outlier: 3.709A pdb=" N SER H 640 " --> pdb=" O SER H 636 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG H 649 " --> pdb=" O TYR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 670 removed outlier: 3.548A pdb=" N ALA H 660 " --> pdb=" O ARG H 656 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU H 661 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP H 670 " --> pdb=" O PHE H 666 " (cutoff:3.500A) Processing helix chain 'H' and resid 688 through 702 removed outlier: 3.615A pdb=" N LYS H 692 " --> pdb=" O ASN H 688 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS H 702 " --> pdb=" O ALA H 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 725 Processing helix chain 'H' and resid 755 through 763 removed outlier: 3.502A pdb=" N LYS H 763 " --> pdb=" O SER H 759 " (cutoff:3.500A) Processing helix chain 'H' and resid 766 through 782 Processing helix chain 'H' and resid 810 through 829 removed outlier: 3.719A pdb=" N ASN H 829 " --> pdb=" O THR H 825 " (cutoff:3.500A) Processing helix chain 'H' and resid 832 through 846 Processing helix chain 'H' and resid 848 through 864 Processing helix chain 'H' and resid 865 through 868 Processing helix chain 'H' and resid 877 through 890 Processing helix chain 'H' and resid 893 through 901 Processing helix chain 'H' and resid 908 through 917 removed outlier: 3.573A pdb=" N ALA H 912 " --> pdb=" O ASP H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 924 through 932 removed outlier: 4.597A pdb=" N TYR H 929 " --> pdb=" O ASP H 926 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP H 930 " --> pdb=" O SER H 927 " (cutoff:3.500A) Processing helix chain 'H' and resid 934 through 948 Processing helix chain 'H' and resid 950 through 962 removed outlier: 3.597A pdb=" N ILE H 956 " --> pdb=" O ASP H 952 " (cutoff:3.500A) Processing helix chain 'H' and resid 974 through 994 Processing helix chain 'I' and resid 110 through 114 removed outlier: 3.759A pdb=" N THR I 114 " --> pdb=" O PRO I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 146 removed outlier: 3.648A pdb=" N ARG I 146 " --> pdb=" O ASN I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'I' and resid 204 through 208 removed outlier: 3.643A pdb=" N ALA I 208 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 291 removed outlier: 3.908A pdb=" N ASN I 291 " --> pdb=" O LEU I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 315 removed outlier: 4.421A pdb=" N LEU I 308 " --> pdb=" O VAL I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 318 No H-bonds generated for 'chain 'I' and resid 316 through 318' Processing helix chain 'I' and resid 332 through 343 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.546A pdb=" N GLU I 366 " --> pdb=" O PHE I 362 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE I 368 " --> pdb=" O HIS I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.904A pdb=" N LYS I 372 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU I 373 " --> pdb=" O GLN I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 404 through 412 Processing helix chain 'I' and resid 453 through 465 removed outlier: 4.054A pdb=" N LYS I 459 " --> pdb=" O ILE I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 602 Processing helix chain 'I' and resid 621 through 623 No H-bonds generated for 'chain 'I' and resid 621 through 623' Processing helix chain 'I' and resid 641 through 653 removed outlier: 3.736A pdb=" N LYS I 653 " --> pdb=" O ASP I 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 4.103A pdb=" N GLU K 88 " --> pdb=" O TYR K 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET K 89 " --> pdb=" O PHE K 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 89' Processing helix chain 'K' and resid 104 through 117 removed outlier: 3.821A pdb=" N ILE K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 121 removed outlier: 3.920A pdb=" N LYS K 121 " --> pdb=" O VAL K 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 118 through 121' Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 219 through 237 removed outlier: 3.561A pdb=" N ARG K 223 " --> pdb=" O SER K 219 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 266 removed outlier: 4.201A pdb=" N LEU K 254 " --> pdb=" O ARG K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 288 removed outlier: 3.643A pdb=" N ALA K 281 " --> pdb=" O LEU K 277 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN K 282 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE K 288 " --> pdb=" O TYR K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 removed outlier: 3.894A pdb=" N ARG K 297 " --> pdb=" O ASN K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.792A pdb=" N ALA K 347 " --> pdb=" O ARG K 344 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY K 348 " --> pdb=" O LYS K 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 344 through 348' Processing helix chain 'K' and resid 365 through 372 Processing helix chain 'K' and resid 400 through 412 removed outlier: 3.643A pdb=" N ILE K 404 " --> pdb=" O ASP K 400 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET K 405 " --> pdb=" O ALA K 401 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 412 " --> pdb=" O VAL K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 440 removed outlier: 3.702A pdb=" N PHE K 428 " --> pdb=" O LYS K 424 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN K 435 " --> pdb=" O GLN K 431 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG K 438 " --> pdb=" O GLU K 434 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 439 " --> pdb=" O GLN K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 476 removed outlier: 3.840A pdb=" N MET K 471 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA K 472 " --> pdb=" O LYS K 468 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY K 474 " --> pdb=" O GLU K 470 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 475 " --> pdb=" O MET K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 509 removed outlier: 3.815A pdb=" N LYS K 506 " --> pdb=" O GLU K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 540 Processing helix chain 'K' and resid 586 through 597 removed outlier: 3.875A pdb=" N LEU K 597 " --> pdb=" O LEU K 593 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 20 removed outlier: 4.145A pdb=" N ASP P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 43 removed outlier: 4.693A pdb=" N SER P 36 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 50 removed outlier: 3.913A pdb=" N GLU P 50 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 57 removed outlier: 4.146A pdb=" N ASP P 57 " --> pdb=" O PRO P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 74 removed outlier: 3.774A pdb=" N GLY P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 86 removed outlier: 3.869A pdb=" N VAL P 86 " --> pdb=" O PRO P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 98 removed outlier: 3.733A pdb=" N LEU P 93 " --> pdb=" O LEU P 89 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR P 98 " --> pdb=" O GLU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 116 Processing helix chain 'P' and resid 120 through 136 removed outlier: 4.912A pdb=" N VAL P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) Proline residue: P 130 - end of helix Processing helix chain 'P' and resid 140 through 148 removed outlier: 3.933A pdb=" N ARG P 144 " --> pdb=" O TRP P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 174 Processing helix chain 'P' and resid 178 through 193 removed outlier: 4.141A pdb=" N ARG P 182 " --> pdb=" O THR P 178 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA P 184 " --> pdb=" O MSE P 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 204 removed outlier: 3.577A pdb=" N VAL P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 204 " --> pdb=" O ASN P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 214 removed outlier: 3.502A pdb=" N MSE P 208 " --> pdb=" O GLU P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 235 removed outlier: 4.196A pdb=" N GLU P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 240 removed outlier: 3.913A pdb=" N ASP P 239 " --> pdb=" O PRO P 236 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU P 240 " --> pdb=" O GLN P 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 236 through 240' Processing helix chain 'P' and resid 244 through 253 removed outlier: 3.758A pdb=" N GLU P 253 " --> pdb=" O ARG P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 266 Processing helix chain 'P' and resid 267 through 274 Processing helix chain 'P' and resid 274 through 282 removed outlier: 4.401A pdb=" N ILE P 278 " --> pdb=" O VAL P 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR P 279 " --> pdb=" O GLY P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 289 removed outlier: 3.858A pdb=" N ALA P 286 " --> pdb=" O ASP P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 312 removed outlier: 3.998A pdb=" N ARG P 299 " --> pdb=" O GLU P 295 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS P 307 " --> pdb=" O SER P 303 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU P 308 " --> pdb=" O HIS P 304 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 325 Processing helix chain 'P' and resid 325 through 335 removed outlier: 3.652A pdb=" N CYS P 329 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER P 335 " --> pdb=" O LYS P 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 349 removed outlier: 3.697A pdb=" N LYS P 342 " --> pdb=" O ASN P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 357 Processing helix chain 'P' and resid 360 through 374 removed outlier: 3.845A pdb=" N HIS P 364 " --> pdb=" O ASN P 360 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU P 366 " --> pdb=" O ILE P 362 " (cutoff:3.500A) Proline residue: P 367 - end of helix Processing helix chain 'P' and resid 377 through 385 removed outlier: 3.794A pdb=" N ARG P 381 " --> pdb=" O CYS P 377 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN P 383 " --> pdb=" O GLU P 379 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 404 Processing helix chain 'P' and resid 404 through 412 removed outlier: 3.830A pdb=" N VAL P 409 " --> pdb=" O LEU P 405 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU P 410 " --> pdb=" O PRO P 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 417 through 427 Processing helix chain 'P' and resid 427 through 432 removed outlier: 4.188A pdb=" N GLY P 432 " --> pdb=" O PRO P 428 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 442 Processing helix chain 'P' and resid 442 through 451 Processing helix chain 'P' and resid 455 through 473 removed outlier: 3.867A pdb=" N ARG P 459 " --> pdb=" O VAL P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 482 through 488 Processing helix chain 'P' and resid 494 through 509 removed outlier: 3.797A pdb=" N ARG P 498 " --> pdb=" O ASN P 494 " (cutoff:3.500A) Processing helix chain 'P' and resid 515 through 520 removed outlier: 4.249A pdb=" N LYS P 519 " --> pdb=" O ASP P 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 521 through 528 removed outlier: 3.523A pdb=" N VAL P 525 " --> pdb=" O MSE P 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 533 through 548 removed outlier: 3.651A pdb=" N ARG P 537 " --> pdb=" O VAL P 533 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE P 538 " --> pdb=" O ALA P 534 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN P 539 " --> pdb=" O ASN P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 552 through 559 removed outlier: 3.516A pdb=" N GLU P 559 " --> pdb=" O THR P 555 " (cutoff:3.500A) Processing helix chain 'P' and resid 559 through 568 Processing helix chain 'P' and resid 573 through 586 Processing helix chain 'Q' and resid 3 through 18 Processing helix chain 'Q' and resid 24 through 40 Processing helix chain 'Q' and resid 61 through 72 Processing helix chain 'Q' and resid 93 through 107 Processing helix chain 'Q' and resid 128 through 137 Processing helix chain 'Q' and resid 140 through 151 removed outlier: 3.832A pdb=" N LYS Q 144 " --> pdb=" O ALA Q 140 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP Q 151 " --> pdb=" O THR Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 182 removed outlier: 3.801A pdb=" N ILE Q 180 " --> pdb=" O THR Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 201 Processing helix chain 'Q' and resid 221 through 231 Processing helix chain 'Q' and resid 264 through 268 Processing helix chain 'U' and resid 82 through 91 Processing helix chain 'U' and resid 98 through 106 removed outlier: 4.418A pdb=" N UNK U 102 " --> pdb=" O UNK U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 119 removed outlier: 3.563A pdb=" N UNK U 116 " --> pdb=" O UNK U 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK U 119 " --> pdb=" O UNK U 115 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 131 Processing helix chain 'U' and resid 139 through 146 Processing helix chain 'U' and resid 149 through 159 removed outlier: 4.295A pdb=" N UNK U 153 " --> pdb=" O UNK U 149 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N UNK U 159 " --> pdb=" O UNK U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 171 removed outlier: 3.545A pdb=" N UNK U 169 " --> pdb=" O UNK U 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK U 171 " --> pdb=" O UNK U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 185 removed outlier: 3.794A pdb=" N UNK U 182 " --> pdb=" O UNK U 178 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK U 183 " --> pdb=" O UNK U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 202 removed outlier: 3.775A pdb=" N UNK U 195 " --> pdb=" O UNK U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 218 Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'U' and resid 253 through 258 Processing helix chain 'U' and resid 259 through 271 removed outlier: 3.588A pdb=" N UNK U 263 " --> pdb=" O UNK U 259 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK U 271 " --> pdb=" O UNK U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 288 removed outlier: 3.539A pdb=" N UNK U 283 " --> pdb=" O UNK U 279 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 309 removed outlier: 4.208A pdb=" N UNK U 297 " --> pdb=" O UNK U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 313 through 323 removed outlier: 3.940A pdb=" N UNK U 317 " --> pdb=" O UNK U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 406 through 418 removed outlier: 3.738A pdb=" N UNK U 418 " --> pdb=" O UNK U 414 " (cutoff:3.500A) Processing helix chain 'U' and resid 422 through 436 Processing helix chain 'U' and resid 507 through 511 removed outlier: 3.850A pdb=" N UNK U 511 " --> pdb=" O UNK U 508 " (cutoff:3.500A) Processing helix chain 'U' and resid 512 through 523 removed outlier: 3.570A pdb=" N UNK U 521 " --> pdb=" O UNK U 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 820 through 821 removed outlier: 3.753A pdb=" N ALA D 820 " --> pdb=" O GLU D 852 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D 886 " --> pdb=" O ARG D 889 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG D 891 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN D 884 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 845 through 847 removed outlier: 3.819A pdb=" N ASP D 846 " --> pdb=" O VAL D 896 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 896 " --> pdb=" O ASP D 846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 872 through 875 removed outlier: 3.530A pdb=" N VAL D 863 " --> pdb=" O ILE D 875 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 911 " --> pdb=" O MET D 929 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET D 929 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 64 removed outlier: 3.923A pdb=" N ALA F 64 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 170 through 171 removed outlier: 5.927A pdb=" N ALA F 170 " --> pdb=" O TYR F 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 231 through 232 Processing sheet with id=AA7, first strand: chain 'F' and resid 307 through 310 removed outlier: 3.627A pdb=" N GLY F 366 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL F 352 " --> pdb=" O PRO F 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AA9, first strand: chain 'G' and resid 831 through 833 removed outlier: 3.588A pdb=" N VAL G 831 " --> pdb=" O THR G 890 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 879 through 881 removed outlier: 3.694A pdb=" N VAL G 881 " --> pdb=" O VAL G 850 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 879 through 881 removed outlier: 3.694A pdb=" N VAL G 881 " --> pdb=" O VAL G 850 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR G 924 " --> pdb=" O VAL G 906 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 32 through 34 removed outlier: 7.942A pdb=" N MET I 32 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE I 99 " --> pdb=" O TYR I 124 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL I 123 " --> pdb=" O GLN I 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 210 through 212 Processing sheet with id=AB5, first strand: chain 'I' and resid 236 through 237 Processing sheet with id=AB6, first strand: chain 'I' and resid 295 through 299 removed outlier: 3.998A pdb=" N THR I 395 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS I 299 " --> pdb=" O THR I 395 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB8, first strand: chain 'I' and resid 606 through 610 removed outlier: 3.807A pdb=" N ARG K 516 " --> pdb=" O THR I 633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE I 635 " --> pdb=" O ARG K 516 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL K 557 " --> pdb=" O LEU K 564 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR K 558 " --> pdb=" O GLN K 550 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN K 550 " --> pdb=" O THR K 558 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 32 through 35 Processing sheet with id=AC1, first strand: chain 'K' and resid 148 through 149 removed outlier: 3.516A pdb=" N VAL K 148 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE K 156 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU K 205 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 180 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE K 207 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU K 206 " --> pdb=" O LEU K 417 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL K 419 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR K 208 " --> pdb=" O VAL K 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 326 through 329 Processing sheet with id=AC3, first strand: chain 'K' and resid 355 through 356 removed outlier: 4.057A pdb=" N MET K 356 " --> pdb=" O GLU K 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'Q' and resid 45 through 48 removed outlier: 6.411A pdb=" N GLN Q 46 " --> pdb=" O LEU Q 158 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL Q 237 " --> pdb=" O VAL Q 257 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE Q 259 " --> pdb=" O VAL Q 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG Q 239 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 52 through 54 Processing sheet with id=AC6, first strand: chain 'Q' and resid 80 through 82 Processing sheet with id=AC7, first strand: chain 'Q' and resid 202 through 203 removed outlier: 6.720A pdb=" N ASP Q 202 " --> pdb=" O PHE Q 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 3098 hydrogen bonds defined for protein. 9087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.84 Time building geometry restraints manager: 19.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 20146 1.37 - 1.52: 16055 1.52 - 1.66: 21926 1.66 - 1.81: 378 1.81 - 1.95: 77 Bond restraints: 58582 Sorted by residual: bond pdb=" C ILE G 198 " pdb=" N PRO G 199 " ideal model delta sigma weight residual 1.337 1.355 -0.019 9.80e-03 1.04e+04 3.70e+00 bond pdb=" N GLY E 741 " pdb=" CA GLY E 741 " ideal model delta sigma weight residual 1.443 1.465 -0.022 1.37e-02 5.33e+03 2.66e+00 bond pdb=" CA GLY K 276 " pdb=" C GLY K 276 " ideal model delta sigma weight residual 1.511 1.527 -0.016 1.02e-02 9.61e+03 2.51e+00 bond pdb=" N GLY A1475 " pdb=" CA GLY A1475 " ideal model delta sigma weight residual 1.443 1.463 -0.020 1.37e-02 5.33e+03 2.23e+00 bond pdb=" C PRO E 760 " pdb=" N PRO E 761 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 ... (remaining 58577 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.61: 1177 105.61 - 112.72: 31826 112.72 - 119.84: 18435 119.84 - 126.95: 27840 126.95 - 134.07: 597 Bond angle restraints: 79875 Sorted by residual: angle pdb=" N PRO E 205 " pdb=" CA PRO E 205 " pdb=" CB PRO E 205 " ideal model delta sigma weight residual 102.65 110.68 -8.03 6.80e-01 2.16e+00 1.39e+02 angle pdb=" N PRO B 57 " pdb=" CA PRO B 57 " pdb=" CB PRO B 57 " ideal model delta sigma weight residual 102.28 110.25 -7.97 7.50e-01 1.78e+00 1.13e+02 angle pdb=" N PRO B 258 " pdb=" CA PRO B 258 " pdb=" CB PRO B 258 " ideal model delta sigma weight residual 102.36 110.44 -8.08 7.80e-01 1.64e+00 1.07e+02 angle pdb=" N PRO I 360 " pdb=" CA PRO I 360 " pdb=" CB PRO I 360 " ideal model delta sigma weight residual 103.08 111.55 -8.47 9.70e-01 1.06e+00 7.62e+01 angle pdb=" N PRO K 324 " pdb=" CA PRO K 324 " pdb=" CB PRO K 324 " ideal model delta sigma weight residual 103.30 110.24 -6.94 8.00e-01 1.56e+00 7.53e+01 ... (remaining 79870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 33467 17.96 - 35.93: 1730 35.93 - 53.89: 220 53.89 - 71.86: 27 71.86 - 89.82: 24 Dihedral angle restraints: 35468 sinusoidal: 11701 harmonic: 23767 Sorted by residual: dihedral pdb=" CA TYR B 848 " pdb=" C TYR B 848 " pdb=" N THR B 849 " pdb=" CA THR B 849 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" N PRO I 360 " pdb=" C PRO I 360 " pdb=" CA PRO I 360 " pdb=" CB PRO I 360 " ideal model delta harmonic sigma weight residual 115.10 125.30 -10.20 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" N PRO E 740 " pdb=" C PRO E 740 " pdb=" CA PRO E 740 " pdb=" CB PRO E 740 " ideal model delta harmonic sigma weight residual 115.10 125.19 -10.09 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 35465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 8467 0.061 - 0.121: 995 0.121 - 0.182: 26 0.182 - 0.243: 76 0.243 - 0.304: 34 Chirality restraints: 9598 Sorted by residual: chirality pdb=" CA PRO I 360 " pdb=" N PRO I 360 " pdb=" C PRO I 360 " pdb=" CB PRO I 360 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA PRO E 740 " pdb=" N PRO E 740 " pdb=" C PRO E 740 " pdb=" CB PRO E 740 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE K 207 " pdb=" CA ILE K 207 " pdb=" CG1 ILE K 207 " pdb=" CG2 ILE K 207 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 9595 not shown) Planarity restraints: 10466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1881 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO A1882 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A1882 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1882 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 706 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO H 707 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 707 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 707 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B1101 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B1102 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B1102 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1102 " 0.030 5.00e-02 4.00e+02 ... (remaining 10463 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 216 2.50 - 3.10: 42258 3.10 - 3.70: 87974 3.70 - 4.30: 116681 4.30 - 4.90: 193054 Nonbonded interactions: 440183 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 85 " pdb="MN MN Q 502 " model vdw 1.905 2.320 nonbonded pdb=" NE2 HIS Q 167 " pdb="MN MN Q 501 " model vdw 1.972 2.400 nonbonded pdb=" ND1 HIS Q 241 " pdb="MN MN Q 501 " model vdw 2.026 2.400 nonbonded pdb=" OD1 ASN Q 117 " pdb="MN MN Q 501 " model vdw 2.061 2.320 nonbonded pdb=" CE1 HIS Q 167 " pdb="MN MN Q 501 " model vdw 2.108 2.540 ... (remaining 440178 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 22.650 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 122.550 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.180 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.002 0.043 58582 Z= 0.152 Angle : 0.639 8.749 79875 Z= 0.416 Chirality : 0.045 0.304 9598 Planarity : 0.003 0.057 10466 Dihedral : 10.977 89.820 19966 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.69 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 7773 helix: -0.46 (0.07), residues: 4279 sheet: -1.98 (0.27), residues: 317 loop : -3.94 (0.09), residues: 3177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 902 HIS 0.008 0.000 HIS E 928 PHE 0.010 0.001 PHE B1041 TYR 0.009 0.001 TYR I 104 ARG 0.005 0.000 ARG D 922 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1024 time to evaluate : 4.989 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: 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 1726 ARG cc_start: 0.5747 (ptt180) cc_final: 0.5455 (mpp80) REVERT: A 2047 MET cc_start: 0.8076 (mmm) cc_final: 0.7335 (mmt) REVERT: A 2101 ASN cc_start: 0.7644 (m-40) cc_final: 0.6985 (m-40) REVERT: B 323 ASN cc_start: 0.7592 (t0) cc_final: 0.7382 (t0) REVERT: B 677 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7277 (tptt) REVERT: B 1195 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6856 (mp0) REVERT: D 552 PHE cc_start: 0.8238 (m-10) cc_final: 0.7744 (m-80) REVERT: D 561 MET cc_start: 0.6619 (tpt) cc_final: 0.5910 (tpt) REVERT: D 642 ASP cc_start: 0.7786 (t70) cc_final: 0.7464 (t0) REVERT: F 126 ILE cc_start: 0.7473 (mm) cc_final: 0.7049 (mm) REVERT: F 130 ASP cc_start: 0.7491 (t0) cc_final: 0.6454 (p0) REVERT: G 221 LEU cc_start: 0.8234 (mt) cc_final: 0.8034 (mt) REVERT: G 748 MET cc_start: 0.8297 (mmm) cc_final: 0.7993 (mmt) REVERT: G 771 TYR cc_start: 0.6019 (t80) cc_final: 0.5666 (t80) REVERT: K 254 LEU cc_start: 0.8778 (mt) cc_final: 0.8448 (tt) REVERT: K 517 PHE cc_start: 0.4777 (m-80) cc_final: 0.4479 (m-80) REVERT: Q 253 ASP cc_start: 0.7247 (t0) cc_final: 0.6899 (t0) outliers start: 0 outliers final: 0 residues processed: 1024 average time/residue: 0.6697 time to fit residues: 1136.8225 Evaluate side-chains 637 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 683 optimal weight: 30.0000 chunk 613 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 413 optimal weight: 0.8980 chunk 327 optimal weight: 0.9980 chunk 634 optimal weight: 0.0370 chunk 245 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 471 optimal weight: 3.9990 chunk 734 optimal weight: 7.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1728 GLN A2154 HIS A2185 HIS B 323 ASN B 338 GLN B 448 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 648 GLN B 695 GLN B 770 GLN B1002 HIS B1067 GLN B1187 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN D 261 GLN D 403 GLN D 441 ASN D 633 GLN D 650 GLN D 667 GLN D 771 HIS D 873 GLN D 884 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN E 445 HIS E 501 GLN E 708 GLN ** E 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 785 HIS E 836 HIS E 926 ASN E 963 GLN E 984 HIS F 293 GLN F 294 ASN G 150 HIS G 281 ASN G 326 HIS G 375 GLN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 532 GLN G 539 HIS G 633 GLN G 670 GLN G 673 GLN G 779 ASN G 797 GLN G 814 ASN G 823 ASN G 826 GLN H 404 ASN H 445 ASN H 588 HIS H 609 GLN H 731 HIS ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 902 GLN H 945 HIS H 955 GLN I 131 GLN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 HIS I 294 ASN ** I 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS I 482 GLN I 484 HIS I 639 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS K 398 HIS K 550 GLN P 211 ASN ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN P 237 GLN ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 320 ASN P 340 HIS P 392 ASN P 479 HIS P 520 HIS P 557 GLN Q 44 ASN Q 59 HIS Q 79 ASN Q 122 GLN Q 139 ASN Q 162 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 58582 Z= 0.230 Angle : 0.605 13.044 79875 Z= 0.293 Chirality : 0.041 0.280 9598 Planarity : 0.004 0.071 10466 Dihedral : 3.208 23.835 8568 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.55 % Favored : 92.19 % Rotamer: Outliers : 1.30 % Allowed : 11.19 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.10), residues: 7773 helix: 0.65 (0.08), residues: 4358 sheet: -1.67 (0.28), residues: 334 loop : -3.66 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 164 HIS 0.011 0.001 HIS E 928 PHE 0.032 0.002 PHE P 538 TYR 0.023 0.001 TYR K 584 ARG 0.006 0.000 ARG F 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 657 time to evaluate : 4.925 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1726 ARG cc_start: 0.5814 (ptt180) cc_final: 0.5534 (mpp80) REVERT: A 2047 MET cc_start: 0.8289 (mmm) cc_final: 0.8039 (mmt) REVERT: B 677 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7355 (tptt) REVERT: B 1195 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7001 (mp0) REVERT: D 552 PHE cc_start: 0.8291 (m-10) cc_final: 0.7847 (m-80) REVERT: D 561 MET cc_start: 0.6926 (tpt) cc_final: 0.6029 (tpt) REVERT: D 642 ASP cc_start: 0.7763 (t70) cc_final: 0.7524 (t0) REVERT: E 926 ASN cc_start: 0.2939 (OUTLIER) cc_final: 0.1588 (t0) REVERT: F 57 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6104 (mt-10) REVERT: F 126 ILE cc_start: 0.7561 (mm) cc_final: 0.7178 (mm) REVERT: F 433 MET cc_start: 0.6544 (ptt) cc_final: 0.6285 (ppp) REVERT: G 748 MET cc_start: 0.8516 (mmm) cc_final: 0.8209 (mmt) REVERT: G 877 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7403 (mtp) REVERT: H 407 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7695 (t80) REVERT: H 764 LEU cc_start: 0.8391 (mt) cc_final: 0.8184 (mt) REVERT: K 254 LEU cc_start: 0.8757 (mt) cc_final: 0.8554 (mt) REVERT: K 517 PHE cc_start: 0.5069 (m-80) cc_final: 0.4364 (m-80) REVERT: Q 253 ASP cc_start: 0.7481 (t0) cc_final: 0.7060 (t0) outliers start: 68 outliers final: 40 residues processed: 695 average time/residue: 0.5146 time to fit residues: 613.2002 Evaluate side-chains 631 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 588 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1640 LEU Chi-restraints excluded: chain A residue 1731 GLU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 326 HIS Chi-restraints excluded: chain G residue 353 TYR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 497 ILE Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 829 LEU Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain H residue 407 PHE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain K residue 304 ASN Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 205 ASP Chi-restraints excluded: chain Q residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 408 optimal weight: 0.1980 chunk 228 optimal weight: 0.9990 chunk 611 optimal weight: 10.0000 chunk 500 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 735 optimal weight: 0.4980 chunk 795 optimal weight: 50.0000 chunk 655 optimal weight: 7.9990 chunk 729 optimal weight: 0.8980 chunk 250 optimal weight: 30.0000 chunk 590 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 523 GLN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN B 700 GLN B 720 HIS ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 868 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 633 GLN D 771 HIS E 500 HIS ** E 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 926 ASN F 378 ASN G 76 ASN G 437 GLN G 522 ASN G 570 HIS ** G 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 879 GLN H 894 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS K 171 GLN K 550 GLN K 603 GLN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 58582 Z= 0.402 Angle : 0.696 10.546 79875 Z= 0.346 Chirality : 0.044 0.306 9598 Planarity : 0.005 0.083 10466 Dihedral : 3.839 26.259 8568 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.45 % Favored : 91.33 % Rotamer: Outliers : 2.45 % Allowed : 14.24 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7773 helix: 0.87 (0.08), residues: 4402 sheet: -1.66 (0.29), residues: 332 loop : -3.46 (0.10), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 727 HIS 0.036 0.002 HIS G 326 PHE 0.042 0.002 PHE H 382 TYR 0.026 0.002 TYR H 855 ARG 0.009 0.001 ARG Q 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 593 time to evaluate : 5.055 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1726 ARG cc_start: 0.6103 (ptt180) cc_final: 0.5787 (mpp80) REVERT: A 2047 MET cc_start: 0.8392 (mmm) cc_final: 0.8052 (mmm) REVERT: B 392 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7923 (t80) REVERT: B 413 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7453 (tp-100) REVERT: B 496 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8895 (tp) REVERT: B 677 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7560 (tptt) REVERT: D 642 ASP cc_start: 0.7843 (t70) cc_final: 0.7613 (t0) REVERT: D 845 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6921 (tp) REVERT: F 57 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6727 (mt-10) REVERT: F 301 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7428 (ptm160) REVERT: G 541 MET cc_start: 0.7249 (mmm) cc_final: 0.6984 (mmp) REVERT: G 675 MET cc_start: 0.8350 (tmm) cc_final: 0.8053 (tmm) REVERT: G 748 MET cc_start: 0.8448 (mmm) cc_final: 0.8095 (mmt) REVERT: G 771 TYR cc_start: 0.6109 (t80) cc_final: 0.5889 (t80) REVERT: G 877 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7569 (mtp) REVERT: H 648 MET cc_start: 0.5792 (ppp) cc_final: 0.5533 (ppp) REVERT: H 667 MET cc_start: 0.7794 (tpp) cc_final: 0.7590 (mmt) REVERT: H 753 TYR cc_start: 0.7760 (m-10) cc_final: 0.7557 (m-10) REVERT: H 966 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8650 (pp) REVERT: P 502 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8933 (mm) REVERT: Q 88 ASP cc_start: 0.7831 (m-30) cc_final: 0.7578 (m-30) REVERT: Q 253 ASP cc_start: 0.7553 (t0) cc_final: 0.7248 (t0) outliers start: 128 outliers final: 78 residues processed: 673 average time/residue: 0.5733 time to fit residues: 666.8245 Evaluate side-chains 604 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 519 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1768 CYS Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 927 MET Chi-restraints excluded: chain E residue 930 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 829 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 407 PHE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 806 LEU Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain K residue 113 TYR Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 502 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 141 ASN Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 727 optimal weight: 3.9990 chunk 553 optimal weight: 0.4980 chunk 381 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 351 optimal weight: 0.3980 chunk 494 optimal weight: 10.0000 chunk 738 optimal weight: 1.9990 chunk 781 optimal weight: 30.0000 chunk 385 optimal weight: 4.9990 chunk 700 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2101 ASN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS ** E 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN G 326 HIS ** G 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 GLN H 480 GLN H 744 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 919 GLN H 955 GLN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 HIS K 550 GLN ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 58582 Z= 0.341 Angle : 0.642 13.159 79875 Z= 0.317 Chirality : 0.042 0.164 9598 Planarity : 0.004 0.076 10466 Dihedral : 3.855 26.230 8568 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.27 % Favored : 91.51 % Rotamer: Outliers : 2.64 % Allowed : 16.13 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 7773 helix: 1.11 (0.08), residues: 4413 sheet: -1.55 (0.29), residues: 339 loop : -3.39 (0.10), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 727 HIS 0.011 0.001 HIS E 928 PHE 0.032 0.002 PHE H 465 TYR 0.019 0.002 TYR D 388 ARG 0.009 0.001 ARG Q 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 545 time to evaluate : 4.942 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1726 ARG cc_start: 0.6234 (ptt180) cc_final: 0.5930 (mpp80) REVERT: A 2047 MET cc_start: 0.8421 (mmm) cc_final: 0.8111 (mmm) REVERT: B 392 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7993 (t80) REVERT: B 413 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7484 (tp-100) REVERT: B 523 GLN cc_start: 0.8208 (mp10) cc_final: 0.7940 (mp10) REVERT: B 677 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7872 (tptt) REVERT: B 772 MET cc_start: 0.8124 (tpt) cc_final: 0.7913 (tpt) REVERT: D 642 ASP cc_start: 0.7778 (t70) cc_final: 0.7549 (t0) REVERT: F 57 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6882 (mt-10) REVERT: F 374 LEU cc_start: 0.8384 (mt) cc_final: 0.8118 (mp) REVERT: F 434 MET cc_start: 0.6684 (ppp) cc_final: 0.6350 (ppp) REVERT: G 541 MET cc_start: 0.7308 (mmm) cc_final: 0.6976 (mmp) REVERT: G 675 MET cc_start: 0.8408 (tmm) cc_final: 0.8139 (tmm) REVERT: G 748 MET cc_start: 0.8334 (mmm) cc_final: 0.8067 (mmt) REVERT: G 877 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7631 (mtp) REVERT: H 648 MET cc_start: 0.5992 (ppp) cc_final: 0.5607 (ppp) REVERT: H 742 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6780 (mt) REVERT: I 55 TRP cc_start: 0.6102 (t60) cc_final: 0.5803 (t60) REVERT: K 257 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8494 (pp) REVERT: K 265 MET cc_start: 0.6429 (ppp) cc_final: 0.5713 (ppp) REVERT: P 67 LEU cc_start: 0.9275 (pp) cc_final: 0.9047 (mp) REVERT: P 502 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8665 (mt) REVERT: Q 86 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (p90) REVERT: Q 253 ASP cc_start: 0.7552 (t0) cc_final: 0.7284 (t0) outliers start: 138 outliers final: 87 residues processed: 639 average time/residue: 0.5251 time to fit residues: 584.5906 Evaluate side-chains 602 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 509 time to evaluate : 4.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1768 CYS Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 829 LEU Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 742 ILE Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 758 LEU Chi-restraints excluded: chain H residue 792 THR Chi-restraints excluded: chain H residue 806 LEU Chi-restraints excluded: chain H residue 816 ILE Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 502 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 141 ASN Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 651 optimal weight: 10.0000 chunk 443 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 582 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 667 optimal weight: 50.0000 chunk 540 optimal weight: 0.0270 chunk 0 optimal weight: 30.0000 chunk 399 optimal weight: 0.8980 chunk 701 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN E 445 HIS E 750 HIS ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 953 HIS ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 58582 Z= 0.410 Angle : 0.680 14.045 79875 Z= 0.335 Chirality : 0.044 0.192 9598 Planarity : 0.004 0.079 10466 Dihedral : 4.031 28.481 8568 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.84 % Favored : 90.96 % Rotamer: Outliers : 3.16 % Allowed : 17.13 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.10), residues: 7773 helix: 1.12 (0.08), residues: 4431 sheet: -1.41 (0.30), residues: 336 loop : -3.33 (0.10), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 727 HIS 0.013 0.001 HIS E 445 PHE 0.035 0.002 PHE H 995 TYR 0.019 0.002 TYR A2050 ARG 0.011 0.001 ARG B 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 527 time to evaluate : 4.968 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1726 ARG cc_start: 0.6342 (ptt180) cc_final: 0.5664 (ptp90) REVERT: A 2047 MET cc_start: 0.8390 (mmm) cc_final: 0.8135 (mmm) REVERT: B 392 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7938 (t80) REVERT: B 413 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7571 (tp-100) REVERT: B 677 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7907 (tptt) REVERT: B 772 MET cc_start: 0.8149 (tpt) cc_final: 0.7854 (tpt) REVERT: D 388 TYR cc_start: 0.7568 (p90) cc_final: 0.7190 (p90) REVERT: D 642 ASP cc_start: 0.7794 (t70) cc_final: 0.7561 (t0) REVERT: F 57 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6947 (mt-10) REVERT: F 301 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7185 (ptm160) REVERT: F 374 LEU cc_start: 0.8403 (mt) cc_final: 0.8132 (mp) REVERT: F 382 MET cc_start: 0.7061 (pmm) cc_final: 0.6721 (pmm) REVERT: G 541 MET cc_start: 0.7433 (mmm) cc_final: 0.7134 (mmp) REVERT: G 675 MET cc_start: 0.8450 (tmm) cc_final: 0.8027 (tmm) REVERT: G 748 MET cc_start: 0.8276 (mmm) cc_final: 0.7975 (mmt) REVERT: G 877 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7593 (mtp) REVERT: H 465 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.4940 (t80) REVERT: H 648 MET cc_start: 0.6428 (ppp) cc_final: 0.5710 (ppp) REVERT: I 55 TRP cc_start: 0.6264 (t60) cc_final: 0.5951 (t60) REVERT: K 257 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8531 (pp) REVERT: K 265 MET cc_start: 0.6372 (ppp) cc_final: 0.5914 (ppp) REVERT: K 517 PHE cc_start: 0.3109 (m-80) cc_final: 0.1698 (m-80) REVERT: P 502 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8894 (mm) REVERT: Q 86 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8096 (p90) REVERT: Q 253 ASP cc_start: 0.7573 (t0) cc_final: 0.7320 (t0) outliers start: 165 outliers final: 122 residues processed: 645 average time/residue: 0.5413 time to fit residues: 612.0586 Evaluate side-chains 629 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 500 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1768 CYS Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain A residue 2152 GLN Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1144 ASP Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 802 THR Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 829 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 573 LEU Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 758 LEU Chi-restraints excluded: chain H residue 792 THR Chi-restraints excluded: chain H residue 816 ILE Chi-restraints excluded: chain H residue 911 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 113 TYR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain P residue 502 LEU Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 141 ASN Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 251 CYS Chi-restraints excluded: chain Q residue 277 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 263 optimal weight: 8.9990 chunk 704 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 459 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 782 optimal weight: 50.0000 chunk 649 optimal weight: 20.0000 chunk 362 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 410 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN E 445 HIS ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 895 ASN H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 550 GLN ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 58582 Z= 0.302 Angle : 0.641 11.747 79875 Z= 0.314 Chirality : 0.042 0.248 9598 Planarity : 0.004 0.080 10466 Dihedral : 3.994 27.803 8568 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.71 % Favored : 91.08 % Rotamer: Outliers : 3.26 % Allowed : 17.99 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 7773 helix: 1.24 (0.08), residues: 4439 sheet: -1.38 (0.30), residues: 338 loop : -3.26 (0.10), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 523 HIS 0.014 0.001 HIS E 928 PHE 0.034 0.001 PHE H 995 TYR 0.016 0.002 TYR G 259 ARG 0.008 0.000 ARG Q 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 523 time to evaluate : 5.027 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: symmetry clash revert: symmetry clash REVERT: A 1726 ARG cc_start: 0.6317 (ptt180) cc_final: 0.5787 (ptp-110) REVERT: A 1789 GLN cc_start: 0.6668 (mp10) cc_final: 0.6364 (mp10) REVERT: A 2047 MET cc_start: 0.8374 (mmm) cc_final: 0.8141 (mmm) REVERT: B 348 MET cc_start: 0.4966 (tmm) cc_final: 0.4504 (tmm) REVERT: B 413 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7618 (tp-100) REVERT: B 496 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8733 (tp) REVERT: B 523 GLN cc_start: 0.8194 (mp10) cc_final: 0.7980 (mp10) REVERT: B 677 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7987 (tptt) REVERT: B 710 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9002 (mp) REVERT: B 985 ASN cc_start: 0.7622 (t0) cc_final: 0.7282 (t0) REVERT: D 642 ASP cc_start: 0.7753 (t70) cc_final: 0.7520 (t0) REVERT: E 927 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7714 (ptm) REVERT: F 374 LEU cc_start: 0.8401 (mt) cc_final: 0.8136 (mp) REVERT: F 382 MET cc_start: 0.7095 (pmm) cc_final: 0.6744 (pmm) REVERT: G 541 MET cc_start: 0.7397 (mmm) cc_final: 0.7098 (mmp) REVERT: G 675 MET cc_start: 0.8441 (tmm) cc_final: 0.8093 (tmm) REVERT: G 748 MET cc_start: 0.8293 (mmm) cc_final: 0.7895 (mmt) REVERT: G 877 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7487 (mtp) REVERT: H 465 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5372 (t80) REVERT: I 55 TRP cc_start: 0.6267 (t60) cc_final: 0.6034 (t60) REVERT: I 250 MET cc_start: 0.3261 (mmm) cc_final: 0.2778 (mmm) REVERT: K 257 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8490 (pp) REVERT: Q 86 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.8046 (p90) REVERT: Q 253 ASP cc_start: 0.7589 (t0) cc_final: 0.7343 (t0) outliers start: 170 outliers final: 119 residues processed: 648 average time/residue: 0.5058 time to fit residues: 572.8176 Evaluate side-chains 621 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 495 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1768 CYS Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1022 CYS Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1144 ASP Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 628 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 894 THR Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 927 MET Chi-restraints excluded: chain E residue 928 HIS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 696 ASP Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 756 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 802 THR Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 573 LEU Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 758 LEU Chi-restraints excluded: chain H residue 792 THR Chi-restraints excluded: chain H residue 816 ILE Chi-restraints excluded: chain H residue 834 SER Chi-restraints excluded: chain H residue 865 ASP Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 911 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain P residue 507 VAL Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 251 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 754 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 445 optimal weight: 0.8980 chunk 571 optimal weight: 0.5980 chunk 442 optimal weight: 3.9990 chunk 658 optimal weight: 5.9990 chunk 437 optimal weight: 0.6980 chunk 779 optimal weight: 50.0000 chunk 487 optimal weight: 1.9990 chunk 475 optimal weight: 20.0000 chunk 359 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 733 GLN E 445 HIS ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** G 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 902 HIS H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58582 Z= 0.264 Angle : 0.632 12.018 79875 Z= 0.309 Chirality : 0.042 0.304 9598 Planarity : 0.004 0.075 10466 Dihedral : 3.957 26.939 8568 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.62 % Favored : 91.19 % Rotamer: Outliers : 3.28 % Allowed : 18.59 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 7773 helix: 1.33 (0.08), residues: 4442 sheet: -1.32 (0.30), residues: 336 loop : -3.19 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 523 HIS 0.015 0.001 HIS E 928 PHE 0.032 0.001 PHE H 995 TYR 0.020 0.001 TYR G 771 ARG 0.008 0.000 ARG Q 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 515 time to evaluate : 4.960 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: A 1726 ARG cc_start: 0.6295 (ptt180) cc_final: 0.5774 (ptp-110) REVERT: A 2047 MET cc_start: 0.8310 (mmm) cc_final: 0.8071 (mmm) REVERT: B 347 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5986 (tp) REVERT: B 348 MET cc_start: 0.4841 (tmm) cc_final: 0.4438 (tmm) REVERT: B 413 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7673 (tp-100) REVERT: B 677 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7929 (tptt) REVERT: B 985 ASN cc_start: 0.7621 (t0) cc_final: 0.7267 (t0) REVERT: D 387 MET cc_start: 0.5585 (tpt) cc_final: 0.5304 (tpt) REVERT: D 642 ASP cc_start: 0.7735 (t70) cc_final: 0.7512 (t0) REVERT: E 927 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7730 (ptm) REVERT: F 301 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7247 (ptm160) REVERT: F 374 LEU cc_start: 0.8424 (mt) cc_final: 0.8144 (mp) REVERT: F 382 MET cc_start: 0.7135 (pmm) cc_final: 0.6832 (pmm) REVERT: G 541 MET cc_start: 0.7412 (mmm) cc_final: 0.7194 (mmp) REVERT: G 675 MET cc_start: 0.8453 (tmm) cc_final: 0.8163 (tmm) REVERT: G 748 MET cc_start: 0.8270 (mmm) cc_final: 0.7855 (mmt) REVERT: G 877 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7456 (mtp) REVERT: H 465 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5414 (t80) REVERT: H 954 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7205 (ttm-80) REVERT: I 55 TRP cc_start: 0.6311 (t60) cc_final: 0.6074 (t60) REVERT: I 250 MET cc_start: 0.3324 (mmm) cc_final: 0.2919 (mmm) REVERT: I 273 ASN cc_start: 0.8146 (p0) cc_final: 0.7883 (t0) REVERT: K 257 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8442 (pp) REVERT: K 265 MET cc_start: 0.6053 (ppp) cc_final: 0.5584 (ppp) REVERT: Q 86 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (p90) REVERT: Q 253 ASP cc_start: 0.7582 (t0) cc_final: 0.7317 (t0) outliers start: 171 outliers final: 124 residues processed: 648 average time/residue: 0.5031 time to fit residues: 569.1493 Evaluate side-chains 631 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 499 time to evaluate : 4.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1699 TRP Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1768 CYS Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 1883 MET Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1144 ASP Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 733 GLN Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 685 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 763 PHE Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 841 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 927 MET Chi-restraints excluded: chain E residue 928 HIS Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 506 SER Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 756 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 802 THR Chi-restraints excluded: chain G residue 806 LEU Chi-restraints excluded: chain G residue 829 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 573 LEU Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 792 THR Chi-restraints excluded: chain H residue 816 ILE Chi-restraints excluded: chain H residue 834 SER Chi-restraints excluded: chain H residue 865 ASP Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 911 THR Chi-restraints excluded: chain H residue 954 ARG Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 429 TYR Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain P residue 490 SER Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 251 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 482 optimal weight: 0.8980 chunk 311 optimal weight: 0.0670 chunk 465 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 495 optimal weight: 9.9990 chunk 531 optimal weight: 0.8980 chunk 385 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 612 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN E 445 HIS ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 HIS H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 550 GLN P 230 ASN ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 GLN Q 139 ASN Q 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 58582 Z= 0.187 Angle : 0.623 14.748 79875 Z= 0.300 Chirality : 0.041 0.397 9598 Planarity : 0.004 0.069 10466 Dihedral : 3.853 27.091 8568 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.46 % Rotamer: Outliers : 2.49 % Allowed : 19.75 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 7773 helix: 1.46 (0.08), residues: 4436 sheet: -1.25 (0.30), residues: 335 loop : -3.14 (0.10), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 523 HIS 0.014 0.001 HIS E 928 PHE 0.028 0.001 PHE H 995 TYR 0.020 0.001 TYR K 584 ARG 0.007 0.000 ARG Q 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 532 time to evaluate : 5.122 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 1726 ARG cc_start: 0.6271 (ptt180) cc_final: 0.5743 (ptp-110) REVERT: A 2047 MET cc_start: 0.8286 (mmm) cc_final: 0.8051 (mmm) REVERT: B 348 MET cc_start: 0.4850 (tmm) cc_final: 0.4538 (tmm) REVERT: B 413 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7631 (tp-100) REVERT: B 677 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7884 (tptt) REVERT: B 985 ASN cc_start: 0.7613 (t0) cc_final: 0.7274 (t0) REVERT: D 387 MET cc_start: 0.5366 (tpt) cc_final: 0.5145 (tpt) REVERT: D 642 ASP cc_start: 0.7702 (t70) cc_final: 0.7474 (t0) REVERT: F 301 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6967 (ptm160) REVERT: F 374 LEU cc_start: 0.8418 (mt) cc_final: 0.8140 (mp) REVERT: F 382 MET cc_start: 0.7129 (pmm) cc_final: 0.6837 (pmm) REVERT: G 675 MET cc_start: 0.8438 (tmm) cc_final: 0.8143 (tmm) REVERT: G 748 MET cc_start: 0.8171 (mmm) cc_final: 0.7836 (mmt) REVERT: G 877 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: H 465 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5411 (t80) REVERT: H 954 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7202 (ttm-80) REVERT: I 55 TRP cc_start: 0.6241 (t60) cc_final: 0.6035 (t60) REVERT: I 250 MET cc_start: 0.3264 (mmm) cc_final: 0.2933 (mmm) REVERT: K 257 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8491 (pp) REVERT: K 265 MET cc_start: 0.6221 (ppp) cc_final: 0.5769 (ppp) REVERT: P 427 MSE cc_start: 0.4622 (ttm) cc_final: 0.4405 (ttt) REVERT: Q 86 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7838 (p90) REVERT: Q 253 ASP cc_start: 0.7597 (t0) cc_final: 0.7315 (t0) outliers start: 130 outliers final: 101 residues processed: 625 average time/residue: 0.5176 time to fit residues: 565.0054 Evaluate side-chains 616 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 509 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 1883 MET Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1144 ASP Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 685 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 928 HIS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 506 SER Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 696 ASP Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 877 MET Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 834 SER Chi-restraints excluded: chain H residue 865 ASP Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 954 ARG Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 429 TYR Chi-restraints excluded: chain I residue 497 MET Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 251 CYS Chi-restraints excluded: chain Q residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 709 optimal weight: 3.9990 chunk 747 optimal weight: 4.9990 chunk 681 optimal weight: 30.0000 chunk 726 optimal weight: 3.9990 chunk 746 optimal weight: 3.9990 chunk 437 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 570 optimal weight: 0.5980 chunk 222 optimal weight: 0.6980 chunk 656 optimal weight: 7.9990 chunk 687 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN E 445 HIS ** E 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS ** G 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 230 ASN ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 58582 Z= 0.237 Angle : 0.641 17.207 79875 Z= 0.310 Chirality : 0.042 0.403 9598 Planarity : 0.004 0.070 10466 Dihedral : 3.860 26.573 8568 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.67 % Favored : 91.15 % Rotamer: Outliers : 2.63 % Allowed : 19.87 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 7773 helix: 1.47 (0.08), residues: 4444 sheet: -1.24 (0.30), residues: 335 loop : -3.10 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 523 HIS 0.014 0.001 HIS E 928 PHE 0.029 0.001 PHE H 995 TYR 0.021 0.001 TYR K 97 ARG 0.008 0.000 ARG G 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 517 time to evaluate : 4.997 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 1726 ARG cc_start: 0.6281 (ptt180) cc_final: 0.5750 (ptp-110) REVERT: A 2047 MET cc_start: 0.8283 (mmm) cc_final: 0.8059 (mmm) REVERT: B 413 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7618 (tp-100) REVERT: B 611 ASN cc_start: 0.8012 (m-40) cc_final: 0.7791 (t0) REVERT: B 677 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7955 (tptt) REVERT: B 985 ASN cc_start: 0.7605 (t0) cc_final: 0.7189 (t0) REVERT: D 499 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6333 (p0) REVERT: D 642 ASP cc_start: 0.7731 (t70) cc_final: 0.7506 (t0) REVERT: D 845 LEU cc_start: 0.6968 (tp) cc_final: 0.6539 (tp) REVERT: F 374 LEU cc_start: 0.8375 (mt) cc_final: 0.8093 (mp) REVERT: F 382 MET cc_start: 0.7113 (pmm) cc_final: 0.6837 (pmm) REVERT: G 675 MET cc_start: 0.8419 (tmm) cc_final: 0.8119 (tmm) REVERT: G 748 MET cc_start: 0.8056 (mmm) cc_final: 0.7707 (mmt) REVERT: H 465 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.5440 (t80) REVERT: H 954 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7231 (ttm-80) REVERT: I 250 MET cc_start: 0.3306 (mmm) cc_final: 0.2984 (mmm) REVERT: K 257 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8487 (pp) REVERT: K 265 MET cc_start: 0.6245 (ppp) cc_final: 0.5797 (ppp) REVERT: P 427 MSE cc_start: 0.4570 (ttm) cc_final: 0.4318 (ttt) REVERT: Q 86 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7818 (p90) REVERT: Q 253 ASP cc_start: 0.7594 (t0) cc_final: 0.7336 (t0) outliers start: 137 outliers final: 110 residues processed: 621 average time/residue: 0.5216 time to fit residues: 569.5422 Evaluate side-chains 623 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 508 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1699 TRP Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1878 LEU Chi-restraints excluded: chain A residue 1883 MET Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1144 ASP Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 685 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 763 PHE Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 841 VAL Chi-restraints excluded: chain E residue 905 GLU Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 928 HIS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 506 SER Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 685 TYR Chi-restraints excluded: chain G residue 696 ASP Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 756 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 701 CYS Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 792 THR Chi-restraints excluded: chain H residue 834 SER Chi-restraints excluded: chain H residue 865 ASP Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 954 ARG Chi-restraints excluded: chain H residue 964 THR Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 497 MET Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain P residue 291 MSE Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain P residue 490 SER Chi-restraints excluded: chain P residue 507 VAL Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 251 CYS Chi-restraints excluded: chain Q residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 724 optimal weight: 2.9990 chunk 477 optimal weight: 0.0070 chunk 768 optimal weight: 0.0980 chunk 468 optimal weight: 0.9990 chunk 364 optimal weight: 20.0000 chunk 534 optimal weight: 2.9990 chunk 805 optimal weight: 50.0000 chunk 741 optimal weight: 1.9990 chunk 641 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 495 optimal weight: 0.7980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN E 445 HIS E 701 ASN ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 HIS ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 573 GLN G 826 GLN H 480 GLN ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 550 GLN ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58582 Z= 0.171 Angle : 0.635 19.276 79875 Z= 0.305 Chirality : 0.041 0.274 9598 Planarity : 0.004 0.069 10466 Dihedral : 3.779 28.572 8568 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.26 % Favored : 91.57 % Rotamer: Outliers : 2.13 % Allowed : 20.50 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7773 helix: 1.59 (0.08), residues: 4429 sheet: -1.07 (0.31), residues: 325 loop : -3.06 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP I 55 HIS 0.013 0.001 HIS E 928 PHE 0.026 0.001 PHE H 995 TYR 0.016 0.001 TYR K 212 ARG 0.009 0.000 ARG F 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15546 Ramachandran restraints generated. 7773 Oldfield, 0 Emsley, 7773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 533 time to evaluate : 5.054 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: A 1726 ARG cc_start: 0.6255 (ptt180) cc_final: 0.5621 (ptp-110) REVERT: A 2047 MET cc_start: 0.8251 (mmm) cc_final: 0.8035 (mmm) REVERT: B 413 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7518 (tp-100) REVERT: B 516 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7339 (tpm170) REVERT: B 677 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7832 (tptt) REVERT: B 985 ASN cc_start: 0.7568 (t0) cc_final: 0.7230 (t0) REVERT: D 499 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6270 (p0) REVERT: D 561 MET cc_start: 0.7153 (tpt) cc_final: 0.6499 (mmm) REVERT: D 642 ASP cc_start: 0.7677 (t70) cc_final: 0.7449 (t0) REVERT: D 679 TRP cc_start: 0.7954 (m-90) cc_final: 0.7652 (m-90) REVERT: F 374 LEU cc_start: 0.8329 (mt) cc_final: 0.8046 (mp) REVERT: F 382 MET cc_start: 0.7148 (pmm) cc_final: 0.6877 (pmm) REVERT: G 675 MET cc_start: 0.8435 (tmm) cc_final: 0.8146 (tmm) REVERT: G 748 MET cc_start: 0.8159 (mmm) cc_final: 0.7838 (mmt) REVERT: H 465 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5365 (t80) REVERT: H 759 SER cc_start: 0.8706 (m) cc_final: 0.8417 (t) REVERT: I 250 MET cc_start: 0.3195 (mmm) cc_final: 0.2943 (mmm) REVERT: K 257 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8463 (pp) REVERT: K 265 MET cc_start: 0.6371 (ppp) cc_final: 0.5891 (ppp) REVERT: K 584 TYR cc_start: -0.2315 (m-10) cc_final: -0.2542 (m-10) REVERT: P 427 MSE cc_start: 0.4550 (ttm) cc_final: 0.4278 (ttt) REVERT: Q 86 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7689 (p90) REVERT: Q 253 ASP cc_start: 0.7572 (t0) cc_final: 0.7320 (t0) outliers start: 111 outliers final: 94 residues processed: 617 average time/residue: 0.5198 time to fit residues: 561.6644 Evaluate side-chains 611 residues out of total 6864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 513 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1699 TRP Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1883 MET Chi-restraints excluded: chain A residue 2136 VAL Chi-restraints excluded: chain B residue 337 TRP Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 568 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 802 MET Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 685 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 701 ASN Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 910 LEU Chi-restraints excluded: chain E residue 928 HIS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 506 SER Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 557 HIS Chi-restraints excluded: chain G residue 696 ASP Chi-restraints excluded: chain G residue 712 LEU Chi-restraints excluded: chain G residue 787 VAL Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 875 ASN Chi-restraints excluded: chain G residue 894 LEU Chi-restraints excluded: chain G residue 910 VAL Chi-restraints excluded: chain H residue 400 SER Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain H residue 465 PHE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 495 VAL Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain H residue 603 PHE Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 701 CYS Chi-restraints excluded: chain H residue 748 THR Chi-restraints excluded: chain H residue 834 SER Chi-restraints excluded: chain H residue 865 ASP Chi-restraints excluded: chain H residue 895 THR Chi-restraints excluded: chain H residue 952 ASP Chi-restraints excluded: chain H residue 966 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 497 MET Chi-restraints excluded: chain I residue 617 VAL Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 392 TYR Chi-restraints excluded: chain P residue 438 PHE Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 455 VAL Chi-restraints excluded: chain P residue 490 SER Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 86 TYR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 187 GLN Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 393 optimal weight: 0.3980 chunk 509 optimal weight: 0.9990 chunk 683 optimal weight: 50.0000 chunk 196 optimal weight: 0.4980 chunk 591 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 178 optimal weight: 40.0000 chunk 642 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 660 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 HIS D 908 GLN E 445 HIS ** E 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN ** K 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.125618 restraints weight = 122868.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122829 restraints weight = 208426.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120769 restraints weight = 170157.282| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58582 Z= 0.248 Angle : 0.653 17.573 79875 Z= 0.316 Chirality : 0.042 0.287 9598 Planarity : 0.004 0.069 10466 Dihedral : 3.820 26.193 8568 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.33 % Rotamer: Outliers : 2.30 % Allowed : 20.60 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7773 helix: 1.58 (0.08), residues: 4429 sheet: -1.05 (0.30), residues: 326 loop : -3.04 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP I 55 HIS 0.014 0.001 HIS E 928 PHE 0.030 0.001 PHE H 995 TYR 0.024 0.001 TYR P 261 ARG 0.011 0.000 ARG E 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11315.05 seconds wall clock time: 199 minutes 40.98 seconds (11980.98 seconds total)