Starting phenix.real_space_refine on Thu Mar 21 03:14:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/03_2024/7chh_30374.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18430 2.51 5 N 4798 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ASP 65": "OD1" <-> "OD2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "K GLU 86": "OE1" <-> "OE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29029 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 52, 'TRANS': 950} Chain breaks: 10 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7652 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7672 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 10 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "G" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.86, per 1000 atoms: 0.51 Number of scatterers: 29029 At special positions: 0 Unit cell: (136.68, 152.76, 227.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5672 8.00 N 4798 7.00 C 18430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 603 " " NAG C1313 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C 717 " Time building additional restraints: 9.29 Conformation dependent library (CDL) restraints added in 4.3 seconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6854 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 59 sheets defined 20.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.692A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.999A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.741A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.913A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.877A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.054A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.910A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.195A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.564A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.815A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.599A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.534A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.641A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.569A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.657A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.566A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.987A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.024A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.776A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.821A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.513A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.829A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.029A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.781A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.958A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL K 88 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.026A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.880A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.260A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.721A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.757A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.343A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.519A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.880A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.345A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.785A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B 392 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.730A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 691 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.547A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.692A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.519A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.830A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.720A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.504A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.051A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.364A pdb=" N PHE C 392 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.688A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.460A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR D 119 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS E 23 " --> pdb=" O PHE E 76 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 76 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 75 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 72 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY E 89 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 41 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR E 54 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.505A pdb=" N THR G 119 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR G 95 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS H 23 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 76 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 72 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 41 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR H 54 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU J 20 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR J 119 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR J 95 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS K 23 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE K 76 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP K 75 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER K 72 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY K 89 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR K 41 " --> pdb=" O TYR K 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU K 42 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU K 51 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR K 54 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 2931 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: 12.93 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 9318 1.35 - 1.48: 8012 1.48 - 1.62: 12165 1.62 - 1.75: 2 1.75 - 1.89: 163 Bond restraints: 29660 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" CA TRP J 109 " pdb=" C TRP J 109 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.72e-02 3.38e+03 8.16e+00 bond pdb=" CB ARG D 43 " pdb=" CG ARG D 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.87e+00 bond pdb=" CB ARG J 43 " pdb=" CG ARG J 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.81e+00 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.39: 310 103.39 - 111.12: 11035 111.12 - 118.85: 12378 118.85 - 126.58: 16273 126.58 - 134.31: 371 Bond angle restraints: 40367 Sorted by residual: angle pdb=" CB ARG G 100 " pdb=" CG ARG G 100 " pdb=" CD ARG G 100 " ideal model delta sigma weight residual 111.30 95.66 15.64 2.30e+00 1.89e-01 4.63e+01 angle pdb=" CB ARG J 100 " pdb=" CG ARG J 100 " pdb=" CD ARG J 100 " ideal model delta sigma weight residual 111.30 95.67 15.63 2.30e+00 1.89e-01 4.62e+01 angle pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " pdb=" CD ARG D 100 " ideal model delta sigma weight residual 111.30 95.72 15.58 2.30e+00 1.89e-01 4.59e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.88 -14.48 2.30e+00 1.89e-01 3.96e+01 angle pdb=" C ASN A 165 " pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sigma weight residual 122.74 111.32 11.42 1.82e+00 3.02e-01 3.94e+01 ... (remaining 40362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 16673 21.99 - 43.98: 1213 43.98 - 65.98: 213 65.98 - 87.97: 39 87.97 - 109.96: 5 Dihedral angle restraints: 18143 sinusoidal: 7454 harmonic: 10689 Sorted by residual: dihedral pdb=" CA LEU B 293 " pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta harmonic sigma weight residual -180.00 -117.24 -62.76 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.81 -85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 177.64 -84.64 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3924 0.082 - 0.164: 689 0.164 - 0.246: 61 0.246 - 0.327: 10 0.327 - 0.409: 10 Chirality restraints: 4694 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C2 NAG C1308 " pdb=" C1 NAG C1308 " pdb=" C3 NAG C1308 " pdb=" N2 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 4691 not shown) Planarity restraints: 5215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " 0.025 2.00e-02 2.50e+03 3.54e-02 2.19e+01 pdb=" CG PHE J 29 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 29 " -0.025 2.00e-02 2.50e+03 3.53e-02 2.18e+01 pdb=" CG PHE D 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 29 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 29 " -0.025 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE G 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE G 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE G 29 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE G 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 5212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1627 2.73 - 3.27: 26607 3.27 - 3.81: 47275 3.81 - 4.36: 54094 4.36 - 4.90: 95682 Nonbonded interactions: 225285 Sorted by model distance: nonbonded pdb=" O GLY D 116 " pdb=" OG SER E 48 " model vdw 2.182 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.253 2.520 nonbonded pdb=" O SER D 85 " pdb=" OG SER D 85 " model vdw 2.257 2.440 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.257 2.440 nonbonded pdb=" O SER J 85 " pdb=" OG SER J 85 " model vdw 2.257 2.440 ... (remaining 225280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 516 or resid 521 through 620 or resid 641 t \ hrough 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or resid 334 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1146 or resid 1301 through 1313)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 334 through 516 or re \ sid 521 through 1146 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.220 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 73.000 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 29660 Z= 0.480 Angle : 1.103 15.643 40367 Z= 0.588 Chirality : 0.063 0.409 4694 Planarity : 0.007 0.085 5183 Dihedral : 15.259 109.961 11157 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 3.56 % Allowed : 1.19 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.12), residues: 3626 helix: -1.01 (0.18), residues: 665 sheet: -0.57 (0.17), residues: 843 loop : -1.85 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP C 353 HIS 0.013 0.002 HIS A1058 PHE 0.080 0.004 PHE J 29 TYR 0.038 0.003 TYR C 423 ARG 0.056 0.002 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 233 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1151 (m-80) cc_final: 0.0764 (m-80) REVERT: A 618 THR cc_start: 0.0081 (m) cc_final: -0.0948 (p) REVERT: A 823 PHE cc_start: 0.0703 (m-10) cc_final: -0.2134 (p90) REVERT: A 1029 MET cc_start: 0.0721 (tpp) cc_final: -0.0305 (tpp) REVERT: A 1110 TYR cc_start: 0.0702 (t80) cc_final: -0.0282 (t80) REVERT: B 206 LYS cc_start: 0.1404 (tttt) cc_final: 0.0928 (tttm) REVERT: B 614 ASP cc_start: -0.0604 (p0) cc_final: -0.0839 (t0) REVERT: B 1014 ARG cc_start: 0.2351 (ttm110) cc_final: 0.0880 (tpt170) REVERT: B 1115 ILE cc_start: 0.2112 (mt) cc_final: 0.1515 (pt) REVERT: E 94 MET cc_start: -0.4673 (ttp) cc_final: -0.4906 (ttp) REVERT: G 4 LEU cc_start: -0.0684 (OUTLIER) cc_final: -0.1367 (mm) REVERT: G 34 MET cc_start: 0.0140 (OUTLIER) cc_final: -0.0383 (tpp) REVERT: G 52 SER cc_start: 0.1959 (OUTLIER) cc_final: 0.1480 (m) REVERT: G 53 ASP cc_start: 0.0272 (OUTLIER) cc_final: -0.0623 (m-30) REVERT: H 41 TYR cc_start: -0.0516 (OUTLIER) cc_final: -0.1296 (m-80) REVERT: H 76 PHE cc_start: 0.0814 (OUTLIER) cc_final: -0.0258 (m-10) REVERT: H 111 ILE cc_start: -0.0088 (OUTLIER) cc_final: -0.0451 (tt) REVERT: J 52 SER cc_start: -0.0323 (OUTLIER) cc_final: -0.0807 (p) REVERT: J 105 TYR cc_start: -0.3500 (m-80) cc_final: -0.3790 (m-80) REVERT: K 11 LEU cc_start: -0.2711 (OUTLIER) cc_final: -0.2953 (tp) REVERT: K 41 TYR cc_start: 0.0873 (OUTLIER) cc_final: 0.0240 (m-80) REVERT: K 51 LEU cc_start: 0.0056 (OUTLIER) cc_final: -0.0369 (tt) outliers start: 111 outliers final: 28 residues processed: 338 average time/residue: 0.4031 time to fit residues: 217.5243 Evaluate side-chains 174 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 41 TYR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 41 TYR Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 3.9990 chunk 278 optimal weight: 40.0000 chunk 154 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 287 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 0.0980 chunk 214 optimal weight: 0.9990 chunk 333 optimal weight: 50.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 901 GLN C 954 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0486 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29660 Z= 0.190 Angle : 0.654 13.285 40367 Z= 0.333 Chirality : 0.046 0.443 4694 Planarity : 0.005 0.089 5183 Dihedral : 8.358 103.197 4902 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 1.48 % Allowed : 7.42 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3626 helix: 0.37 (0.20), residues: 665 sheet: -0.40 (0.17), residues: 894 loop : -1.52 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 47 HIS 0.006 0.001 HIS K 31 PHE 0.024 0.002 PHE B 238 TYR 0.026 0.002 TYR B 204 ARG 0.008 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 157 time to evaluate : 2.863 Fit side-chains revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1149 (m-80) cc_final: 0.0757 (m-80) REVERT: A 618 THR cc_start: 0.0442 (m) cc_final: -0.0801 (p) REVERT: A 823 PHE cc_start: 0.1522 (m-10) cc_final: -0.2020 (t80) REVERT: A 1110 TYR cc_start: 0.1362 (t80) cc_final: 0.0031 (t80) REVERT: B 614 ASP cc_start: 0.0110 (p0) cc_final: -0.0154 (t0) REVERT: B 877 LEU cc_start: 0.3390 (mt) cc_final: 0.2809 (mt) REVERT: B 1014 ARG cc_start: 0.2261 (ttm110) cc_final: 0.0261 (tpp-160) REVERT: C 95 THR cc_start: 0.4066 (p) cc_final: 0.3606 (m) REVERT: C 355 ARG cc_start: -0.0229 (OUTLIER) cc_final: -0.2765 (ptt180) REVERT: C 1089 PHE cc_start: 0.3038 (m-80) cc_final: 0.2540 (m-80) REVERT: C 1111 GLU cc_start: 0.0136 (tt0) cc_final: -0.0510 (mm-30) REVERT: D 36 TRP cc_start: 0.0365 (m100) cc_final: 0.0156 (m100) REVERT: D 94 TYR cc_start: 0.3239 (m-80) cc_final: 0.2803 (m-80) REVERT: E 94 MET cc_start: -0.4537 (ttp) cc_final: -0.4781 (ttp) REVERT: G 4 LEU cc_start: -0.0427 (OUTLIER) cc_final: -0.0713 (mt) REVERT: H 54 TYR cc_start: -0.0567 (OUTLIER) cc_final: -0.1313 (p90) REVERT: J 105 TYR cc_start: -0.3616 (m-80) cc_final: -0.4104 (m-80) outliers start: 46 outliers final: 22 residues processed: 192 average time/residue: 0.4280 time to fit residues: 132.5232 Evaluate side-chains 155 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 94 MET Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 333 optimal weight: 8.9990 chunk 360 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 267 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 658 ASN A 901 GLN A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 957 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1064 HIS B1101 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0767 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29660 Z= 0.201 Angle : 0.633 11.756 40367 Z= 0.320 Chirality : 0.046 0.260 4694 Planarity : 0.005 0.115 5183 Dihedral : 7.123 99.595 4844 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 1.93 % Allowed : 10.30 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3626 helix: 0.62 (0.20), residues: 655 sheet: -0.34 (0.17), residues: 907 loop : -1.41 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 40 HIS 0.010 0.001 HIS B1048 PHE 0.024 0.002 PHE A 718 TYR 0.020 0.001 TYR C1067 ARG 0.011 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 146 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.4817 (pm20) cc_final: 0.4006 (tm-30) REVERT: A 451 TYR cc_start: 0.1245 (m-80) cc_final: 0.0861 (m-80) REVERT: A 536 ASN cc_start: 0.0159 (OUTLIER) cc_final: -0.0480 (m-40) REVERT: A 853 GLN cc_start: 0.5712 (tm-30) cc_final: 0.3581 (mm110) REVERT: A 898 PHE cc_start: 0.0662 (t80) cc_final: 0.0353 (t80) REVERT: A 990 GLU cc_start: 0.4806 (OUTLIER) cc_final: 0.3941 (tt0) REVERT: A 1110 TYR cc_start: 0.2289 (t80) cc_final: 0.0585 (t80) REVERT: A 1130 ILE cc_start: -0.0558 (OUTLIER) cc_final: -0.0865 (mp) REVERT: B 614 ASP cc_start: 0.0100 (p0) cc_final: -0.0328 (t0) REVERT: B 796 ASP cc_start: 0.2814 (OUTLIER) cc_final: 0.2539 (p0) REVERT: B 877 LEU cc_start: 0.3684 (mt) cc_final: 0.1964 (pp) REVERT: C 300 LYS cc_start: 0.2370 (ttmt) cc_final: 0.1748 (mmtm) REVERT: C 432 CYS cc_start: 0.0952 (OUTLIER) cc_final: 0.0402 (p) REVERT: C 484 GLU cc_start: 0.3102 (pt0) cc_final: 0.2674 (mp0) REVERT: C 1089 PHE cc_start: 0.3349 (m-80) cc_final: 0.2521 (m-80) REVERT: C 1111 GLU cc_start: 0.0114 (tt0) cc_final: -0.0327 (mm-30) REVERT: D 95 TYR cc_start: 0.1999 (OUTLIER) cc_final: 0.1460 (p90) REVERT: E 94 MET cc_start: -0.4427 (ttp) cc_final: -0.4670 (ttp) outliers start: 60 outliers final: 28 residues processed: 193 average time/residue: 0.3756 time to fit residues: 122.1627 Evaluate side-chains 163 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 50.0000 chunk 251 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 159 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 chunk 335 optimal weight: 40.0000 chunk 354 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 317 optimal weight: 50.0000 chunk 95 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 949 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 901 GLN B 913 GLN B1048 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0898 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 29660 Z= 0.189 Angle : 0.607 10.723 40367 Z= 0.304 Chirality : 0.045 0.268 4694 Planarity : 0.005 0.084 5183 Dihedral : 6.874 94.473 4833 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 1.93 % Allowed : 12.91 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3626 helix: 0.71 (0.20), residues: 661 sheet: -0.44 (0.17), residues: 941 loop : -1.32 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 109 HIS 0.019 0.001 HIS K 31 PHE 0.021 0.002 PHE B 927 TYR 0.022 0.001 TYR K 37 ARG 0.010 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 132 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1185 (m-80) cc_final: 0.0797 (m-80) REVERT: A 536 ASN cc_start: 0.0162 (OUTLIER) cc_final: -0.0070 (m-40) REVERT: A 714 ILE cc_start: -0.1734 (OUTLIER) cc_final: -0.2010 (pt) REVERT: A 853 GLN cc_start: 0.5901 (tm-30) cc_final: 0.3746 (mm110) REVERT: A 898 PHE cc_start: 0.1117 (t80) cc_final: 0.0753 (t80) REVERT: A 1110 TYR cc_start: 0.3140 (t80) cc_final: 0.1221 (t80) REVERT: B 796 ASP cc_start: 0.3153 (OUTLIER) cc_final: 0.2949 (p0) REVERT: B 797 PHE cc_start: 0.3071 (m-10) cc_final: 0.2064 (m-80) REVERT: B 1014 ARG cc_start: 0.2665 (ttm110) cc_final: 0.0416 (tpp-160) REVERT: B 1138 TYR cc_start: -0.0403 (t80) cc_final: -0.0726 (t80) REVERT: C 300 LYS cc_start: 0.2238 (ttmt) cc_final: 0.1660 (mmtm) REVERT: C 388 ASN cc_start: 0.1573 (OUTLIER) cc_final: 0.0753 (t0) REVERT: C 432 CYS cc_start: 0.0840 (OUTLIER) cc_final: 0.0438 (p) REVERT: C 484 GLU cc_start: 0.3271 (pt0) cc_final: 0.2926 (mp0) REVERT: C 1089 PHE cc_start: 0.3611 (m-80) cc_final: 0.2653 (m-80) REVERT: C 1111 GLU cc_start: 0.0046 (tt0) cc_final: -0.0354 (mm-30) REVERT: D 94 TYR cc_start: 0.3030 (m-80) cc_final: 0.2724 (m-80) REVERT: J 105 TYR cc_start: -0.3108 (m-80) cc_final: -0.4673 (m-80) REVERT: K 4 MET cc_start: -0.1023 (tpp) cc_final: -0.1978 (tpp) REVERT: K 94 MET cc_start: 0.1474 (tmm) cc_final: 0.0855 (ppp) outliers start: 60 outliers final: 28 residues processed: 184 average time/residue: 0.3699 time to fit residues: 115.5123 Evaluate side-chains 153 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 318 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 409 GLN B 949 GLN B1058 HIS B1106 GLN C 343 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1149 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 29660 Z= 0.249 Angle : 0.690 13.493 40367 Z= 0.346 Chirality : 0.048 0.286 4694 Planarity : 0.005 0.088 5183 Dihedral : 7.069 89.258 4828 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 2.76 % Allowed : 14.03 % Favored : 83.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3626 helix: 0.41 (0.20), residues: 648 sheet: -0.46 (0.16), residues: 953 loop : -1.46 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 36 HIS 0.047 0.002 HIS K 31 PHE 0.021 0.002 PHE B 927 TYR 0.022 0.002 TYR A1067 ARG 0.013 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 132 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2396 (OUTLIER) cc_final: 0.1620 (m) REVERT: A 400 PHE cc_start: 0.3901 (OUTLIER) cc_final: 0.3470 (p90) REVERT: A 451 TYR cc_start: 0.1071 (m-80) cc_final: 0.0561 (m-80) REVERT: A 714 ILE cc_start: -0.1440 (OUTLIER) cc_final: -0.2237 (pt) REVERT: A 779 GLN cc_start: 0.0306 (OUTLIER) cc_final: -0.0921 (mt0) REVERT: A 853 GLN cc_start: 0.6073 (tm-30) cc_final: 0.3771 (mm110) REVERT: A 898 PHE cc_start: 0.1287 (t80) cc_final: 0.0956 (t80) REVERT: A 1135 ASN cc_start: -0.0541 (OUTLIER) cc_final: -0.1285 (t0) REVERT: B 313 TYR cc_start: 0.2548 (m-80) cc_final: 0.0558 (t80) REVERT: B 714 ILE cc_start: -0.1693 (OUTLIER) cc_final: -0.2426 (mt) REVERT: B 796 ASP cc_start: 0.2962 (OUTLIER) cc_final: 0.2690 (p0) REVERT: B 797 PHE cc_start: 0.3407 (m-10) cc_final: 0.2487 (m-80) REVERT: B 1038 LYS cc_start: 0.0861 (OUTLIER) cc_final: 0.0489 (pttm) REVERT: B 1058 HIS cc_start: 0.0757 (OUTLIER) cc_final: 0.0245 (m-70) REVERT: B 1138 TYR cc_start: 0.0055 (t80) cc_final: -0.0317 (t80) REVERT: C 300 LYS cc_start: 0.2467 (ttmt) cc_final: 0.1890 (mmtm) REVERT: C 388 ASN cc_start: 0.1467 (OUTLIER) cc_final: 0.0278 (t0) REVERT: C 432 CYS cc_start: 0.0718 (OUTLIER) cc_final: 0.0249 (p) REVERT: C 484 GLU cc_start: 0.3538 (pt0) cc_final: 0.3228 (mp0) REVERT: C 1089 PHE cc_start: 0.3309 (m-80) cc_final: 0.2384 (m-80) REVERT: C 1111 GLU cc_start: 0.0223 (tt0) cc_final: -0.0347 (mm-30) REVERT: G 34 MET cc_start: 0.0437 (tpp) cc_final: 0.0218 (tpp) REVERT: K 94 MET cc_start: 0.1490 (tmm) cc_final: 0.0788 (ppp) outliers start: 86 outliers final: 42 residues processed: 204 average time/residue: 0.3970 time to fit residues: 133.7707 Evaluate side-chains 176 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 123 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 1.9990 chunk 319 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 208 optimal weight: 50.0000 chunk 87 optimal weight: 0.9980 chunk 355 optimal weight: 0.0980 chunk 294 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1140 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29660 Z= 0.182 Angle : 0.610 10.758 40367 Z= 0.302 Chirality : 0.046 0.433 4694 Planarity : 0.005 0.075 5183 Dihedral : 6.787 81.660 4828 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 2.47 % Allowed : 15.44 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3626 helix: 0.71 (0.21), residues: 635 sheet: -0.37 (0.17), residues: 931 loop : -1.36 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 109 HIS 0.038 0.002 HIS B1058 PHE 0.016 0.001 PHE B 927 TYR 0.026 0.001 TYR B 204 ARG 0.008 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 129 time to evaluate : 2.896 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2328 (OUTLIER) cc_final: 0.1458 (m) REVERT: A 378 LYS cc_start: 0.4929 (tttm) cc_final: 0.4592 (tttm) REVERT: A 400 PHE cc_start: 0.3626 (OUTLIER) cc_final: 0.3267 (p90) REVERT: A 451 TYR cc_start: 0.0746 (m-80) cc_final: 0.0206 (m-80) REVERT: A 515 PHE cc_start: -0.1735 (OUTLIER) cc_final: -0.4055 (p90) REVERT: A 655 HIS cc_start: 0.2821 (OUTLIER) cc_final: -0.0349 (t-170) REVERT: A 762 GLN cc_start: 0.2901 (mm110) cc_final: 0.1716 (tp40) REVERT: A 779 GLN cc_start: 0.0326 (OUTLIER) cc_final: -0.0629 (mt0) REVERT: A 853 GLN cc_start: 0.5941 (tm-30) cc_final: 0.3800 (mm110) REVERT: A 898 PHE cc_start: 0.1366 (t80) cc_final: 0.0984 (t80) REVERT: A 1130 ILE cc_start: 0.0128 (OUTLIER) cc_final: -0.0253 (mt) REVERT: B 313 TYR cc_start: 0.2540 (m-80) cc_final: 0.0850 (t80) REVERT: B 670 ILE cc_start: 0.1497 (OUTLIER) cc_final: 0.0966 (pt) REVERT: B 714 ILE cc_start: -0.1530 (OUTLIER) cc_final: -0.2253 (mt) REVERT: B 797 PHE cc_start: 0.3516 (m-10) cc_final: 0.2752 (m-80) REVERT: B 819 GLU cc_start: 0.2110 (mp0) cc_final: 0.1837 (mm-30) REVERT: B 1058 HIS cc_start: 0.1594 (OUTLIER) cc_final: -0.0454 (m90) REVERT: B 1071 GLN cc_start: 0.3913 (mp10) cc_final: 0.2361 (tt0) REVERT: B 1138 TYR cc_start: 0.0275 (t80) cc_final: 0.0022 (t80) REVERT: C 300 LYS cc_start: 0.2504 (ttmt) cc_final: 0.1928 (mmtm) REVERT: C 364 ASP cc_start: 0.2341 (t0) cc_final: 0.1633 (p0) REVERT: C 388 ASN cc_start: 0.1553 (OUTLIER) cc_final: 0.0389 (t0) REVERT: C 432 CYS cc_start: 0.0719 (OUTLIER) cc_final: 0.0264 (p) REVERT: C 484 GLU cc_start: 0.3803 (pt0) cc_final: 0.3389 (mp0) REVERT: C 1089 PHE cc_start: 0.3182 (m-80) cc_final: 0.2129 (m-80) REVERT: C 1111 GLU cc_start: 0.0080 (tt0) cc_final: -0.0430 (mm-30) REVERT: G 34 MET cc_start: 0.0544 (tpp) cc_final: 0.0307 (tpp) REVERT: K 94 MET cc_start: 0.1211 (tmm) cc_final: 0.0673 (ppp) REVERT: K 95 GLN cc_start: 0.3417 (pp30) cc_final: -0.0588 (pt0) outliers start: 77 outliers final: 41 residues processed: 197 average time/residue: 0.3556 time to fit residues: 120.1238 Evaluate side-chains 176 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 124 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 259 optimal weight: 0.1980 chunk 200 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 198 optimal weight: 0.0030 chunk 353 optimal weight: 0.9990 chunk 221 optimal weight: 0.0970 chunk 215 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 777 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1087 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29660 Z= 0.146 Angle : 0.553 11.204 40367 Z= 0.275 Chirality : 0.044 0.280 4694 Planarity : 0.004 0.069 5183 Dihedral : 6.323 71.224 4828 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 1.73 % Allowed : 16.60 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3626 helix: 1.15 (0.21), residues: 622 sheet: -0.24 (0.17), residues: 922 loop : -1.30 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 109 HIS 0.036 0.001 HIS B1058 PHE 0.012 0.001 PHE B 759 TYR 0.019 0.001 TYR B 204 ARG 0.004 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 2.809 Fit side-chains REVERT: A 29 THR cc_start: 0.2155 (OUTLIER) cc_final: 0.1225 (m) REVERT: A 378 LYS cc_start: 0.4895 (tttm) cc_final: 0.4557 (tttm) REVERT: A 400 PHE cc_start: 0.3614 (OUTLIER) cc_final: 0.3255 (p90) REVERT: A 451 TYR cc_start: 0.0572 (m-80) cc_final: 0.0032 (m-80) REVERT: A 515 PHE cc_start: -0.1857 (OUTLIER) cc_final: -0.4040 (p90) REVERT: A 762 GLN cc_start: 0.2817 (mm110) cc_final: 0.1667 (tp40) REVERT: A 779 GLN cc_start: 0.0137 (OUTLIER) cc_final: -0.0795 (mt0) REVERT: A 853 GLN cc_start: 0.5768 (tm-30) cc_final: 0.3962 (mm110) REVERT: A 898 PHE cc_start: 0.1118 (t80) cc_final: 0.0791 (t80) REVERT: A 1029 MET cc_start: -0.0306 (ttt) cc_final: -0.1366 (mtp) REVERT: B 313 TYR cc_start: 0.2536 (m-80) cc_final: 0.0863 (t80) REVERT: B 386 LYS cc_start: -0.1266 (ptpt) cc_final: -0.1498 (mtmt) REVERT: B 670 ILE cc_start: 0.1509 (OUTLIER) cc_final: 0.0112 (mm) REVERT: B 714 ILE cc_start: -0.1566 (OUTLIER) cc_final: -0.2268 (mt) REVERT: B 797 PHE cc_start: 0.3430 (m-10) cc_final: 0.2639 (m-80) REVERT: B 883 THR cc_start: 0.4930 (p) cc_final: 0.4579 (p) REVERT: B 1071 GLN cc_start: 0.3700 (mp10) cc_final: 0.2365 (tt0) REVERT: C 300 LYS cc_start: 0.2473 (ttmt) cc_final: 0.1911 (mmtm) REVERT: C 364 ASP cc_start: 0.2439 (t0) cc_final: 0.1503 (p0) REVERT: C 388 ASN cc_start: 0.1353 (OUTLIER) cc_final: 0.0299 (t0) REVERT: C 432 CYS cc_start: 0.0669 (OUTLIER) cc_final: 0.0309 (p) REVERT: C 484 GLU cc_start: 0.3995 (pt0) cc_final: 0.3520 (mp0) REVERT: C 1089 PHE cc_start: 0.3029 (m-80) cc_final: 0.1813 (m-80) REVERT: C 1111 GLU cc_start: -0.0163 (tt0) cc_final: -0.0609 (mm-30) REVERT: G 34 MET cc_start: 0.0659 (tpp) cc_final: 0.0365 (tpp) REVERT: K 95 GLN cc_start: 0.3336 (pp30) cc_final: -0.0397 (pt0) outliers start: 54 outliers final: 38 residues processed: 182 average time/residue: 0.3821 time to fit residues: 115.5562 Evaluate side-chains 177 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 0.3980 chunk 141 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 224 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 278 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 544 ASN B 564 GLN B1058 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1114 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29660 Z= 0.149 Angle : 0.552 10.273 40367 Z= 0.274 Chirality : 0.044 0.279 4694 Planarity : 0.004 0.068 5183 Dihedral : 5.988 56.487 4826 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.31 % Allowed : 16.31 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3626 helix: 1.20 (0.21), residues: 630 sheet: -0.21 (0.17), residues: 921 loop : -1.24 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 109 HIS 0.004 0.001 HIS B1058 PHE 0.016 0.001 PHE B 782 TYR 0.022 0.001 TYR B 453 ARG 0.004 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 140 time to evaluate : 2.994 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2170 (OUTLIER) cc_final: 0.1240 (m) REVERT: A 378 LYS cc_start: 0.4889 (tttm) cc_final: 0.4408 (tttm) REVERT: A 400 PHE cc_start: 0.3628 (OUTLIER) cc_final: 0.3208 (p90) REVERT: A 451 TYR cc_start: 0.0579 (m-80) cc_final: 0.0039 (m-80) REVERT: A 515 PHE cc_start: -0.1981 (OUTLIER) cc_final: -0.4061 (p90) REVERT: A 569 ILE cc_start: -0.1558 (OUTLIER) cc_final: -0.2101 (mm) REVERT: A 655 HIS cc_start: 0.2721 (OUTLIER) cc_final: -0.0338 (t-170) REVERT: A 762 GLN cc_start: 0.3188 (mm110) cc_final: 0.1853 (tp40) REVERT: A 779 GLN cc_start: -0.0032 (OUTLIER) cc_final: -0.0764 (mt0) REVERT: A 853 GLN cc_start: 0.5816 (tm-30) cc_final: 0.4094 (mm110) REVERT: A 898 PHE cc_start: 0.1294 (t80) cc_final: 0.0882 (t80) REVERT: A 1029 MET cc_start: 0.0068 (ttt) cc_final: -0.1045 (mtp) REVERT: B 313 TYR cc_start: 0.2588 (m-80) cc_final: 0.1399 (m-80) REVERT: B 670 ILE cc_start: 0.1474 (OUTLIER) cc_final: 0.0149 (mm) REVERT: B 714 ILE cc_start: -0.1708 (OUTLIER) cc_final: -0.2436 (mt) REVERT: B 797 PHE cc_start: 0.3347 (m-10) cc_final: 0.2539 (m-80) REVERT: B 1058 HIS cc_start: 0.1243 (m90) cc_final: 0.0662 (m-70) REVERT: B 1071 GLN cc_start: 0.3810 (mp10) cc_final: 0.2663 (tt0) REVERT: C 364 ASP cc_start: 0.2524 (t0) cc_final: 0.1577 (p0) REVERT: C 388 ASN cc_start: 0.1454 (OUTLIER) cc_final: 0.0318 (t0) REVERT: C 432 CYS cc_start: 0.0708 (OUTLIER) cc_final: 0.0329 (p) REVERT: C 983 ARG cc_start: 0.2183 (ttp80) cc_final: 0.1949 (ttm110) REVERT: C 1089 PHE cc_start: 0.3058 (m-80) cc_final: 0.1729 (m-80) REVERT: C 1111 GLU cc_start: -0.0246 (tt0) cc_final: -0.0596 (mm-30) REVERT: K 95 GLN cc_start: 0.3347 (pp30) cc_final: -0.0117 (mt0) REVERT: K 97 LEU cc_start: 0.2249 (mm) cc_final: 0.2038 (mm) outliers start: 72 outliers final: 44 residues processed: 203 average time/residue: 0.3733 time to fit residues: 128.1059 Evaluate side-chains 185 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 131 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 329 optimal weight: 50.0000 chunk 198 optimal weight: 0.6980 chunk 143 optimal weight: 40.0000 chunk 258 optimal weight: 0.0050 chunk 101 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 311 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 564 GLN B 804 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1258 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 29660 Z= 0.205 Angle : 0.636 14.186 40367 Z= 0.316 Chirality : 0.049 1.043 4694 Planarity : 0.005 0.072 5183 Dihedral : 6.738 103.130 4826 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.44 % Allowed : 16.28 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3626 helix: 0.90 (0.21), residues: 621 sheet: -0.25 (0.17), residues: 914 loop : -1.31 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 109 HIS 0.007 0.001 HIS A1048 PHE 0.028 0.002 PHE C 377 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 141 time to evaluate : 2.811 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.1914 (OUTLIER) cc_final: 0.1065 (m) REVERT: A 220 PHE cc_start: 0.0549 (t80) cc_final: -0.0173 (p90) REVERT: A 340 GLU cc_start: 0.5769 (pm20) cc_final: 0.5563 (pm20) REVERT: A 346 ARG cc_start: 0.1817 (tmt-80) cc_final: 0.0530 (mtt180) REVERT: A 400 PHE cc_start: 0.3747 (OUTLIER) cc_final: 0.3239 (p90) REVERT: A 451 TYR cc_start: 0.0656 (m-80) cc_final: 0.0088 (m-80) REVERT: A 515 PHE cc_start: -0.2011 (OUTLIER) cc_final: -0.4041 (p90) REVERT: A 581 THR cc_start: 0.1288 (OUTLIER) cc_final: 0.1075 (m) REVERT: A 655 HIS cc_start: 0.2603 (OUTLIER) cc_final: -0.0504 (t-170) REVERT: A 762 GLN cc_start: 0.3227 (mm110) cc_final: 0.1922 (tp40) REVERT: A 779 GLN cc_start: -0.0009 (OUTLIER) cc_final: -0.0884 (mt0) REVERT: A 853 GLN cc_start: 0.5811 (tm-30) cc_final: 0.3983 (mm110) REVERT: A 1029 MET cc_start: -0.0347 (ttt) cc_final: -0.1354 (mtp) REVERT: A 1091 ARG cc_start: 0.3057 (mtp85) cc_final: 0.2361 (mpt-90) REVERT: B 386 LYS cc_start: -0.1338 (ptpt) cc_final: -0.1575 (mtmt) REVERT: B 670 ILE cc_start: 0.1839 (OUTLIER) cc_final: 0.1324 (pt) REVERT: B 714 ILE cc_start: -0.1709 (OUTLIER) cc_final: -0.2458 (mt) REVERT: B 797 PHE cc_start: 0.3676 (m-10) cc_final: 0.2879 (m-80) REVERT: C 223 LEU cc_start: 0.0079 (tp) cc_final: -0.0323 (mt) REVERT: C 241 LEU cc_start: 0.3971 (mm) cc_final: 0.3354 (mm) REVERT: C 300 LYS cc_start: 0.2763 (ttmt) cc_final: 0.2149 (mmtt) REVERT: C 364 ASP cc_start: 0.2624 (t0) cc_final: 0.1485 (p0) REVERT: C 432 CYS cc_start: 0.0919 (OUTLIER) cc_final: 0.0502 (p) REVERT: C 613 GLN cc_start: 0.0830 (OUTLIER) cc_final: 0.0607 (mm-40) REVERT: C 983 ARG cc_start: 0.2212 (ttp80) cc_final: 0.1995 (ttm110) REVERT: C 1089 PHE cc_start: 0.3694 (m-80) cc_final: 0.2396 (m-80) REVERT: C 1111 GLU cc_start: -0.0366 (tt0) cc_final: -0.0592 (mm-30) REVERT: D 36 TRP cc_start: 0.0262 (m100) cc_final: 0.0024 (m100) REVERT: J 109 TRP cc_start: -0.0523 (p90) cc_final: -0.0951 (p90) REVERT: K 95 GLN cc_start: 0.2969 (pp30) cc_final: -0.0076 (mt0) outliers start: 76 outliers final: 54 residues processed: 209 average time/residue: 0.3678 time to fit residues: 128.7414 Evaluate side-chains 199 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 135 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 365 optimal weight: 9.9990 chunk 336 optimal weight: 0.1980 chunk 291 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 907 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1680 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 29660 Z= 0.498 Angle : 1.082 28.419 40367 Z= 0.553 Chirality : 0.062 0.506 4694 Planarity : 0.008 0.152 5183 Dihedral : 8.947 120.095 4826 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.34 % Allowed : 17.05 % Favored : 80.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.14 % 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: -2.09 (0.13), residues: 3626 helix: -0.89 (0.20), residues: 615 sheet: -0.93 (0.17), residues: 906 loop : -1.78 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP B 886 HIS 0.024 0.003 HIS A1048 PHE 0.060 0.004 PHE B 927 TYR 0.043 0.003 TYR A 37 ARG 0.014 0.001 ARG C1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 156 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.5087 (t60) cc_final: 0.4499 (t60) REVERT: A 220 PHE cc_start: 0.1421 (t80) cc_final: 0.0578 (p90) REVERT: A 343 ASN cc_start: 0.0757 (m-40) cc_final: 0.0367 (t0) REVERT: A 346 ARG cc_start: 0.2007 (tmt-80) cc_final: 0.0605 (mtt180) REVERT: A 451 TYR cc_start: 0.0716 (m-80) cc_final: 0.0179 (m-80) REVERT: A 655 HIS cc_start: 0.2476 (OUTLIER) cc_final: -0.0301 (t-170) REVERT: A 762 GLN cc_start: 0.4396 (mm110) cc_final: 0.2817 (tp40) REVERT: A 779 GLN cc_start: 0.0744 (OUTLIER) cc_final: -0.1134 (mt0) REVERT: A 853 GLN cc_start: 0.6240 (tm-30) cc_final: 0.4429 (mm110) REVERT: A 990 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5393 (tt0) REVERT: A 1091 ARG cc_start: 0.3804 (mtp85) cc_final: 0.2416 (ptt180) REVERT: B 224 GLU cc_start: 0.1566 (OUTLIER) cc_final: 0.0445 (mt-10) REVERT: B 386 LYS cc_start: -0.1405 (ptpt) cc_final: -0.1726 (mtmm) REVERT: B 670 ILE cc_start: 0.1897 (OUTLIER) cc_final: 0.1534 (pt) REVERT: B 697 MET cc_start: 0.0576 (mtt) cc_final: -0.2605 (mtp) REVERT: B 714 ILE cc_start: -0.1068 (OUTLIER) cc_final: -0.1714 (mt) REVERT: B 797 PHE cc_start: 0.3706 (m-10) cc_final: 0.2672 (m-80) REVERT: B 800 PHE cc_start: 0.1919 (m-80) cc_final: 0.1592 (m-80) REVERT: B 894 LEU cc_start: 0.4777 (mt) cc_final: 0.4471 (mp) REVERT: B 1109 PHE cc_start: 0.2284 (t80) cc_final: 0.1189 (t80) REVERT: C 300 LYS cc_start: 0.3176 (ttmt) cc_final: 0.2587 (mmtt) REVERT: C 408 ARG cc_start: 0.0799 (tmm-80) cc_final: -0.0796 (mtm-85) REVERT: C 424 LYS cc_start: 0.2672 (mttt) cc_final: 0.2457 (mtmt) REVERT: C 432 CYS cc_start: 0.1209 (OUTLIER) cc_final: 0.0963 (p) REVERT: C 728 PRO cc_start: 0.3825 (Cg_endo) cc_final: 0.3402 (Cg_exo) REVERT: C 731 MET cc_start: 0.0862 (ptp) cc_final: 0.0642 (ptp) REVERT: C 784 GLN cc_start: 0.0927 (mt0) cc_final: 0.0278 (pt0) REVERT: C 1089 PHE cc_start: 0.3662 (m-80) cc_final: 0.3052 (m-80) REVERT: J 109 TRP cc_start: -0.0016 (p90) cc_final: -0.0455 (p90) outliers start: 73 outliers final: 57 residues processed: 221 average time/residue: 0.4298 time to fit residues: 157.5228 Evaluate side-chains 203 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 139 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1052 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 94 MET Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 3.9990 chunk 310 optimal weight: 50.0000 chunk 89 optimal weight: 0.8980 chunk 268 optimal weight: 50.0000 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 291 optimal weight: 0.9980 chunk 122 optimal weight: 0.0070 chunk 299 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.297663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.296769 restraints weight = 69770.784| |-----------------------------------------------------------------------------| r_work (start): 0.5313 rms_B_bonded: 0.17 r_work: 0.5295 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.5276 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work (final): 0.5276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1476 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.387 29660 Z= 0.504 Angle : 1.135 65.900 40367 Z= 0.596 Chirality : 0.060 0.512 4694 Planarity : 0.009 0.203 5183 Dihedral : 8.934 120.263 4826 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.34 % Allowed : 17.34 % Favored : 80.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.17 % 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: -2.12 (0.13), residues: 3626 helix: -0.93 (0.20), residues: 615 sheet: -0.96 (0.17), residues: 906 loop : -1.80 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 886 HIS 0.022 0.003 HIS A1048 PHE 0.057 0.003 PHE B 927 TYR 0.042 0.003 TYR A1067 ARG 0.025 0.001 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5165.08 seconds wall clock time: 95 minutes 23.93 seconds (5723.93 seconds total)