Starting phenix.real_space_refine on Fri Mar 22 00:58:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6t_32335/03_2024/7w6t_32335.pdb" } resolution = 3.85 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= -0.005 sd= 0.059 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 178 5.16 5 C 20432 2.51 5 N 5326 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ASP 263": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E ASP 180": "OD1" <-> "OD2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "E ASP 194": "OD1" <-> "OD2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F ASP 39": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 263": "OD1" <-> "OD2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ASP 213": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 139": "NH1" <-> "NH2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "H ARG 308": "NH1" <-> "NH2" Residue "H PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 289": "OE1" <-> "OE2" Residue "I ASP 313": "OD1" <-> "OD2" Residue "I ASP 314": "OD1" <-> "OD2" Residue "I GLU 362": "OE1" <-> "OE2" Residue "I GLU 364": "OE1" <-> "OE2" Residue "I GLU 375": "OE1" <-> "OE2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 445": "OE1" <-> "OE2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 470": "OD1" <-> "OD2" Residue "I GLU 473": "OE1" <-> "OE2" Residue "I PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 520": "OE1" <-> "OE2" Residue "I GLU 541": "OE1" <-> "OE2" Residue "I ASP 542": "OD1" <-> "OD2" Residue "I PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 578": "OE1" <-> "OE2" Residue "I GLU 614": "OE1" <-> "OE2" Residue "I PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 629": "OE1" <-> "OE2" Residue "I TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 693": "OE1" <-> "OE2" Residue "I TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 741": "OE1" <-> "OE2" Residue "I TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 790": "OD1" <-> "OD2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 364": "OE1" <-> "OE2" Residue "J GLU 366": "OE1" <-> "OE2" Residue "J GLU 374": "OE1" <-> "OE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 445": "OE1" <-> "OE2" Residue "J TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 460": "OD1" <-> "OD2" Residue "J GLU 473": "OE1" <-> "OE2" Residue "J PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 520": "OE1" <-> "OE2" Residue "J GLU 534": "OE1" <-> "OE2" Residue "J ASP 542": "OD1" <-> "OD2" Residue "J PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 568": "OD1" <-> "OD2" Residue "J GLU 578": "OE1" <-> "OE2" Residue "J PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 581": "OE1" <-> "OE2" Residue "J PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 623": "OE1" <-> "OE2" Residue "J GLU 624": "OE1" <-> "OE2" Residue "J ASP 626": "OD1" <-> "OD2" Residue "J PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 683": "OD1" <-> "OD2" Residue "J GLU 693": "OE1" <-> "OE2" Residue "J TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 719": "OE1" <-> "OE2" Residue "J PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 761": "OE1" <-> "OE2" Residue "J PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 790": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31768 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "G" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Chain: "I" Number of atoms: 6024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6024 Classifications: {'peptide': 749} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 715} Chain breaks: 1 Chain: "J" Number of atoms: 6024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6024 Classifications: {'peptide': 749} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 715} Chain breaks: 1 Time building chain proxies: 16.77, per 1000 atoms: 0.53 Number of scatterers: 31768 At special positions: 0 Unit cell: (199.758, 162.24, 209.898, 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 178 16.00 O 5832 8.00 N 5326 7.00 C 20432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS I 357 " distance=2.03 Simple disulfide: pdb=" SG CYS I 466 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS I 475 " - pdb=" SG CYS I 493 " distance=2.02 Simple disulfide: pdb=" SG CYS I 674 " - pdb=" SG CYS I 785 " distance=2.02 Simple disulfide: pdb=" SG CYS J 350 " - pdb=" SG CYS J 357 " distance=2.02 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS J 469 " distance=2.03 Simple disulfide: pdb=" SG CYS J 475 " - pdb=" SG CYS J 493 " distance=2.02 Simple disulfide: pdb=" SG CYS J 674 " - pdb=" SG CYS J 785 " 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 Time building additional restraints: 14.75 Conformation dependent library (CDL) restraints added in 6.0 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7448 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 31 sheets defined 51.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.622A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.340A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 removed outlier: 4.037A pdb=" N ASN A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.557A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.624A pdb=" N ARG A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.727A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.958A pdb=" N LYS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 23 Proline residue: B 21 - end of helix No H-bonds generated for 'chain 'B' and resid 18 through 23' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 74 removed outlier: 4.154A pdb=" N PHE B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.211A pdb=" N PHE B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.776A pdb=" N LYS B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 179 through 203 removed outlier: 3.529A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.506A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.986A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 303 removed outlier: 3.606A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.098A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 removed outlier: 3.655A pdb=" N LEU B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.798A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 397 removed outlier: 3.906A pdb=" N LYS B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.684A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 4.228A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.735A pdb=" N ALA C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.925A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.613A pdb=" N PHE C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 removed outlier: 3.805A pdb=" N TYR C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 4.205A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 154 through 170 removed outlier: 4.044A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 170 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 removed outlier: 4.182A pdb=" N VAL C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.698A pdb=" N ALA D 7 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 18 through 23 removed outlier: 4.483A pdb=" N VAL D 22 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.994A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.565A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 292 through 303 removed outlier: 4.188A pdb=" N ARG D 296 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 298 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 4.038A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.825A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 357 through 365 Processing helix chain 'D' and resid 380 through 396 Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.380A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.830A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.567A pdb=" N PHE E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 106 removed outlier: 4.168A pdb=" N TYR E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 131 removed outlier: 3.735A pdb=" N ALA E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.612A pdb=" N MET E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 194 removed outlier: 3.873A pdb=" N VAL E 186 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'F' and resid 8 through 16 removed outlier: 3.865A pdb=" N ALA F 12 " --> pdb=" O TRP F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 69 through 74 removed outlier: 3.945A pdb=" N GLU F 72 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 73 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.828A pdb=" N CYS F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 94 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.512A pdb=" N TYR F 114 " --> pdb=" O CYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.567A pdb=" N ASN F 175 " --> pdb=" O ARG F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 179 through 203 removed outlier: 3.749A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.592A pdb=" N LEU F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 276 removed outlier: 3.528A pdb=" N ILE F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.887A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.806A pdb=" N ASP F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 292 through 303 removed outlier: 4.310A pdb=" N ARG F 296 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 299 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 343 removed outlier: 3.933A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 321 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 366 removed outlier: 4.390A pdb=" N TYR F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 396 Processing helix chain 'F' and resid 397 through 425 removed outlier: 4.400A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.667A pdb=" N LEU F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 486 No H-bonds generated for 'chain 'F' and resid 484 through 486' Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 61 through 75 removed outlier: 4.004A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.891A pdb=" N GLN G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 110 removed outlier: 4.801A pdb=" N TYR G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 105 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 removed outlier: 3.871A pdb=" N ALA G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.936A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 194 removed outlier: 4.155A pdb=" N VAL G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 189 " --> pdb=" O HIS G 185 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS G 192 " --> pdb=" O VAL G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 213 through 221 removed outlier: 3.780A pdb=" N MET G 217 " --> pdb=" O ASP G 213 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 8 through 16 removed outlier: 3.530A pdb=" N ALA H 12 " --> pdb=" O TRP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 89 through 101 removed outlier: 3.565A pdb=" N CYS H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.746A pdb=" N ILE H 128 " --> pdb=" O PRO H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 180 through 203 removed outlier: 3.796A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 Processing helix chain 'H' and resid 257 through 276 removed outlier: 4.291A pdb=" N ILE H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Proline residue: H 269 - end of helix Processing helix chain 'H' and resid 277 through 281 removed outlier: 3.847A pdb=" N ASP H 281 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 293 removed outlier: 3.940A pdb=" N PHE H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL H 287 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 302 removed outlier: 3.613A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.808A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS H 317 " --> pdb=" O THR H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 342 removed outlier: 3.534A pdb=" N LEU H 321 " --> pdb=" O CYS H 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 356 No H-bonds generated for 'chain 'H' and resid 354 through 356' Processing helix chain 'H' and resid 357 through 366 removed outlier: 3.975A pdb=" N THR H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 396 removed outlier: 4.027A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 426 removed outlier: 4.609A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG H 426 " --> pdb=" O GLN H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.889A pdb=" N LEU H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 480 " --> pdb=" O HIS H 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 56 removed outlier: 3.742A pdb=" N LEU I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU I 43 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL I 50 " --> pdb=" O CYS I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 76 Processing helix chain 'I' and resid 77 through 81 Processing helix chain 'I' and resid 119 through 125 removed outlier: 3.591A pdb=" N ILE I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU I 124 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER I 125 " --> pdb=" O LYS I 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 119 through 125' Processing helix chain 'I' and resid 229 through 235 Processing helix chain 'I' and resid 314 through 318 Processing helix chain 'I' and resid 394 through 396 No H-bonds generated for 'chain 'I' and resid 394 through 396' Processing helix chain 'I' and resid 518 through 528 removed outlier: 3.779A pdb=" N ASN I 526 " --> pdb=" O GLN I 522 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP I 527 " --> pdb=" O LYS I 523 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG I 528 " --> pdb=" O ALA I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 590 Processing helix chain 'I' and resid 607 through 613 removed outlier: 4.458A pdb=" N LEU I 611 " --> pdb=" O GLN I 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU I 612 " --> pdb=" O GLY I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 616 No H-bonds generated for 'chain 'I' and resid 614 through 616' Processing helix chain 'I' and resid 620 through 637 removed outlier: 3.846A pdb=" N LYS I 625 " --> pdb=" O PHE I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 652 through 661 Processing helix chain 'I' and resid 683 through 687 Processing helix chain 'I' and resid 688 through 697 removed outlier: 3.851A pdb=" N TYR I 695 " --> pdb=" O PHE I 691 " (cutoff:3.500A) Processing helix chain 'I' and resid 703 through 709 Processing helix chain 'I' and resid 710 through 716 removed outlier: 3.987A pdb=" N ARG I 714 " --> pdb=" O LYS I 710 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER I 716 " --> pdb=" O ALA I 712 " (cutoff:3.500A) Processing helix chain 'I' and resid 736 through 750 removed outlier: 4.320A pdb=" N LEU I 742 " --> pdb=" O HIS I 738 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN I 745 " --> pdb=" O GLU I 741 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 786 removed outlier: 3.725A pdb=" N HIS I 773 " --> pdb=" O ALA I 769 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU I 784 " --> pdb=" O GLY I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 56 removed outlier: 3.545A pdb=" N LEU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 394 through 396 No H-bonds generated for 'chain 'J' and resid 394 through 396' Processing helix chain 'J' and resid 518 through 526 removed outlier: 3.647A pdb=" N ASN J 526 " --> pdb=" O GLN J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 592 removed outlier: 3.563A pdb=" N VAL J 587 " --> pdb=" O THR J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 613 Processing helix chain 'J' and resid 614 through 616 No H-bonds generated for 'chain 'J' and resid 614 through 616' Processing helix chain 'J' and resid 620 through 635 removed outlier: 3.549A pdb=" N GLU J 624 " --> pdb=" O GLY J 620 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS J 625 " --> pdb=" O PHE J 621 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL J 631 " --> pdb=" O GLN J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 661 Processing helix chain 'J' and resid 688 through 696 removed outlier: 4.289A pdb=" N TYR J 695 " --> pdb=" O PHE J 691 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU J 696 " --> pdb=" O SER J 692 " (cutoff:3.500A) Processing helix chain 'J' and resid 703 through 710 removed outlier: 3.821A pdb=" N GLU J 707 " --> pdb=" O ASN J 703 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET J 708 " --> pdb=" O ARG J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 716 removed outlier: 4.586A pdb=" N SER J 716 " --> pdb=" O ALA J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 735 through 738 Processing helix chain 'J' and resid 739 through 750 removed outlier: 3.661A pdb=" N THR J 744 " --> pdb=" O ALA J 740 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN J 745 " --> pdb=" O GLU J 741 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 787 removed outlier: 4.105A pdb=" N GLU J 784 " --> pdb=" O GLY J 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 removed outlier: 3.703A pdb=" N TYR B 82 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 49 through 54 Processing sheet with id=AA4, first strand: chain 'F' and resid 49 through 54 removed outlier: 3.663A pdb=" N TYR F 82 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 154 Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 54 removed outlier: 8.665A pdb=" N TYR H 82 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL H 43 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE H 84 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN H 45 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 88 through 89 removed outlier: 3.563A pdb=" N LYS I 88 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 96 " --> pdb=" O LYS I 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 139 through 147 removed outlier: 3.727A pdb=" N TYR I 157 " --> pdb=" O TYR I 144 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL I 146 " --> pdb=" O THR I 155 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR I 155 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR I 158 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 183 through 186 removed outlier: 4.164A pdb=" N PHE I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'I' and resid 266 through 267 removed outlier: 3.955A pdb=" N LEU I 267 " --> pdb=" O LYS I 279 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 279 " --> pdb=" O LEU I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 295 through 296 removed outlier: 3.868A pdb=" N LEU I 295 " --> pdb=" O MET I 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 320 through 322 removed outlier: 3.541A pdb=" N LEU I 338 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL I 344 " --> pdb=" O ASN I 339 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER I 345 " --> pdb=" O GLU I 362 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU I 362 " --> pdb=" O SER I 345 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU I 347 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 377 through 378 removed outlier: 3.516A pdb=" N ARG I 389 " --> pdb=" O HIS I 401 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 426 through 433 removed outlier: 6.980A pdb=" N TYR I 440 " --> pdb=" O LEU I 430 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR I 432 " --> pdb=" O LYS I 438 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS I 438 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 478 through 480 removed outlier: 6.593A pdb=" N VAL I 501 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU I 515 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN I 505 " --> pdb=" O ARG I 511 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG I 511 " --> pdb=" O ASN I 505 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 532 through 540 removed outlier: 4.285A pdb=" N VAL I 596 " --> pdb=" O LEU I 550 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL I 597 " --> pdb=" O PRO I 562 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU I 564 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR I 561 " --> pdb=" O ASP I 641 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR I 643 " --> pdb=" O TYR I 561 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU I 563 " --> pdb=" O THR I 643 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL I 645 " --> pdb=" O LEU I 563 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU I 565 " --> pdb=" O VAL I 645 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL I 647 " --> pdb=" O LEU I 565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 677 through 678 removed outlier: 5.976A pdb=" N ALA I 677 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE I 725 " --> pdb=" O GLN I 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 94 through 98 removed outlier: 7.327A pdb=" N VAL J 104 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU J 117 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 130 through 132 removed outlier: 4.133A pdb=" N ARG J 130 " --> pdb=" O SER J 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 130 through 132 removed outlier: 4.133A pdb=" N ARG J 130 " --> pdb=" O SER J 143 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY J 156 " --> pdb=" O LEU J 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 183 through 186 removed outlier: 4.174A pdb=" N TYR J 183 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE J 196 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY J 185 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 194 " --> pdb=" O GLY J 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.985A pdb=" N LEU J 295 " --> pdb=" O MET J 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 264 through 267 Processing sheet with id=AC7, first strand: chain 'J' and resid 325 through 326 removed outlier: 4.270A pdb=" N LYS J 326 " --> pdb=" O ALA J 334 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA J 334 " --> pdb=" O LYS J 326 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER J 345 " --> pdb=" O GLU J 362 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU J 362 " --> pdb=" O SER J 345 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU J 347 " --> pdb=" O LYS J 360 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS J 360 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 387 through 392 removed outlier: 3.909A pdb=" N ARG J 389 " --> pdb=" O HIS J 401 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 426 through 431 removed outlier: 7.664A pdb=" N LEU J 442 " --> pdb=" O THR J 427 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE J 429 " --> pdb=" O TYR J 440 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR J 440 " --> pdb=" O ILE J 429 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER J 431 " --> pdb=" O LYS J 438 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LYS J 438 " --> pdb=" O SER J 431 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE J 441 " --> pdb=" O TYR J 454 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER J 443 " --> pdb=" O HIS J 452 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS J 452 " --> pdb=" O SER J 443 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 478 through 482 Processing sheet with id=AD2, first strand: chain 'J' and resid 532 through 539 removed outlier: 3.746A pdb=" N VAL J 595 " --> pdb=" O PRO J 562 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 597 " --> pdb=" O LEU J 564 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR J 561 " --> pdb=" O ASP J 641 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR J 643 " --> pdb=" O TYR J 561 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU J 563 " --> pdb=" O THR J 643 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL J 645 " --> pdb=" O LEU J 563 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU J 565 " --> pdb=" O VAL J 645 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL J 647 " --> pdb=" O LEU J 565 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 674 through 675 Processing sheet with id=AD4, first strand: chain 'J' and resid 725 through 728 1357 hydrogen bonds defined for protein. 3807 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: 11.54 Time building geometry restraints manager: 15.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7874 1.33 - 1.45: 6800 1.45 - 1.57: 17590 1.57 - 1.69: 0 1.69 - 1.81: 278 Bond restraints: 32542 Sorted by residual: bond pdb=" CA LYS D 350 " pdb=" C LYS D 350 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.37e-02 5.33e+03 1.68e+01 bond pdb=" CA LYS F 350 " pdb=" C LYS F 350 " ideal model delta sigma weight residual 1.522 1.461 0.061 1.72e-02 3.38e+03 1.26e+01 bond pdb=" CA ASN B 45 " pdb=" CB ASN B 45 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C PHE I 95 " pdb=" N ILE I 96 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.14e-02 7.69e+03 8.41e+00 bond pdb=" CA LYS B 350 " pdb=" C LYS B 350 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.39e-02 5.18e+03 6.27e+00 ... (remaining 32537 not shown) Histogram of bond angle deviations from ideal: 98.86 - 106.66: 884 106.66 - 114.47: 18860 114.47 - 122.27: 19429 122.27 - 130.07: 4693 130.07 - 137.88: 202 Bond angle restraints: 44068 Sorted by residual: angle pdb=" C PRO I 284 " pdb=" N LYS I 285 " pdb=" CA LYS I 285 " ideal model delta sigma weight residual 122.77 114.78 7.99 1.33e+00 5.65e-01 3.61e+01 angle pdb=" C GLY J 495 " pdb=" N PRO J 496 " pdb=" CD PRO J 496 " ideal model delta sigma weight residual 120.60 109.99 10.61 2.20e+00 2.07e-01 2.33e+01 angle pdb=" C GLY J 495 " pdb=" N PRO J 496 " pdb=" CA PRO J 496 " ideal model delta sigma weight residual 127.00 137.88 -10.88 2.40e+00 1.74e-01 2.05e+01 angle pdb=" N TYR I 652 " pdb=" CA TYR I 652 " pdb=" C TYR I 652 " ideal model delta sigma weight residual 114.62 109.67 4.95 1.14e+00 7.69e-01 1.89e+01 angle pdb=" C HIS I 560 " pdb=" N TYR I 561 " pdb=" CA TYR I 561 " ideal model delta sigma weight residual 122.74 112.41 10.33 2.44e+00 1.68e-01 1.79e+01 ... (remaining 44063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17173 17.77 - 35.54: 1856 35.54 - 53.31: 281 53.31 - 71.08: 47 71.08 - 88.85: 17 Dihedral angle restraints: 19374 sinusoidal: 7818 harmonic: 11556 Sorted by residual: dihedral pdb=" CA LEU I 267 " pdb=" C LEU I 267 " pdb=" N PRO I 268 " pdb=" CA PRO I 268 " ideal model delta harmonic sigma weight residual -180.00 -144.26 -35.74 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA GLY G 78 " pdb=" C GLY G 78 " pdb=" N VAL G 79 " pdb=" CA VAL G 79 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ASP I 760 " pdb=" C ASP I 760 " pdb=" N GLU I 761 " pdb=" CA GLU I 761 " ideal model delta harmonic sigma weight residual 180.00 147.35 32.65 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 19371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3007 0.039 - 0.077: 1389 0.077 - 0.116: 376 0.116 - 0.154: 75 0.154 - 0.193: 9 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CB VAL D 401 " pdb=" CA VAL D 401 " pdb=" CG1 VAL D 401 " pdb=" CG2 VAL D 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CB VAL J 567 " pdb=" CA VAL J 567 " pdb=" CG1 VAL J 567 " pdb=" CG2 VAL J 567 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CG LEU J 307 " pdb=" CB LEU J 307 " pdb=" CD1 LEU J 307 " pdb=" CD2 LEU J 307 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 4853 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 477 " -0.031 2.00e-02 2.50e+03 2.18e-02 9.54e+00 pdb=" CG TYR J 477 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR J 477 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 477 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 477 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 477 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 477 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN J 290 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO J 291 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO J 291 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 291 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 354 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO F 355 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " 0.040 5.00e-02 4.00e+02 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 739 2.61 - 3.18: 32719 3.18 - 3.75: 54629 3.75 - 4.33: 76093 4.33 - 4.90: 114062 Nonbonded interactions: 278242 Sorted by model distance: nonbonded pdb=" OH TYR B 370 " pdb=" OG1 THR D 364 " model vdw 2.034 2.440 nonbonded pdb=" OG1 THR H 64 " pdb=" OH TYR H 98 " model vdw 2.040 2.440 nonbonded pdb=" O LYS J 285 " pdb=" OG SER J 689 " model vdw 2.063 2.440 nonbonded pdb=" OH TYR I 150 " pdb=" OH TYR I 224 " model vdw 2.084 2.440 nonbonded pdb=" O HIS D 104 " pdb=" OH TYR D 114 " model vdw 2.085 2.440 ... (remaining 278237 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.020 Extract box with map and model: 6.390 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 86.730 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 : 0.006 0.064 32542 Z= 0.375 Angle : 0.866 10.876 44068 Z= 0.510 Chirality : 0.046 0.193 4856 Planarity : 0.005 0.072 5610 Dihedral : 14.587 88.852 11902 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.71 % Favored : 89.24 % Rotamer: Outliers : 0.29 % Allowed : 9.98 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.16 % 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: -4.74 (0.10), residues: 3894 helix: -3.03 (0.09), residues: 1770 sheet: -2.97 (0.26), residues: 303 loop : -3.26 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 230 HIS 0.020 0.002 HIS J 727 PHE 0.028 0.002 PHE I 489 TYR 0.052 0.002 TYR J 477 ARG 0.011 0.001 ARG I 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 348 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 MET cc_start: 0.9026 (ptm) cc_final: 0.8782 (ptp) REVERT: B 235 MET cc_start: 0.9134 (ttp) cc_final: 0.8729 (tmm) REVERT: B 328 LEU cc_start: 0.9274 (mt) cc_final: 0.8979 (mt) REVERT: B 339 MET cc_start: 0.8477 (mmm) cc_final: 0.8069 (mmm) REVERT: C 158 MET cc_start: 0.4240 (ptm) cc_final: 0.3720 (ptm) REVERT: E 58 ASN cc_start: 0.7782 (t0) cc_final: 0.7575 (t0) REVERT: E 143 ASN cc_start: 0.7185 (m110) cc_final: 0.6801 (t0) REVERT: E 168 MET cc_start: 0.6314 (ptp) cc_final: 0.5627 (ptp) REVERT: E 217 MET cc_start: 0.1700 (tpt) cc_final: 0.1386 (tpp) REVERT: G 97 ASP cc_start: 0.8745 (t0) cc_final: 0.8416 (t0) REVERT: G 217 MET cc_start: 0.7596 (mpp) cc_final: 0.6975 (mpp) REVERT: I 650 LYS cc_start: 0.6685 (pptt) cc_final: 0.6275 (pptt) REVERT: I 761 GLU cc_start: 0.6858 (tp30) cc_final: 0.6564 (tp30) REVERT: I 766 HIS cc_start: 0.6187 (p-80) cc_final: 0.5847 (m90) REVERT: J 317 MET cc_start: 0.2830 (mmp) cc_final: 0.2053 (mmp) REVERT: J 525 ILE cc_start: 0.8492 (pt) cc_final: 0.8270 (pt) REVERT: J 547 MET cc_start: 0.6271 (tmm) cc_final: 0.5792 (tmm) REVERT: J 595 VAL cc_start: 0.7627 (t) cc_final: 0.6917 (t) REVERT: J 626 ASP cc_start: 0.7252 (m-30) cc_final: 0.6945 (t0) REVERT: J 652 TYR cc_start: 0.7092 (t80) cc_final: 0.5969 (t80) REVERT: J 722 GLN cc_start: 0.8261 (mt0) cc_final: 0.7926 (tm-30) REVERT: J 743 ILE cc_start: 0.5468 (tt) cc_final: 0.5203 (tp) outliers start: 10 outliers final: 3 residues processed: 358 average time/residue: 0.4459 time to fit residues: 253.8758 Evaluate side-chains 254 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain J residue 290 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.0040 chunk 294 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 198 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 196 ASN B 177 HIS ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 58 ASN C 185 HIS C 191 GLN D 177 HIS D 422 GLN D 477 HIS E 58 ASN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN F 96 ASN F 177 HIS F 405 ASN G 58 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN H 177 HIS I 112 ASN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN ** I 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN I 474 ASN I 613 GLN I 670 GLN I 713 HIS ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 437 ASN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 613 GLN ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 763 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32542 Z= 0.265 Angle : 0.725 9.166 44068 Z= 0.381 Chirality : 0.046 0.251 4856 Planarity : 0.005 0.072 5610 Dihedral : 6.203 51.394 4329 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 28.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.13 % Allowed : 16.42 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.46 (0.12), residues: 3894 helix: -1.77 (0.11), residues: 1841 sheet: -2.65 (0.25), residues: 326 loop : -2.75 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 245 HIS 0.012 0.001 HIS I 152 PHE 0.037 0.002 PHE J 197 TYR 0.034 0.002 TYR J 477 ARG 0.009 0.001 ARG F 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 288 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.5253 (tpt) cc_final: 0.4028 (ptt) REVERT: B 235 MET cc_start: 0.9072 (ttp) cc_final: 0.8503 (tmm) REVERT: B 328 LEU cc_start: 0.9240 (mt) cc_final: 0.8916 (mt) REVERT: D 276 MET cc_start: 0.8615 (mmt) cc_final: 0.8401 (mmm) REVERT: E 168 MET cc_start: 0.5950 (ptp) cc_final: 0.5656 (ptp) REVERT: E 220 LEU cc_start: 0.2083 (tp) cc_final: 0.1616 (mp) REVERT: G 217 MET cc_start: 0.7488 (mpp) cc_final: 0.6702 (mpp) REVERT: H 259 MET cc_start: 0.8071 (mmt) cc_final: 0.7271 (mmm) REVERT: H 263 ASP cc_start: 0.9217 (m-30) cc_final: 0.8973 (m-30) REVERT: I 84 ASP cc_start: -0.1024 (OUTLIER) cc_final: -0.2134 (p0) REVERT: I 220 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4456 (pm20) REVERT: I 317 MET cc_start: 0.3344 (tpp) cc_final: 0.3111 (mmm) REVERT: I 327 TRP cc_start: 0.0391 (m100) cc_final: 0.0116 (m100) REVERT: I 600 ASP cc_start: 0.0554 (OUTLIER) cc_final: 0.0229 (t0) REVERT: I 650 LYS cc_start: 0.6491 (pptt) cc_final: 0.6159 (pptt) REVERT: I 761 GLU cc_start: 0.6727 (tp30) cc_final: 0.6362 (tp30) REVERT: I 766 HIS cc_start: 0.6288 (p-80) cc_final: 0.5625 (m170) REVERT: J 317 MET cc_start: 0.2417 (mmp) cc_final: 0.1671 (mmp) REVERT: J 324 MET cc_start: -0.0419 (tmm) cc_final: -0.0907 (mmm) REVERT: J 547 MET cc_start: 0.6407 (tmm) cc_final: 0.6108 (ppp) REVERT: J 652 TYR cc_start: 0.6751 (t80) cc_final: 0.6190 (t80) REVERT: J 722 GLN cc_start: 0.7998 (mt0) cc_final: 0.7690 (tm-30) outliers start: 74 outliers final: 36 residues processed: 346 average time/residue: 0.3963 time to fit residues: 227.7903 Evaluate side-chains 287 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 383 ARG Chi-restraints excluded: chain J residue 629 GLU Chi-restraints excluded: chain J residue 744 THR Chi-restraints excluded: chain J residue 752 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 50.0000 chunk 109 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 352 optimal weight: 30.0000 chunk 381 optimal weight: 40.0000 chunk 314 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN G 103 HIS ** I 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN ** I 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 745 GLN ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32542 Z= 0.312 Angle : 0.723 12.107 44068 Z= 0.380 Chirality : 0.046 0.194 4856 Planarity : 0.005 0.065 5610 Dihedral : 6.107 58.506 4329 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.57 % Allowed : 18.60 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.08 % 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: -2.98 (0.12), residues: 3894 helix: -1.33 (0.11), residues: 1857 sheet: -2.58 (0.25), residues: 338 loop : -2.53 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 245 HIS 0.013 0.002 HIS I 152 PHE 0.033 0.002 PHE J 197 TYR 0.036 0.002 TYR C 104 ARG 0.009 0.001 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 259 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9058 (ttp) cc_final: 0.8594 (tmm) REVERT: B 328 LEU cc_start: 0.9300 (mt) cc_final: 0.8974 (mt) REVERT: C 173 THR cc_start: 0.5885 (OUTLIER) cc_final: 0.5651 (m) REVERT: D 169 MET cc_start: 0.8962 (ptt) cc_final: 0.8702 (ptt) REVERT: D 276 MET cc_start: 0.8637 (mmt) cc_final: 0.8386 (mmm) REVERT: E 168 MET cc_start: 0.6113 (ptp) cc_final: 0.5579 (ptp) REVERT: E 220 LEU cc_start: 0.2594 (tp) cc_final: 0.2009 (mp) REVERT: F 1 MET cc_start: 0.4818 (mtt) cc_final: 0.4261 (mtt) REVERT: G 158 MET cc_start: 0.6966 (pmm) cc_final: 0.6762 (pmm) REVERT: G 217 MET cc_start: 0.7521 (mpp) cc_final: 0.6703 (mpp) REVERT: H 42 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6368 (mm) REVERT: H 259 MET cc_start: 0.8148 (mmt) cc_final: 0.7487 (mmm) REVERT: H 263 ASP cc_start: 0.9206 (m-30) cc_final: 0.8912 (m-30) REVERT: I 309 MET cc_start: -0.4342 (mmt) cc_final: -0.4576 (mtt) REVERT: I 600 ASP cc_start: 0.0890 (OUTLIER) cc_final: 0.0048 (t0) REVERT: I 650 LYS cc_start: 0.6889 (pptt) cc_final: 0.6417 (pptt) REVERT: I 766 HIS cc_start: 0.6278 (p-80) cc_final: 0.5794 (m170) REVERT: J 84 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7641 (t0) REVERT: J 317 MET cc_start: 0.2821 (mmp) cc_final: 0.0274 (tpp) REVERT: J 530 MET cc_start: 0.8401 (mpp) cc_final: 0.8138 (mpp) REVERT: J 547 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.6091 (ppp) REVERT: J 628 MET cc_start: 0.5953 (mtt) cc_final: 0.5475 (mmm) REVERT: J 652 TYR cc_start: 0.6798 (t80) cc_final: 0.6410 (t80) REVERT: J 660 ILE cc_start: 0.9366 (mt) cc_final: 0.9130 (mp) REVERT: J 722 GLN cc_start: 0.7954 (mt0) cc_final: 0.7649 (tm-30) outliers start: 124 outliers final: 72 residues processed: 360 average time/residue: 0.3860 time to fit residues: 232.6552 Evaluate side-chains 323 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 246 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 385 SER Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 547 MET Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 629 GLU Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 744 THR Chi-restraints excluded: chain J residue 752 ASN Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 183 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 chunk 375 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN ** I 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 522 GLN J 526 ASN ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32542 Z= 0.220 Angle : 0.669 10.319 44068 Z= 0.346 Chirality : 0.044 0.233 4856 Planarity : 0.005 0.062 5610 Dihedral : 5.790 58.162 4329 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.85 % Allowed : 19.93 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.46 (0.13), residues: 3894 helix: -0.88 (0.12), residues: 1829 sheet: -2.31 (0.26), residues: 332 loop : -2.28 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 245 HIS 0.013 0.001 HIS J 699 PHE 0.036 0.002 PHE J 197 TYR 0.028 0.002 TYR B 360 ARG 0.007 0.000 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 270 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TRP cc_start: 0.7977 (t60) cc_final: 0.7669 (t60) REVERT: A 193 MET cc_start: 0.4197 (mmm) cc_final: 0.3587 (mmp) REVERT: B 235 MET cc_start: 0.9064 (ttp) cc_final: 0.8465 (ppp) REVERT: B 328 LEU cc_start: 0.9273 (mt) cc_final: 0.8965 (mt) REVERT: C 173 THR cc_start: 0.5927 (OUTLIER) cc_final: 0.5680 (m) REVERT: D 276 MET cc_start: 0.8657 (mmt) cc_final: 0.8408 (mmm) REVERT: E 220 LEU cc_start: 0.2726 (tp) cc_final: 0.2163 (mp) REVERT: G 217 MET cc_start: 0.7487 (mpp) cc_final: 0.6877 (mpp) REVERT: H 1 MET cc_start: 0.5628 (mpp) cc_final: 0.5056 (mmt) REVERT: H 42 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6365 (mm) REVERT: H 259 MET cc_start: 0.8111 (mmt) cc_final: 0.7518 (mmm) REVERT: H 263 ASP cc_start: 0.9194 (m-30) cc_final: 0.8891 (m-30) REVERT: I 84 ASP cc_start: -0.1088 (OUTLIER) cc_final: -0.1700 (p0) REVERT: I 220 GLU cc_start: 0.4871 (OUTLIER) cc_final: 0.4635 (pm20) REVERT: I 317 MET cc_start: 0.3394 (tpp) cc_final: 0.3190 (mmm) REVERT: I 327 TRP cc_start: -0.0164 (m100) cc_final: -0.0421 (m100) REVERT: I 486 MET cc_start: -0.2386 (mpp) cc_final: -0.3762 (mmt) REVERT: I 494 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: I 600 ASP cc_start: 0.0759 (OUTLIER) cc_final: 0.0435 (t0) REVERT: I 650 LYS cc_start: 0.6865 (pptt) cc_final: 0.6594 (pptt) REVERT: I 766 HIS cc_start: 0.6209 (p-80) cc_final: 0.5371 (m170) REVERT: J 317 MET cc_start: 0.2313 (mmp) cc_final: -0.0239 (tpp) REVERT: J 530 MET cc_start: 0.8349 (mpp) cc_final: 0.8099 (mpp) REVERT: J 547 MET cc_start: 0.6355 (tmm) cc_final: 0.5684 (tmm) REVERT: J 628 MET cc_start: 0.5813 (mtt) cc_final: 0.5331 (mmt) REVERT: J 652 TYR cc_start: 0.6595 (t80) cc_final: 0.6321 (t80) REVERT: J 660 ILE cc_start: 0.9358 (mt) cc_final: 0.9007 (mp) REVERT: J 733 LYS cc_start: 0.7861 (tttt) cc_final: 0.7314 (tptp) REVERT: J 767 SER cc_start: 0.8128 (m) cc_final: 0.7602 (t) outliers start: 134 outliers final: 74 residues processed: 373 average time/residue: 0.3841 time to fit residues: 240.4438 Evaluate side-chains 324 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 244 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 276 MET Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 385 SER Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 301 ASN Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 744 THR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 191 optimal weight: 50.0000 chunk 336 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32542 Z= 0.264 Angle : 0.685 9.566 44068 Z= 0.356 Chirality : 0.045 0.198 4856 Planarity : 0.005 0.057 5610 Dihedral : 5.741 56.992 4329 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.34 % Allowed : 20.90 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -2.27 (0.13), residues: 3894 helix: -0.74 (0.12), residues: 1842 sheet: -2.14 (0.26), residues: 329 loop : -2.18 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 245 HIS 0.013 0.001 HIS G 103 PHE 0.041 0.002 PHE J 197 TYR 0.024 0.002 TYR J 150 ARG 0.008 0.000 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 253 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TRP cc_start: 0.7971 (t60) cc_final: 0.7669 (t60) REVERT: B 235 MET cc_start: 0.9000 (ttp) cc_final: 0.8395 (ppp) REVERT: B 328 LEU cc_start: 0.9314 (mt) cc_final: 0.8959 (mt) REVERT: C 173 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5868 (m) REVERT: D 128 ILE cc_start: 0.8347 (mt) cc_final: 0.8115 (mt) REVERT: D 276 MET cc_start: 0.8642 (mmt) cc_final: 0.8403 (mmm) REVERT: E 220 LEU cc_start: 0.2807 (tp) cc_final: 0.2240 (mt) REVERT: G 168 MET cc_start: 0.8368 (mmm) cc_final: 0.8164 (mmm) REVERT: G 217 MET cc_start: 0.7426 (mpp) cc_final: 0.6936 (mpp) REVERT: H 1 MET cc_start: 0.5691 (mpp) cc_final: 0.4644 (mpp) REVERT: H 268 MET cc_start: 0.8664 (mmm) cc_final: 0.8462 (mmm) REVERT: I 124 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.5180 (pm20) REVERT: I 309 MET cc_start: -0.4452 (mmt) cc_final: -0.4931 (mtt) REVERT: I 327 TRP cc_start: -0.0192 (m100) cc_final: -0.0416 (m100) REVERT: I 494 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: I 600 ASP cc_start: 0.1240 (OUTLIER) cc_final: 0.0743 (t0) REVERT: I 650 LYS cc_start: 0.7209 (pptt) cc_final: 0.6918 (pptt) REVERT: I 782 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.4228 (m-80) REVERT: J 317 MET cc_start: 0.2515 (mmp) cc_final: 0.0197 (tpp) REVERT: J 530 MET cc_start: 0.8336 (mpp) cc_final: 0.8128 (mpp) REVERT: J 547 MET cc_start: 0.6426 (tmm) cc_final: 0.6107 (tmm) REVERT: J 628 MET cc_start: 0.5938 (mtt) cc_final: 0.5487 (mmt) REVERT: J 652 TYR cc_start: 0.6618 (t80) cc_final: 0.6378 (t80) REVERT: J 660 ILE cc_start: 0.9362 (mt) cc_final: 0.9034 (mt) REVERT: J 722 GLN cc_start: 0.7991 (mt0) cc_final: 0.7472 (tp-100) REVERT: J 767 SER cc_start: 0.8064 (m) cc_final: 0.7552 (t) outliers start: 151 outliers final: 100 residues processed: 383 average time/residue: 0.3897 time to fit residues: 248.2672 Evaluate side-chains 344 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 239 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 385 SER Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 301 ASN Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 746 LEU Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain I residue 782 PHE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 265 MET Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 50.0000 chunk 337 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 375 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 197 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 HIS ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 627 GLN ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32542 Z= 0.234 Angle : 0.675 14.586 44068 Z= 0.346 Chirality : 0.044 0.214 4856 Planarity : 0.005 0.055 5610 Dihedral : 5.612 56.798 4329 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.14 % Allowed : 21.91 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -2.08 (0.13), residues: 3894 helix: -0.58 (0.12), residues: 1840 sheet: -2.04 (0.25), residues: 339 loop : -2.08 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 245 HIS 0.015 0.001 HIS I 152 PHE 0.037 0.002 PHE J 197 TYR 0.030 0.002 TYR I 454 ARG 0.007 0.000 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 253 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TRP cc_start: 0.7942 (t60) cc_final: 0.7638 (t60) REVERT: A 169 MET cc_start: 0.5553 (tpt) cc_final: 0.4569 (tmm) REVERT: A 193 MET cc_start: 0.4113 (mmm) cc_final: 0.3488 (mmp) REVERT: B 191 PHE cc_start: 0.7473 (m-80) cc_final: 0.7193 (m-80) REVERT: B 235 MET cc_start: 0.9023 (ttp) cc_final: 0.8395 (ppp) REVERT: B 289 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8572 (tp) REVERT: B 328 LEU cc_start: 0.9308 (mt) cc_final: 0.8992 (mt) REVERT: C 169 MET cc_start: 0.3947 (tmm) cc_final: 0.3412 (tmm) REVERT: C 173 THR cc_start: 0.6090 (OUTLIER) cc_final: 0.5370 (m) REVERT: D 128 ILE cc_start: 0.8338 (mt) cc_final: 0.8121 (mt) REVERT: D 276 MET cc_start: 0.8642 (mmt) cc_final: 0.8392 (mmm) REVERT: E 220 LEU cc_start: 0.2796 (tp) cc_final: 0.2281 (mp) REVERT: G 158 MET cc_start: 0.6884 (pmm) cc_final: 0.6683 (pmm) REVERT: G 217 MET cc_start: 0.7678 (mpp) cc_final: 0.7023 (mpp) REVERT: H 169 MET cc_start: 0.8445 (ptt) cc_final: 0.8238 (ptt) REVERT: H 259 MET cc_start: 0.8443 (mmm) cc_final: 0.8101 (mmm) REVERT: H 263 ASP cc_start: 0.9218 (m-30) cc_final: 0.8953 (m-30) REVERT: H 393 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8704 (mp) REVERT: I 124 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5174 (pm20) REVERT: I 327 TRP cc_start: -0.0243 (m100) cc_final: -0.0486 (m100) REVERT: I 494 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: I 600 ASP cc_start: 0.1001 (OUTLIER) cc_final: 0.0469 (t0) REVERT: I 650 LYS cc_start: 0.7061 (pptt) cc_final: 0.6730 (pptt) REVERT: I 651 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: J 175 GLU cc_start: 0.7382 (mp0) cc_final: 0.6738 (pp20) REVERT: J 317 MET cc_start: 0.2481 (mmp) cc_final: 0.0167 (tpp) REVERT: J 523 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (pttp) REVERT: J 530 MET cc_start: 0.8353 (mpp) cc_final: 0.8058 (mpp) REVERT: J 547 MET cc_start: 0.6527 (tmm) cc_final: 0.6154 (ppp) REVERT: J 628 MET cc_start: 0.6010 (mtt) cc_final: 0.5606 (mmt) REVERT: J 652 TYR cc_start: 0.6601 (t80) cc_final: 0.6298 (t80) REVERT: J 660 ILE cc_start: 0.9341 (mt) cc_final: 0.8968 (mt) REVERT: J 722 GLN cc_start: 0.7950 (mt0) cc_final: 0.7633 (tm-30) REVERT: J 767 SER cc_start: 0.8034 (m) cc_final: 0.7554 (t) outliers start: 144 outliers final: 96 residues processed: 374 average time/residue: 0.3801 time to fit residues: 238.9095 Evaluate side-chains 344 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 240 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 276 MET Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 301 ASN Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 523 LYS Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN ** H 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32542 Z= 0.282 Angle : 0.709 14.725 44068 Z= 0.363 Chirality : 0.045 0.221 4856 Planarity : 0.005 0.055 5610 Dihedral : 5.668 53.190 4329 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.08 % Allowed : 22.94 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -2.04 (0.13), residues: 3894 helix: -0.54 (0.12), residues: 1840 sheet: -2.03 (0.26), residues: 343 loop : -2.07 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 245 HIS 0.016 0.001 HIS I 152 PHE 0.054 0.002 PHE H 383 TYR 0.027 0.002 TYR C 104 ARG 0.007 0.001 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 247 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TRP cc_start: 0.7922 (t60) cc_final: 0.7589 (t60) REVERT: A 169 MET cc_start: 0.5740 (tpt) cc_final: 0.4727 (tmm) REVERT: A 193 MET cc_start: 0.4198 (mmm) cc_final: 0.3565 (mmp) REVERT: B 192 PHE cc_start: 0.8394 (m-80) cc_final: 0.8112 (m-80) REVERT: B 235 MET cc_start: 0.9025 (ttp) cc_final: 0.8399 (ppp) REVERT: B 328 LEU cc_start: 0.9316 (mt) cc_final: 0.8976 (mt) REVERT: C 169 MET cc_start: 0.4016 (tmm) cc_final: 0.3477 (tmm) REVERT: C 173 THR cc_start: 0.6116 (OUTLIER) cc_final: 0.5368 (m) REVERT: D 128 ILE cc_start: 0.8338 (mt) cc_final: 0.8136 (mt) REVERT: D 276 MET cc_start: 0.8643 (mmt) cc_final: 0.8398 (mmm) REVERT: E 59 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6859 (t80) REVERT: E 220 LEU cc_start: 0.2950 (tp) cc_final: 0.2331 (mp) REVERT: G 158 MET cc_start: 0.7008 (pmm) cc_final: 0.6746 (pmm) REVERT: G 217 MET cc_start: 0.7666 (mpp) cc_final: 0.7027 (mpp) REVERT: H 1 MET cc_start: 0.5344 (mpp) cc_final: 0.4509 (mmp) REVERT: H 259 MET cc_start: 0.8591 (mmm) cc_final: 0.8194 (mmm) REVERT: H 263 ASP cc_start: 0.9230 (m-30) cc_final: 0.8939 (m-30) REVERT: H 393 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8704 (mp) REVERT: I 124 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5173 (pm20) REVERT: I 327 TRP cc_start: -0.0064 (m100) cc_final: -0.0356 (m100) REVERT: I 486 MET cc_start: -0.1736 (mpp) cc_final: -0.3844 (mtm) REVERT: I 494 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: I 600 ASP cc_start: 0.1374 (OUTLIER) cc_final: 0.0632 (t0) REVERT: I 651 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: I 782 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4184 (m-80) REVERT: J 105 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5239 (mm) REVERT: J 317 MET cc_start: 0.2733 (mmp) cc_final: 0.0418 (tpp) REVERT: J 530 MET cc_start: 0.8329 (mpp) cc_final: 0.8045 (mpp) REVERT: J 538 ILE cc_start: 0.8548 (mm) cc_final: 0.8247 (mp) REVERT: J 547 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6146 (ppp) REVERT: J 628 MET cc_start: 0.6208 (mtt) cc_final: 0.5857 (mmt) REVERT: J 660 ILE cc_start: 0.9382 (mt) cc_final: 0.9058 (mt) REVERT: J 722 GLN cc_start: 0.7983 (mt0) cc_final: 0.7640 (tm-30) REVERT: J 767 SER cc_start: 0.8056 (m) cc_final: 0.7548 (t) outliers start: 142 outliers final: 107 residues processed: 365 average time/residue: 0.3801 time to fit residues: 235.0812 Evaluate side-chains 353 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 236 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 385 SER Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 600 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 746 LEU Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 777 SER Chi-restraints excluded: chain I residue 782 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 470 ASP Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 547 MET Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 743 ILE Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 0.0050 chunk 149 optimal weight: 0.0980 chunk 223 optimal weight: 30.0000 chunk 112 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 184 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 422 GLN F 96 ASN ** H 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32542 Z= 0.184 Angle : 0.674 13.841 44068 Z= 0.339 Chirality : 0.044 0.239 4856 Planarity : 0.004 0.053 5610 Dihedral : 5.383 57.765 4329 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.88 % Allowed : 24.12 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3894 helix: -0.39 (0.12), residues: 1848 sheet: -1.85 (0.26), residues: 338 loop : -1.85 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 245 HIS 0.016 0.001 HIS I 152 PHE 0.055 0.002 PHE J 197 TYR 0.030 0.002 TYR G 101 ARG 0.006 0.000 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 279 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6880 (m) REVERT: A 140 TRP cc_start: 0.7840 (t60) cc_final: 0.7498 (t60) REVERT: A 169 MET cc_start: 0.5554 (tpt) cc_final: 0.4608 (tmm) REVERT: B 235 MET cc_start: 0.8994 (ttp) cc_final: 0.8695 (ppp) REVERT: B 259 MET cc_start: 0.8109 (mtp) cc_final: 0.7901 (ttm) REVERT: B 289 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 328 LEU cc_start: 0.9308 (mt) cc_final: 0.9092 (mt) REVERT: C 168 MET cc_start: 0.6320 (mpp) cc_final: 0.5765 (mpp) REVERT: C 169 MET cc_start: 0.3870 (tmm) cc_final: 0.3308 (tmm) REVERT: C 173 THR cc_start: 0.6049 (OUTLIER) cc_final: 0.5291 (m) REVERT: D 276 MET cc_start: 0.8627 (mmt) cc_final: 0.8368 (mmm) REVERT: E 59 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6590 (t80) REVERT: E 169 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5563 (mpp) REVERT: E 211 GLN cc_start: -0.4124 (OUTLIER) cc_final: -0.4542 (mm110) REVERT: E 217 MET cc_start: 0.2696 (tpt) cc_final: 0.2099 (tpp) REVERT: F 27 MET cc_start: 0.8197 (tpp) cc_final: 0.7906 (ptt) REVERT: G 158 MET cc_start: 0.6898 (pmm) cc_final: 0.6653 (pmm) REVERT: G 183 ARG cc_start: 0.9543 (mmm-85) cc_final: 0.9082 (tpm170) REVERT: H 1 MET cc_start: 0.5618 (mpp) cc_final: 0.4685 (mmp) REVERT: H 169 MET cc_start: 0.8348 (ptt) cc_final: 0.7828 (mmt) REVERT: H 263 ASP cc_start: 0.9181 (m-30) cc_final: 0.8906 (m-30) REVERT: I 327 TRP cc_start: -0.0547 (m100) cc_final: -0.0906 (m100) REVERT: I 486 MET cc_start: -0.2000 (mpp) cc_final: -0.3961 (mtm) REVERT: I 494 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: I 708 MET cc_start: 0.7699 (mmp) cc_final: 0.7490 (mmp) REVERT: J 105 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5287 (mm) REVERT: J 198 GLU cc_start: 0.8021 (pm20) cc_final: 0.7165 (tm-30) REVERT: J 235 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6186 (mm-30) REVERT: J 265 MET cc_start: 0.5036 (ppp) cc_final: 0.4408 (ppp) REVERT: J 317 MET cc_start: 0.1961 (mmp) cc_final: -0.0343 (tpp) REVERT: J 324 MET cc_start: -0.0372 (tmm) cc_final: -0.1337 (ttt) REVERT: J 530 MET cc_start: 0.8348 (mpp) cc_final: 0.8121 (mpp) REVERT: J 538 ILE cc_start: 0.8555 (mm) cc_final: 0.8252 (mp) REVERT: J 547 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.6162 (ppp) REVERT: J 628 MET cc_start: 0.6155 (mtt) cc_final: 0.5818 (mmt) REVERT: J 660 ILE cc_start: 0.9334 (mt) cc_final: 0.9110 (mt) REVERT: J 722 GLN cc_start: 0.7820 (mt0) cc_final: 0.7553 (tm-30) REVERT: J 767 SER cc_start: 0.7871 (m) cc_final: 0.7395 (t) outliers start: 100 outliers final: 72 residues processed: 358 average time/residue: 0.3864 time to fit residues: 233.6007 Evaluate side-chains 338 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 257 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 276 MET Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 76 PHE Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 582 VAL Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 547 MET Chi-restraints excluded: chain J residue 549 ILE Chi-restraints excluded: chain J residue 567 VAL Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 655 TYR Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 0.0970 chunk 358 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 347 optimal weight: 0.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32542 Z= 0.221 Angle : 0.693 13.509 44068 Z= 0.350 Chirality : 0.044 0.230 4856 Planarity : 0.004 0.050 5610 Dihedral : 5.318 53.042 4328 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.88 % Allowed : 25.01 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3894 helix: -0.24 (0.12), residues: 1825 sheet: -1.83 (0.26), residues: 343 loop : -1.78 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 327 HIS 0.017 0.001 HIS I 152 PHE 0.044 0.002 PHE H 383 TYR 0.023 0.002 TYR C 104 ARG 0.017 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 260 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7116 (OUTLIER) cc_final: 0.6892 (m) REVERT: A 140 TRP cc_start: 0.7845 (t60) cc_final: 0.7535 (t60) REVERT: A 169 MET cc_start: 0.5635 (tpt) cc_final: 0.4817 (tmm) REVERT: A 193 MET cc_start: 0.3799 (mmm) cc_final: 0.3130 (mmp) REVERT: B 235 MET cc_start: 0.9011 (ttp) cc_final: 0.8358 (ppp) REVERT: B 259 MET cc_start: 0.7986 (mtp) cc_final: 0.7485 (ttt) REVERT: B 328 LEU cc_start: 0.9364 (mt) cc_final: 0.9144 (mt) REVERT: C 168 MET cc_start: 0.6281 (mpp) cc_final: 0.5747 (mpp) REVERT: C 169 MET cc_start: 0.3744 (tmm) cc_final: 0.3165 (tmm) REVERT: C 173 THR cc_start: 0.6042 (OUTLIER) cc_final: 0.5289 (m) REVERT: D 276 MET cc_start: 0.8568 (mmt) cc_final: 0.8322 (mmm) REVERT: E 59 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6818 (t80) REVERT: E 211 GLN cc_start: -0.4021 (OUTLIER) cc_final: -0.4419 (mm110) REVERT: F 27 MET cc_start: 0.8166 (tpp) cc_final: 0.7850 (ptt) REVERT: H 1 MET cc_start: 0.5598 (mpp) cc_final: 0.4666 (mmp) REVERT: H 263 ASP cc_start: 0.9206 (m-30) cc_final: 0.8923 (m-30) REVERT: H 393 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (mp) REVERT: I 234 GLU cc_start: 0.0136 (OUTLIER) cc_final: -0.0252 (mp0) REVERT: I 327 TRP cc_start: -0.0458 (m100) cc_final: -0.0795 (m100) REVERT: I 486 MET cc_start: -0.2050 (mpp) cc_final: -0.3852 (mtm) REVERT: I 494 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: J 84 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7212 (t0) REVERT: J 105 ILE cc_start: 0.5782 (OUTLIER) cc_final: 0.5240 (mm) REVERT: J 193 LEU cc_start: 0.1292 (OUTLIER) cc_final: 0.0980 (pp) REVERT: J 198 GLU cc_start: 0.8003 (pm20) cc_final: 0.7117 (tm-30) REVERT: J 235 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6231 (mm-30) REVERT: J 265 MET cc_start: 0.5309 (ppp) cc_final: 0.4558 (ppp) REVERT: J 317 MET cc_start: 0.2158 (mmp) cc_final: -0.0126 (tpp) REVERT: J 530 MET cc_start: 0.8421 (mpp) cc_final: 0.8210 (mpp) REVERT: J 538 ILE cc_start: 0.8656 (mm) cc_final: 0.8369 (mp) REVERT: J 547 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6085 (ppp) REVERT: J 722 GLN cc_start: 0.7850 (mt0) cc_final: 0.7582 (tm-30) outliers start: 100 outliers final: 73 residues processed: 341 average time/residue: 0.3880 time to fit residues: 222.8189 Evaluate side-chains 337 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 253 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 174 GLU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 301 ASN Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 679 SER Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 547 MET Chi-restraints excluded: chain J residue 549 ILE Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Chi-restraints excluded: chain J residue 764 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 2.9990 chunk 368 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 355 optimal weight: 40.0000 chunk 307 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32542 Z= 0.272 Angle : 0.728 14.543 44068 Z= 0.371 Chirality : 0.045 0.219 4856 Planarity : 0.005 0.077 5610 Dihedral : 5.466 52.308 4328 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.93 % Allowed : 25.01 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3894 helix: -0.32 (0.12), residues: 1830 sheet: -1.90 (0.26), residues: 353 loop : -1.81 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 245 HIS 0.016 0.001 HIS I 152 PHE 0.046 0.002 PHE H 383 TYR 0.031 0.002 TYR G 101 ARG 0.009 0.000 ARG B 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 248 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6859 (m) REVERT: A 140 TRP cc_start: 0.7793 (t60) cc_final: 0.7474 (t60) REVERT: A 158 MET cc_start: -0.2039 (OUTLIER) cc_final: -0.2245 (pmm) REVERT: A 169 MET cc_start: 0.5816 (tpt) cc_final: 0.5011 (tmm) REVERT: A 193 MET cc_start: 0.3718 (mmm) cc_final: 0.3030 (mmp) REVERT: B 1 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.2399 (tpt) REVERT: B 235 MET cc_start: 0.9036 (ttp) cc_final: 0.8386 (ppp) REVERT: B 328 LEU cc_start: 0.9355 (mt) cc_final: 0.9055 (mt) REVERT: C 145 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6340 (t80) REVERT: C 168 MET cc_start: 0.6185 (mpp) cc_final: 0.5653 (mpp) REVERT: C 169 MET cc_start: 0.3823 (tmm) cc_final: 0.3284 (tmm) REVERT: C 173 THR cc_start: 0.6013 (OUTLIER) cc_final: 0.5280 (m) REVERT: D 276 MET cc_start: 0.8572 (mmt) cc_final: 0.8317 (mmm) REVERT: E 59 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.7007 (t80) REVERT: E 168 MET cc_start: 0.5269 (ptt) cc_final: 0.4949 (ptt) REVERT: E 211 GLN cc_start: -0.3941 (OUTLIER) cc_final: -0.4368 (mm110) REVERT: F 27 MET cc_start: 0.8226 (tpp) cc_final: 0.7875 (ptt) REVERT: G 183 ARG cc_start: 0.9520 (mmm-85) cc_final: 0.8883 (tpm170) REVERT: H 1 MET cc_start: 0.5557 (mpp) cc_final: 0.4977 (mmp) REVERT: H 263 ASP cc_start: 0.9212 (m-30) cc_final: 0.8917 (m-30) REVERT: I 234 GLU cc_start: -0.0531 (OUTLIER) cc_final: -0.0894 (mp0) REVERT: I 327 TRP cc_start: -0.0297 (m100) cc_final: -0.0615 (m100) REVERT: I 486 MET cc_start: -0.2105 (mpp) cc_final: -0.3821 (mtm) REVERT: I 494 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: J 105 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5218 (mm) REVERT: J 193 LEU cc_start: 0.1493 (OUTLIER) cc_final: 0.1180 (pp) REVERT: J 198 GLU cc_start: 0.7907 (pm20) cc_final: 0.6798 (tm-30) REVERT: J 235 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6288 (mm-30) REVERT: J 265 MET cc_start: 0.5620 (ppp) cc_final: 0.4987 (ppp) REVERT: J 317 MET cc_start: 0.2487 (mmp) cc_final: 0.0353 (tpp) REVERT: J 547 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6188 (ppp) REVERT: J 628 MET cc_start: 0.6522 (mmt) cc_final: 0.6282 (mmt) REVERT: J 722 GLN cc_start: 0.7902 (mt0) cc_final: 0.7663 (tm-30) REVERT: J 767 SER cc_start: 0.7857 (m) cc_final: 0.7409 (t) outliers start: 102 outliers final: 72 residues processed: 330 average time/residue: 0.3867 time to fit residues: 213.8991 Evaluate side-chains 325 residues out of total 3482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 241 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 133 TYR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 192 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 240 HIS Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 464 ARG Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 494 GLU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 564 LEU Chi-restraints excluded: chain I residue 660 ILE Chi-restraints excluded: chain I residue 735 HIS Chi-restraints excluded: chain I residue 743 ILE Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 281 TYR Chi-restraints excluded: chain J residue 290 ASN Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 356 VAL Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 518 ASN Chi-restraints excluded: chain J residue 527 ASP Chi-restraints excluded: chain J residue 547 MET Chi-restraints excluded: chain J residue 582 VAL Chi-restraints excluded: chain J residue 689 SER Chi-restraints excluded: chain J residue 695 TYR Chi-restraints excluded: chain J residue 727 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.0980 chunk 327 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 283 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 316 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 200 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN F 200 ASN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN H 476 HIS ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 373 ASN ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.107160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.090324 restraints weight = 239464.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.089647 restraints weight = 141856.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.089959 restraints weight = 113401.297| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 32542 Z= 0.189 Angle : 0.693 13.411 44068 Z= 0.350 Chirality : 0.044 0.289 4856 Planarity : 0.004 0.057 5610 Dihedral : 5.264 55.318 4328 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.67 % Allowed : 25.24 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.53 (0.13), residues: 3894 helix: -0.20 (0.12), residues: 1830 sheet: -1.90 (0.25), residues: 400 loop : -1.63 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 327 HIS 0.015 0.001 HIS I 152 PHE 0.037 0.002 PHE H 383 TYR 0.037 0.002 TYR G 101 ARG 0.015 0.000 ARG B 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.94 seconds wall clock time: 113 minutes 25.34 seconds (6805.34 seconds total)