Starting phenix.real_space_refine on Wed May 21 20:12:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.map" model { file = "/net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tox_41461/05_2025/8tox_41461.cif" } resolution = 2.3 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= 0.001 sd= 0.014 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 132 5.16 5 C 13533 2.51 5 N 3528 2.21 5 O 4815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22008 Number of models: 1 Model: "" Number of chains: 78 Chain: "B" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "A" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "C" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 14.77, per 1000 atoms: 0.67 Number of scatterers: 22008 At special positions: 0 Unit cell: (151.89, 158.53, 131.14, 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 132 16.00 O 4815 8.00 N 3528 7.00 C 13533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 2 4 " - " MAN 2 5 " " MAN U 4 " - " MAN U 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 6 " " BMA 3 3 " - " MAN 3 5 " " BMA O 3 " - " MAN O 5 " " BMA U 3 " - " MAN U 6 " " BMA V 3 " - " MAN V 5 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 5 " " BMA l 3 " - " MAN l 6 " " BMA m 3 " - " MAN m 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN I 234 " " NAG 1 1 " - " ASN I 241 " " NAG 2 1 " - " ASN I 262 " " NAG 3 1 " - " ASN I 276 " " NAG 4 1 " - " ASN I 295 " " NAG 5 1 " - " ASN I 301 " " NAG 6 1 " - " ASN I 355 " " NAG 7 1 " - " ASN I 386 " " NAG 8 1 " - " ASN I 392 " " NAG 9 1 " - " ASN I 448 " " NAG A 701 " - " ASN A 618 " " NAG B 701 " - " ASN B 618 " " NAG C 601 " - " ASN C 137 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 363 " " NAG F 701 " - " ASN F 618 " " NAG G 601 " - " ASN G 137 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 363 " " NAG I 601 " - " ASN I 137 " " NAG I 602 " - " ASN I 339 " " NAG I 603 " - " ASN I 363 " " NAG M 1 " - " ASN B 611 " " NAG N 1 " - " ASN B 637 " " NAG O 1 " - " ASN G 88 " " NAG P 1 " - " ASN G 133 " " NAG Q 1 " - " ASN G 160 " " NAG R 1 " - " ASN G 197 " " NAG S 1 " - " ASN G 234 " " NAG T 1 " - " ASN G 241 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 276 " " NAG W 1 " - " ASN G 295 " " NAG X 1 " - " ASN G 301 " " NAG Y 1 " - " ASN G 355 " " NAG Z 1 " - " ASN G 386 " " NAG a 1 " - " ASN G 392 " " NAG b 1 " - " ASN G 448 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN A 611 " " NAG e 1 " - " ASN A 637 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 133 " " NAG h 1 " - " ASN C 160 " " NAG i 1 " - " ASN C 197 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 241 " " NAG l 1 " - " ASN C 262 " " NAG m 1 " - " ASN C 276 " " NAG n 1 " - " ASN C 295 " " NAG o 1 " - " ASN C 301 " " NAG p 1 " - " ASN C 355 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 392 " " NAG s 1 " - " ASN C 448 " " NAG t 1 " - " ASN C 156 " " NAG u 1 " - " ASN F 611 " " NAG v 1 " - " ASN F 637 " " NAG w 1 " - " ASN I 88 " " NAG x 1 " - " ASN I 133 " " NAG y 1 " - " ASN I 160 " " NAG z 1 " - " ASN I 197 " " NAGAA 1 " - " ASN I 156 " Time building additional restraints: 7.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4566 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 23.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.568A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'G' and resid 57 through 64 removed outlier: 4.269A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 73 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.059A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 334 through 354 removed outlier: 3.791A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 458 through 462 removed outlier: 4.430A pdb=" N THR G 461 " --> pdb=" O GLY G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.568A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.270A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.060A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.791A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 458 through 462 removed outlier: 4.430A pdb=" N THR C 461 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.567A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'I' and resid 57 through 64 removed outlier: 4.269A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 73 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.059A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.792A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 458 through 462 removed outlier: 4.431A pdb=" N THR I 461 " --> pdb=" O GLY I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR J 87 " --> pdb=" O THR J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 513 through 515 Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.363A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.727A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 323 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.353A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.726A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'F' and resid 513 through 515 Processing sheet with id=AB9, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.350A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 261 current: chain 'I' and resid 284 through 312 removed outlier: 6.726A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.773A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 102 through 103 Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.773A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 102 through 103 Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.772A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1764 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: 7.44 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3345 1.30 - 1.43: 5993 1.43 - 1.56: 12541 1.56 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 22059 Sorted by residual: bond pdb=" C HIS C 216 " pdb=" O HIS C 216 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.21e-02 6.83e+03 2.35e+01 bond pdb=" C HIS G 216 " pdb=" O HIS G 216 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.21e-02 6.83e+03 2.34e+01 bond pdb=" C HIS I 216 " pdb=" O HIS I 216 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.21e-02 6.83e+03 2.29e+01 bond pdb=" C ASN C 156 " pdb=" N CYS C 157 " ideal model delta sigma weight residual 1.330 1.274 0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" C ASN G 156 " pdb=" N CYS G 157 " ideal model delta sigma weight residual 1.330 1.275 0.055 1.40e-02 5.10e+03 1.54e+01 ... (remaining 22054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 27893 1.29 - 2.58: 1460 2.58 - 3.87: 346 3.87 - 5.16: 129 5.16 - 6.46: 79 Bond angle restraints: 29907 Sorted by residual: angle pdb=" C ILE E 29 " pdb=" N LYS E 30 " pdb=" CA LYS E 30 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 angle pdb=" C ILE L 29 " pdb=" N LYS L 30 " pdb=" CA LYS L 30 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.36e+00 angle pdb=" C ILE K 29 " pdb=" N LYS K 30 " pdb=" CA LYS K 30 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.34e+00 angle pdb=" C GLU I 87 " pdb=" N ASN I 88 " pdb=" CA ASN I 88 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.19e+00 angle pdb=" C GLU C 87 " pdb=" N ASN C 88 " pdb=" CA ASN C 88 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.08e+00 ... (remaining 29902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 13668 21.81 - 43.62: 1083 43.62 - 65.43: 177 65.43 - 87.25: 183 87.25 - 109.06: 87 Dihedral angle restraints: 15198 sinusoidal: 8085 harmonic: 7113 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.14 57.14 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.13 57.13 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.12 57.12 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3460 0.095 - 0.190: 311 0.190 - 0.284: 21 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 3798 Sorted by residual: chirality pdb=" C1 BMA w 3 " pdb=" O4 NAG w 2 " pdb=" C2 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.61e+02 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.60e+02 chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.59e+02 ... (remaining 3795 not shown) Planarity restraints: 3648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " 0.145 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" C7 NAG Z 1 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " -0.190 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.144 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG Z 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.188 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 216 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C HIS G 216 " -0.037 2.00e-02 2.50e+03 pdb=" O HIS G 216 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR G 217 " 0.012 2.00e-02 2.50e+03 ... (remaining 3645 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2178 2.74 - 3.28: 21339 3.28 - 3.82: 38018 3.82 - 4.36: 46857 4.36 - 4.90: 75626 Nonbonded interactions: 184018 Sorted by model distance: nonbonded pdb=" O ASN A 637 " pdb=" O HOH A 801 " model vdw 2.205 3.040 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.212 3.040 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 460 " pdb=" OG1 THR C 461 " model vdw 2.212 3.040 nonbonded pdb=" O GLU B 634 " pdb=" O HOH B 801 " model vdw 2.218 3.040 ... (remaining 184013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '3' selection = chain 'AA' selection = chain 'O' selection = chain 'V' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'a' selection = chain 'h' selection = chain 'r' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 52.210 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 0.161 22260 Z= 0.277 Angle : 0.797 17.073 30468 Z= 0.333 Chirality : 0.053 0.474 3798 Planarity : 0.004 0.119 3585 Dihedral : 19.291 109.057 10506 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.51 % Allowed : 18.41 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.18), residues: 2448 helix: 2.17 (0.27), residues: 420 sheet: 0.46 (0.19), residues: 759 loop : 0.02 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 96 HIS 0.006 0.001 HIS I 216 PHE 0.014 0.001 PHE C 53 TYR 0.007 0.001 TYR L 91 ARG 0.003 0.000 ARG I 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 63) link_NAG-ASN : angle 1.80187 ( 189) link_ALPHA1-6 : bond 0.00306 ( 12) link_ALPHA1-6 : angle 2.14561 ( 36) link_BETA1-4 : bond 0.03471 ( 69) link_BETA1-4 : angle 2.56694 ( 207) link_ALPHA1-2 : bond 0.00203 ( 3) link_ALPHA1-2 : angle 1.88473 ( 9) link_ALPHA1-3 : bond 0.00464 ( 12) link_ALPHA1-3 : angle 2.86193 ( 36) hydrogen bonds : bond 0.12662 ( 654) hydrogen bonds : angle 6.31023 ( 1764) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.56077 ( 84) covalent geometry : bond 0.00519 (22059) covalent geometry : angle 0.75050 (29907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 2.445 Fit side-chains REVERT: I 302 MET cc_start: 0.9279 (mmt) cc_final: 0.9027 (mmt) REVERT: L 69 THR cc_start: 0.8569 (m) cc_final: 0.8275 (m) outliers start: 11 outliers final: 7 residues processed: 316 average time/residue: 1.2232 time to fit residues: 445.8268 Evaluate side-chains 277 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 270 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 220 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS G 130 GLN C 72 HIS C 94 ASN C 130 GLN I 72 HIS I 94 ASN I 130 GLN H 76 ASN L 38 GLN D 39 GLN E 34 ASN J 76 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062632 restraints weight = 40161.307| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.32 r_work: 0.2678 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22260 Z= 0.126 Angle : 0.627 7.978 30468 Z= 0.293 Chirality : 0.046 0.282 3798 Planarity : 0.003 0.042 3585 Dihedral : 12.903 77.792 5915 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.18 % Allowed : 17.29 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.97 (0.17), residues: 2448 helix: 2.52 (0.26), residues: 417 sheet: 0.65 (0.19), residues: 756 loop : 0.08 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.003 0.001 HIS E 49 PHE 0.011 0.001 PHE G 53 TYR 0.012 0.001 TYR L 91 ARG 0.007 0.000 ARG J 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 63) link_NAG-ASN : angle 1.74447 ( 189) link_ALPHA1-6 : bond 0.00758 ( 12) link_ALPHA1-6 : angle 1.80922 ( 36) link_BETA1-4 : bond 0.00519 ( 69) link_BETA1-4 : angle 1.53065 ( 207) link_ALPHA1-2 : bond 0.00582 ( 3) link_ALPHA1-2 : angle 2.24501 ( 9) link_ALPHA1-3 : bond 0.01352 ( 12) link_ALPHA1-3 : angle 2.44897 ( 36) hydrogen bonds : bond 0.04097 ( 654) hydrogen bonds : angle 5.00594 ( 1764) SS BOND : bond 0.00357 ( 42) SS BOND : angle 1.28127 ( 84) covalent geometry : bond 0.00275 (22059) covalent geometry : angle 0.59019 (29907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 519 PHE cc_start: 0.8641 (m-80) cc_final: 0.8389 (m-80) REVERT: A 621 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7460 (mt-10) REVERT: F 621 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7569 (mt-10) REVERT: F 625 ASN cc_start: 0.8388 (t0) cc_final: 0.8185 (m110) REVERT: H 3 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8089 (tm130) REVERT: H 72 ASP cc_start: 0.8214 (t70) cc_final: 0.7120 (t70) REVERT: L 4 MET cc_start: 0.7270 (mmm) cc_final: 0.6861 (mmm) REVERT: D 72 ASP cc_start: 0.8027 (t70) cc_final: 0.7080 (t70) REVERT: D 77 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7305 (mmtm) REVERT: E 34 ASN cc_start: 0.8882 (m-40) cc_final: 0.8556 (m110) REVERT: E 95 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: J 72 ASP cc_start: 0.8231 (t70) cc_final: 0.7307 (t70) REVERT: J 74 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8002 (mp0) REVERT: K 23 CYS cc_start: 0.5749 (t) cc_final: 0.5482 (t) REVERT: K 34 ASN cc_start: 0.8932 (m110) cc_final: 0.8444 (m-40) outliers start: 47 outliers final: 27 residues processed: 310 average time/residue: 1.2323 time to fit residues: 440.2443 Evaluate side-chains 294 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 164 optimal weight: 0.6980 chunk 106 optimal weight: 0.0000 chunk 167 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN E 38 GLN E 55 GLN K 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062061 restraints weight = 40275.440| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.35 r_work: 0.2713 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22260 Z= 0.122 Angle : 0.605 10.429 30468 Z= 0.280 Chirality : 0.046 0.308 3798 Planarity : 0.003 0.041 3585 Dihedral : 9.907 65.791 5907 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.09 % Allowed : 17.39 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.95 (0.17), residues: 2448 helix: 2.44 (0.26), residues: 423 sheet: 0.66 (0.18), residues: 756 loop : 0.05 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.002 0.001 HIS C 216 PHE 0.011 0.001 PHE G 53 TYR 0.013 0.001 TYR L 91 ARG 0.012 0.000 ARG G 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 63) link_NAG-ASN : angle 1.71621 ( 189) link_ALPHA1-6 : bond 0.00452 ( 12) link_ALPHA1-6 : angle 1.69829 ( 36) link_BETA1-4 : bond 0.00453 ( 69) link_BETA1-4 : angle 1.40494 ( 207) link_ALPHA1-2 : bond 0.00596 ( 3) link_ALPHA1-2 : angle 2.10450 ( 9) link_ALPHA1-3 : bond 0.01390 ( 12) link_ALPHA1-3 : angle 2.47287 ( 36) hydrogen bonds : bond 0.03750 ( 654) hydrogen bonds : angle 4.82604 ( 1764) SS BOND : bond 0.00424 ( 42) SS BOND : angle 0.76894 ( 84) covalent geometry : bond 0.00266 (22059) covalent geometry : angle 0.57164 (29907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7752 (mt-10) REVERT: G 103 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8812 (tt0) REVERT: G 151 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.8293 (mtt-85) REVERT: A 519 PHE cc_start: 0.8568 (m-80) cc_final: 0.8357 (m-80) REVERT: A 621 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7628 (mt-10) REVERT: C 500 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8499 (mtt90) REVERT: F 621 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7669 (mt-10) REVERT: H 18 LEU cc_start: 0.7628 (tp) cc_final: 0.7419 (tp) REVERT: H 72 ASP cc_start: 0.8125 (t70) cc_final: 0.7552 (t70) REVERT: H 77 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7090 (ttmm) REVERT: H 82 MET cc_start: 0.7772 (mtm) cc_final: 0.6797 (mpp) REVERT: L 4 MET cc_start: 0.7234 (mmm) cc_final: 0.6987 (mmm) REVERT: L 95 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8062 (mp10) REVERT: D 72 ASP cc_start: 0.7983 (t70) cc_final: 0.7571 (t70) REVERT: D 83 ARG cc_start: 0.8385 (mpt-90) cc_final: 0.7849 (mmt90) REVERT: E 95 GLN cc_start: 0.8630 (mt0) cc_final: 0.8379 (mp10) REVERT: J 60 SER cc_start: 0.7407 (t) cc_final: 0.7004 (p) REVERT: J 72 ASP cc_start: 0.8276 (t70) cc_final: 0.7550 (t70) REVERT: J 77 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7365 (ttmm) outliers start: 45 outliers final: 22 residues processed: 304 average time/residue: 1.2144 time to fit residues: 426.2325 Evaluate side-chains 289 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 123 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 239 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 148 optimal weight: 0.0010 chunk 69 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 76 ASN K 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061304 restraints weight = 40797.036| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.39 r_work: 0.2666 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22260 Z= 0.116 Angle : 0.593 10.088 30468 Z= 0.276 Chirality : 0.046 0.321 3798 Planarity : 0.003 0.031 3585 Dihedral : 8.493 57.165 5907 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.46 % Allowed : 17.57 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.17), residues: 2448 helix: 2.50 (0.26), residues: 420 sheet: 0.77 (0.19), residues: 741 loop : 0.02 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE G 53 TYR 0.008 0.001 TYR E 91 ARG 0.008 0.000 ARG J 100F Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 63) link_NAG-ASN : angle 1.68243 ( 189) link_ALPHA1-6 : bond 0.00471 ( 12) link_ALPHA1-6 : angle 1.72033 ( 36) link_BETA1-4 : bond 0.00432 ( 69) link_BETA1-4 : angle 1.40720 ( 207) link_ALPHA1-2 : bond 0.00624 ( 3) link_ALPHA1-2 : angle 2.05245 ( 9) link_ALPHA1-3 : bond 0.01436 ( 12) link_ALPHA1-3 : angle 2.50410 ( 36) hydrogen bonds : bond 0.03617 ( 654) hydrogen bonds : angle 4.71237 ( 1764) SS BOND : bond 0.00133 ( 42) SS BOND : angle 0.76314 ( 84) covalent geometry : bond 0.00255 (22059) covalent geometry : angle 0.55900 (29907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7640 (mt-10) REVERT: G 103 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8742 (tt0) REVERT: A 519 PHE cc_start: 0.8507 (m-80) cc_final: 0.8306 (m-80) REVERT: A 621 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 155 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8254 (mttp) REVERT: C 500 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8404 (mtt90) REVERT: F 621 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7597 (mt-10) REVERT: I 155 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: H 72 ASP cc_start: 0.8256 (t70) cc_final: 0.7279 (t70) REVERT: H 74 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7983 (mp0) REVERT: H 77 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7568 (ttmm) REVERT: H 82 MET cc_start: 0.8214 (mtm) cc_final: 0.7750 (mtm) REVERT: H 83 ARG cc_start: 0.8512 (mpt-90) cc_final: 0.8306 (mtp-110) REVERT: L 4 MET cc_start: 0.7164 (mmm) cc_final: 0.6579 (mmm) REVERT: L 95 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8044 (mp10) REVERT: D 72 ASP cc_start: 0.8163 (t70) cc_final: 0.7247 (t70) REVERT: D 74 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7945 (mp0) REVERT: D 77 LYS cc_start: 0.7722 (ttmm) cc_final: 0.6952 (ttmm) REVERT: D 100 MET cc_start: 0.8124 (mtm) cc_final: 0.7567 (mpt) REVERT: E 95 GLN cc_start: 0.8600 (mt0) cc_final: 0.8330 (mp10) REVERT: J 30 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8800 (pttt) REVERT: J 72 ASP cc_start: 0.8260 (t70) cc_final: 0.7442 (t70) REVERT: J 77 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7100 (ttmm) REVERT: K 33 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7895 (tm) REVERT: K 34 ASN cc_start: 0.8862 (m-40) cc_final: 0.8542 (m110) REVERT: K 36 TYR cc_start: 0.7705 (m-80) cc_final: 0.7396 (m-80) outliers start: 53 outliers final: 26 residues processed: 308 average time/residue: 1.3341 time to fit residues: 470.6322 Evaluate side-chains 291 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 171 optimal weight: 1.9990 chunk 216 optimal weight: 0.0970 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN E 24 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.061109 restraints weight = 40995.813| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.31 r_work: 0.2697 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22260 Z= 0.124 Angle : 0.595 10.355 30468 Z= 0.277 Chirality : 0.045 0.312 3798 Planarity : 0.003 0.065 3585 Dihedral : 7.716 54.367 5907 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 17.62 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.02 (0.17), residues: 2448 helix: 2.43 (0.26), residues: 423 sheet: 0.76 (0.18), residues: 756 loop : 0.09 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 35 HIS 0.002 0.001 HIS E 70 PHE 0.011 0.001 PHE G 53 TYR 0.009 0.001 TYR K 86 ARG 0.016 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 63) link_NAG-ASN : angle 1.69640 ( 189) link_ALPHA1-6 : bond 0.00478 ( 12) link_ALPHA1-6 : angle 1.64179 ( 36) link_BETA1-4 : bond 0.00422 ( 69) link_BETA1-4 : angle 1.40541 ( 207) link_ALPHA1-2 : bond 0.00609 ( 3) link_ALPHA1-2 : angle 2.00236 ( 9) link_ALPHA1-3 : bond 0.01375 ( 12) link_ALPHA1-3 : angle 2.48407 ( 36) hydrogen bonds : bond 0.03689 ( 654) hydrogen bonds : angle 4.70757 ( 1764) SS BOND : bond 0.00144 ( 42) SS BOND : angle 0.69158 ( 84) covalent geometry : bond 0.00278 (22059) covalent geometry : angle 0.56141 (29907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 2.381 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8574 (tmt170) REVERT: B 621 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7794 (mt-10) REVERT: G 210 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: G 500 ARG cc_start: 0.8816 (mtp-110) cc_final: 0.8432 (mtt90) REVERT: G 504 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6943 (mmt90) REVERT: A 621 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 103 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: C 155 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: C 500 ARG cc_start: 0.8916 (mtp-110) cc_final: 0.8492 (mtt90) REVERT: F 621 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7706 (mt-10) REVERT: I 155 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8385 (mttp) REVERT: H 72 ASP cc_start: 0.8337 (t70) cc_final: 0.7335 (t70) REVERT: H 74 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7978 (mp0) REVERT: L 4 MET cc_start: 0.7481 (mmm) cc_final: 0.6909 (mmm) REVERT: L 95 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8057 (mp10) REVERT: D 36 TRP cc_start: 0.8292 (m100) cc_final: 0.8033 (m100) REVERT: D 60 SER cc_start: 0.7411 (t) cc_final: 0.7088 (p) REVERT: D 72 ASP cc_start: 0.8294 (t70) cc_final: 0.7281 (t70) REVERT: D 74 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7924 (mp0) REVERT: D 100 MET cc_start: 0.8225 (mtm) cc_final: 0.7734 (mpt) REVERT: E 38 GLN cc_start: 0.7520 (tt0) cc_final: 0.7291 (tt0) REVERT: E 95 GLN cc_start: 0.8651 (mt0) cc_final: 0.8367 (mp10) REVERT: J 30 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8847 (pttt) REVERT: J 72 ASP cc_start: 0.8351 (t70) cc_final: 0.7533 (t70) REVERT: J 77 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7773 (ttmm) REVERT: J 82 MET cc_start: 0.6759 (mtm) cc_final: 0.6518 (mtm) REVERT: K 33 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8021 (tm) REVERT: K 34 ASN cc_start: 0.8889 (m-40) cc_final: 0.8675 (m110) outliers start: 50 outliers final: 28 residues processed: 312 average time/residue: 1.2254 time to fit residues: 439.5086 Evaluate side-chains 300 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 196 optimal weight: 0.0070 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 34 ASN K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.059645 restraints weight = 40884.911| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.45 r_work: 0.2679 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22260 Z= 0.139 Angle : 0.611 12.093 30468 Z= 0.283 Chirality : 0.046 0.306 3798 Planarity : 0.003 0.049 3585 Dihedral : 7.333 54.400 5907 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.64 % Allowed : 17.48 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.17), residues: 2448 helix: 2.38 (0.26), residues: 423 sheet: 0.73 (0.18), residues: 756 loop : 0.09 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 35 HIS 0.003 0.001 HIS E 70 PHE 0.011 0.001 PHE G 53 TYR 0.009 0.001 TYR H 91 ARG 0.012 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 63) link_NAG-ASN : angle 1.71903 ( 189) link_ALPHA1-6 : bond 0.00461 ( 12) link_ALPHA1-6 : angle 1.59936 ( 36) link_BETA1-4 : bond 0.00413 ( 69) link_BETA1-4 : angle 1.43573 ( 207) link_ALPHA1-2 : bond 0.00585 ( 3) link_ALPHA1-2 : angle 1.96722 ( 9) link_ALPHA1-3 : bond 0.01351 ( 12) link_ALPHA1-3 : angle 2.45813 ( 36) hydrogen bonds : bond 0.03834 ( 654) hydrogen bonds : angle 4.69915 ( 1764) SS BOND : bond 0.00238 ( 42) SS BOND : angle 0.90516 ( 84) covalent geometry : bond 0.00316 (22059) covalent geometry : angle 0.57746 (29907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8613 (ttt180) REVERT: B 621 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7802 (mt-10) REVERT: G 210 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: G 504 ARG cc_start: 0.7253 (mmm160) cc_final: 0.7035 (mmt90) REVERT: A 621 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 103 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: C 117 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8612 (mtmt) REVERT: C 155 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: C 500 ARG cc_start: 0.8916 (mtp-110) cc_final: 0.8487 (mtt90) REVERT: F 621 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7718 (mt-10) REVERT: I 155 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8399 (mttp) REVERT: H 72 ASP cc_start: 0.8371 (t70) cc_final: 0.7599 (t70) REVERT: H 77 LYS cc_start: 0.7808 (ttmm) cc_final: 0.6967 (ttmm) REVERT: L 4 MET cc_start: 0.7430 (mmm) cc_final: 0.6703 (mmm) REVERT: D 19 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7561 (ttp-170) REVERT: D 36 TRP cc_start: 0.8290 (m100) cc_final: 0.8029 (m100) REVERT: D 72 ASP cc_start: 0.8285 (t70) cc_final: 0.7527 (t70) REVERT: D 77 LYS cc_start: 0.7687 (ttmm) cc_final: 0.6934 (ttmm) REVERT: D 100 MET cc_start: 0.8224 (mtm) cc_final: 0.7462 (mpt) REVERT: E 89 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: E 95 GLN cc_start: 0.8649 (mt0) cc_final: 0.8360 (mp10) REVERT: J 30 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8842 (pttt) REVERT: J 72 ASP cc_start: 0.8363 (t70) cc_final: 0.7486 (t70) REVERT: J 77 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7298 (ttmm) REVERT: K 33 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8026 (tm) outliers start: 57 outliers final: 33 residues processed: 311 average time/residue: 1.1943 time to fit residues: 427.4662 Evaluate side-chains 308 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 30 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 76 ASN K 24 GLN K 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059508 restraints weight = 40796.944| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.39 r_work: 0.2667 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22260 Z= 0.167 Angle : 0.627 12.001 30468 Z= 0.291 Chirality : 0.046 0.293 3798 Planarity : 0.004 0.070 3585 Dihedral : 7.105 54.592 5907 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 17.90 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.17), residues: 2448 helix: 2.10 (0.26), residues: 441 sheet: 0.79 (0.18), residues: 771 loop : 0.21 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 35 HIS 0.002 0.001 HIS D 35 PHE 0.024 0.001 PHE E 62 TYR 0.011 0.001 TYR D 90 ARG 0.007 0.000 ARG J 100F Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 63) link_NAG-ASN : angle 1.79707 ( 189) link_ALPHA1-6 : bond 0.00442 ( 12) link_ALPHA1-6 : angle 1.56694 ( 36) link_BETA1-4 : bond 0.00415 ( 69) link_BETA1-4 : angle 1.49185 ( 207) link_ALPHA1-2 : bond 0.00557 ( 3) link_ALPHA1-2 : angle 1.93833 ( 9) link_ALPHA1-3 : bond 0.01316 ( 12) link_ALPHA1-3 : angle 2.41669 ( 36) hydrogen bonds : bond 0.04071 ( 654) hydrogen bonds : angle 4.71301 ( 1764) SS BOND : bond 0.00195 ( 42) SS BOND : angle 0.88451 ( 84) covalent geometry : bond 0.00384 (22059) covalent geometry : angle 0.59286 (29907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8666 (ttt180) REVERT: B 621 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7816 (mt-10) REVERT: G 210 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6936 (m-10) REVERT: G 504 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7171 (mmt90) REVERT: A 621 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 103 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: C 117 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8642 (mtmt) REVERT: C 155 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: C 500 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8481 (mtt90) REVERT: F 621 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7724 (mt-10) REVERT: I 155 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: I 302 MET cc_start: 0.9268 (mmt) cc_final: 0.8937 (mmt) REVERT: H 72 ASP cc_start: 0.8378 (t70) cc_final: 0.7491 (t70) REVERT: L 4 MET cc_start: 0.7571 (mmm) cc_final: 0.6797 (mmm) REVERT: L 95 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8005 (mp10) REVERT: D 19 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7619 (ttp-170) REVERT: D 36 TRP cc_start: 0.8350 (m100) cc_final: 0.8044 (m100) REVERT: D 72 ASP cc_start: 0.8320 (t70) cc_final: 0.7558 (t70) REVERT: D 77 LYS cc_start: 0.7743 (ttmm) cc_final: 0.6945 (ttmm) REVERT: D 100 MET cc_start: 0.8282 (mtm) cc_final: 0.7801 (mpt) REVERT: E 95 GLN cc_start: 0.8658 (mt0) cc_final: 0.8368 (mp10) REVERT: J 60 SER cc_start: 0.7675 (t) cc_final: 0.7319 (p) REVERT: J 72 ASP cc_start: 0.8401 (t70) cc_final: 0.7513 (t70) REVERT: J 77 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7307 (ttmm) REVERT: K 4 MET cc_start: 0.7305 (mmm) cc_final: 0.7046 (mmm) REVERT: K 33 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8070 (tm) outliers start: 53 outliers final: 31 residues processed: 306 average time/residue: 1.2296 time to fit residues: 434.8133 Evaluate side-chains 303 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 169 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 150 optimal weight: 0.0870 chunk 181 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.059044 restraints weight = 41081.541| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.49 r_work: 0.2678 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22260 Z= 0.126 Angle : 0.616 12.842 30468 Z= 0.284 Chirality : 0.045 0.286 3798 Planarity : 0.003 0.047 3585 Dihedral : 6.738 54.285 5907 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.95 % Allowed : 18.31 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.17), residues: 2448 helix: 2.13 (0.26), residues: 441 sheet: 0.72 (0.19), residues: 747 loop : 0.18 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 35 HIS 0.002 0.001 HIS I 72 PHE 0.025 0.001 PHE E 62 TYR 0.014 0.001 TYR D 90 ARG 0.012 0.000 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 63) link_NAG-ASN : angle 1.70896 ( 189) link_ALPHA1-6 : bond 0.00465 ( 12) link_ALPHA1-6 : angle 1.51142 ( 36) link_BETA1-4 : bond 0.00414 ( 69) link_BETA1-4 : angle 1.43995 ( 207) link_ALPHA1-2 : bond 0.00552 ( 3) link_ALPHA1-2 : angle 1.91586 ( 9) link_ALPHA1-3 : bond 0.01327 ( 12) link_ALPHA1-3 : angle 2.40130 ( 36) hydrogen bonds : bond 0.03748 ( 654) hydrogen bonds : angle 4.68890 ( 1764) SS BOND : bond 0.00188 ( 42) SS BOND : angle 1.05635 ( 84) covalent geometry : bond 0.00283 (22059) covalent geometry : angle 0.58248 (29907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7857 (mt-10) REVERT: G 207 LYS cc_start: 0.8760 (mppt) cc_final: 0.8416 (mmpt) REVERT: G 210 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: G 504 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7173 (mmt90) REVERT: A 621 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 103 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: C 117 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8606 (mtmt) REVERT: C 155 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: C 207 LYS cc_start: 0.8816 (mppt) cc_final: 0.8474 (mmpt) REVERT: C 500 ARG cc_start: 0.8918 (mtp-110) cc_final: 0.8480 (mtt90) REVERT: F 621 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7740 (mt-10) REVERT: I 155 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8404 (mttp) REVERT: I 207 LYS cc_start: 0.8856 (mppt) cc_final: 0.8471 (mmpt) REVERT: H 72 ASP cc_start: 0.8388 (t70) cc_final: 0.7537 (t70) REVERT: H 77 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7393 (ttmm) REVERT: L 4 MET cc_start: 0.7540 (mmm) cc_final: 0.6782 (mmm) REVERT: D 36 TRP cc_start: 0.8323 (m100) cc_final: 0.7987 (m100) REVERT: D 72 ASP cc_start: 0.8367 (t70) cc_final: 0.7606 (t70) REVERT: D 77 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7079 (ttmm) REVERT: D 82 MET cc_start: 0.7798 (mmt) cc_final: 0.7097 (mpt) REVERT: D 100 MET cc_start: 0.8320 (mtm) cc_final: 0.7848 (mpt) REVERT: E 36 TYR cc_start: 0.8185 (m-80) cc_final: 0.7658 (m-80) REVERT: E 95 GLN cc_start: 0.8659 (mt0) cc_final: 0.8347 (mp10) REVERT: J 72 ASP cc_start: 0.8380 (t70) cc_final: 0.7488 (t70) REVERT: J 77 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7304 (ttmm) REVERT: K 33 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (tm) outliers start: 42 outliers final: 29 residues processed: 299 average time/residue: 1.2064 time to fit residues: 415.5564 Evaluate side-chains 298 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 217 optimal weight: 0.0670 chunk 10 optimal weight: 0.0570 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060984 restraints weight = 40875.233| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.36 r_work: 0.2662 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22260 Z= 0.110 Angle : 0.598 12.656 30468 Z= 0.278 Chirality : 0.044 0.274 3798 Planarity : 0.003 0.060 3585 Dihedral : 6.442 56.983 5907 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.81 % Allowed : 18.68 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.17), residues: 2448 helix: 2.71 (0.26), residues: 405 sheet: 0.74 (0.18), residues: 768 loop : 0.11 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP K 35 HIS 0.002 0.001 HIS I 72 PHE 0.022 0.001 PHE E 62 TYR 0.011 0.001 TYR D 90 ARG 0.015 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 63) link_NAG-ASN : angle 1.63736 ( 189) link_ALPHA1-6 : bond 0.00441 ( 12) link_ALPHA1-6 : angle 1.49097 ( 36) link_BETA1-4 : bond 0.00425 ( 69) link_BETA1-4 : angle 1.42153 ( 207) link_ALPHA1-2 : bond 0.00537 ( 3) link_ALPHA1-2 : angle 1.89609 ( 9) link_ALPHA1-3 : bond 0.01320 ( 12) link_ALPHA1-3 : angle 2.36332 ( 36) hydrogen bonds : bond 0.03517 ( 654) hydrogen bonds : angle 4.61118 ( 1764) SS BOND : bond 0.00174 ( 42) SS BOND : angle 0.85820 ( 84) covalent geometry : bond 0.00243 (22059) covalent geometry : angle 0.56663 (29907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7775 (mt-10) REVERT: G 103 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: G 210 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: G 504 ARG cc_start: 0.7318 (mmm160) cc_final: 0.7089 (mmt90) REVERT: A 621 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 103 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: C 117 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8530 (mtmt) REVERT: C 155 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8280 (mttp) REVERT: C 500 ARG cc_start: 0.8840 (mtp-110) cc_final: 0.8384 (mtt90) REVERT: C 504 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7048 (mmt90) REVERT: F 621 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7613 (mt-10) REVERT: I 155 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8238 (mttp) REVERT: I 210 PHE cc_start: 0.8080 (p90) cc_final: 0.6892 (m-10) REVERT: I 302 MET cc_start: 0.9188 (mmt) cc_final: 0.8857 (mmt) REVERT: H 72 ASP cc_start: 0.8244 (t70) cc_final: 0.7434 (t70) REVERT: H 77 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7166 (ttmm) REVERT: H 82 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7873 (mpt) REVERT: L 4 MET cc_start: 0.7525 (mmm) cc_final: 0.6786 (mmm) REVERT: L 95 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7996 (mp10) REVERT: D 36 TRP cc_start: 0.8150 (m100) cc_final: 0.7783 (m100) REVERT: D 72 ASP cc_start: 0.8244 (t70) cc_final: 0.7448 (t70) REVERT: D 77 LYS cc_start: 0.7667 (ttmm) cc_final: 0.6962 (ttmm) REVERT: D 82 MET cc_start: 0.7761 (mmt) cc_final: 0.7115 (mpt) REVERT: D 100 MET cc_start: 0.8234 (mtm) cc_final: 0.7884 (mpt) REVERT: E 89 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: E 95 GLN cc_start: 0.8623 (mt0) cc_final: 0.8298 (mp10) REVERT: J 72 ASP cc_start: 0.8338 (t70) cc_final: 0.7397 (t70) REVERT: J 77 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7206 (ttmm) REVERT: K 33 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8076 (tm) REVERT: K 34 ASN cc_start: 0.8632 (m-40) cc_final: 0.8426 (m-40) REVERT: K 36 TYR cc_start: 0.7516 (m-80) cc_final: 0.7298 (m-80) outliers start: 39 outliers final: 26 residues processed: 292 average time/residue: 1.2312 time to fit residues: 413.5852 Evaluate side-chains 299 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 43 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 220 optimal weight: 0.0060 chunk 120 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060142 restraints weight = 40766.354| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.40 r_work: 0.2671 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22260 Z= 0.159 Angle : 0.626 12.395 30468 Z= 0.292 Chirality : 0.045 0.258 3798 Planarity : 0.004 0.058 3585 Dihedral : 6.491 59.107 5907 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.72 % Allowed : 18.87 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.17), residues: 2448 helix: 2.29 (0.26), residues: 423 sheet: 0.84 (0.19), residues: 720 loop : 0.07 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP K 35 HIS 0.003 0.001 HIS I 72 PHE 0.024 0.001 PHE E 62 TYR 0.012 0.001 TYR D 90 ARG 0.014 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 63) link_NAG-ASN : angle 1.78342 ( 189) link_ALPHA1-6 : bond 0.00356 ( 12) link_ALPHA1-6 : angle 1.53564 ( 36) link_BETA1-4 : bond 0.00409 ( 69) link_BETA1-4 : angle 1.52301 ( 207) link_ALPHA1-2 : bond 0.00490 ( 3) link_ALPHA1-2 : angle 1.86964 ( 9) link_ALPHA1-3 : bond 0.01213 ( 12) link_ALPHA1-3 : angle 2.30037 ( 36) hydrogen bonds : bond 0.04018 ( 654) hydrogen bonds : angle 4.63505 ( 1764) SS BOND : bond 0.00211 ( 42) SS BOND : angle 0.74105 ( 84) covalent geometry : bond 0.00366 (22059) covalent geometry : angle 0.59306 (29907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7858 (mt-10) REVERT: G 103 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: G 207 LYS cc_start: 0.8768 (mppt) cc_final: 0.8429 (mmpt) REVERT: G 210 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: A 621 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 103 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: C 117 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8628 (mtmt) REVERT: C 155 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8412 (mttp) REVERT: C 207 LYS cc_start: 0.8835 (mppt) cc_final: 0.8480 (mmpt) REVERT: C 500 ARG cc_start: 0.8910 (mtp-110) cc_final: 0.8472 (mtt90) REVERT: C 504 ARG cc_start: 0.7436 (mmm160) cc_final: 0.7206 (mmt90) REVERT: F 621 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7729 (mt-10) REVERT: I 155 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: I 207 LYS cc_start: 0.8845 (mppt) cc_final: 0.8465 (mmpt) REVERT: I 302 MET cc_start: 0.9261 (mmt) cc_final: 0.8937 (mmt) REVERT: H 72 ASP cc_start: 0.8393 (t70) cc_final: 0.7586 (t70) REVERT: H 77 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7360 (ttmm) REVERT: H 82 MET cc_start: 0.8073 (mpp) cc_final: 0.7728 (mpt) REVERT: L 4 MET cc_start: 0.7625 (mmm) cc_final: 0.7377 (mmm) REVERT: D 36 TRP cc_start: 0.8271 (m100) cc_final: 0.7889 (m100) REVERT: D 72 ASP cc_start: 0.8339 (t70) cc_final: 0.7575 (t70) REVERT: D 77 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7056 (ttmm) REVERT: D 82 MET cc_start: 0.7854 (mmt) cc_final: 0.7200 (mpt) REVERT: D 100 MET cc_start: 0.8350 (mtm) cc_final: 0.7988 (mpt) REVERT: E 89 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: E 95 GLN cc_start: 0.8662 (mt0) cc_final: 0.8351 (mp10) REVERT: J 72 ASP cc_start: 0.8389 (t70) cc_final: 0.7449 (t70) REVERT: J 77 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7308 (ttmm) REVERT: K 33 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8089 (tm) REVERT: K 34 ASN cc_start: 0.8632 (m-40) cc_final: 0.8416 (m-40) REVERT: K 95 GLN cc_start: 0.8503 (mt0) cc_final: 0.8162 (mp10) outliers start: 37 outliers final: 26 residues processed: 291 average time/residue: 1.2539 time to fit residues: 422.1401 Evaluate side-chains 296 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN J 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.058465 restraints weight = 41036.397| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.49 r_work: 0.2651 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22260 Z= 0.178 Angle : 0.640 13.063 30468 Z= 0.298 Chirality : 0.045 0.250 3798 Planarity : 0.004 0.055 3585 Dihedral : 6.516 57.607 5907 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.81 % Allowed : 18.73 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.93 (0.17), residues: 2448 helix: 1.98 (0.26), residues: 441 sheet: 0.69 (0.18), residues: 741 loop : 0.18 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP K 35 HIS 0.003 0.001 HIS I 72 PHE 0.023 0.001 PHE E 62 TYR 0.015 0.001 TYR D 90 ARG 0.016 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 63) link_NAG-ASN : angle 1.84400 ( 189) link_ALPHA1-6 : bond 0.00341 ( 12) link_ALPHA1-6 : angle 1.54102 ( 36) link_BETA1-4 : bond 0.00400 ( 69) link_BETA1-4 : angle 1.54333 ( 207) link_ALPHA1-2 : bond 0.00463 ( 3) link_ALPHA1-2 : angle 1.83292 ( 9) link_ALPHA1-3 : bond 0.01167 ( 12) link_ALPHA1-3 : angle 2.28236 ( 36) hydrogen bonds : bond 0.04159 ( 654) hydrogen bonds : angle 4.65903 ( 1764) SS BOND : bond 0.00239 ( 42) SS BOND : angle 0.94264 ( 84) covalent geometry : bond 0.00412 (22059) covalent geometry : angle 0.60514 (29907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27175.13 seconds wall clock time: 468 minutes 17.51 seconds (28097.51 seconds total)