Starting phenix.real_space_refine on Thu Jun 19 00:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tox_41461/06_2025/8tox_41461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tox_41461/06_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_41461/06_2025/8tox_41461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tox_41461/06_2025/8tox_41461.map" model { file = "/net/cci-nas-00/data/ceres_data/8tox_41461/06_2025/8tox_41461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tox_41461/06_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-5710/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: 15.80, per 1000 atoms: 0.72 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: 7.64 Conformation dependent library (CDL) restraints added in 3.1 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: 2.70 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: 8.21 Time building geometry restraints manager: 8.68 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: 0.05 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: 10.130 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 54.810 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.390 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.110 ------------------------------------------------------------------------------- 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 : 2.548 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: 1.3177 time to fit residues: 480.0630 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 : 2.598 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.106374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062849 restraints weight = 40231.084| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.22 r_work: 0.2683 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 519 PHE cc_start: 0.8643 (m-80) cc_final: 0.8393 (m-80) REVERT: A 621 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7479 (mt-10) REVERT: F 621 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7585 (mt-10) REVERT: H 3 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8096 (tm130) REVERT: H 72 ASP cc_start: 0.8237 (t70) cc_final: 0.7140 (t70) REVERT: L 4 MET cc_start: 0.7307 (mmm) cc_final: 0.6903 (mmm) REVERT: D 72 ASP cc_start: 0.8054 (t70) cc_final: 0.7103 (t70) REVERT: D 77 LYS cc_start: 0.7792 (mmmm) cc_final: 0.7330 (mmtm) REVERT: E 34 ASN cc_start: 0.8906 (m-40) cc_final: 0.8583 (m110) REVERT: E 95 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: J 72 ASP cc_start: 0.8252 (t70) cc_final: 0.7327 (t70) REVERT: J 74 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8002 (mp0) REVERT: K 23 CYS cc_start: 0.5764 (t) cc_final: 0.5499 (t) REVERT: K 34 ASN cc_start: 0.8954 (m110) cc_final: 0.8472 (m-40) outliers start: 47 outliers final: 27 residues processed: 310 average time/residue: 1.8067 time to fit residues: 650.2754 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 : 6.625 ------------------------------------------------------------------------------- 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: 0.2980 chunk 106 optimal weight: 0.0870 chunk 167 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.106501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061539 restraints weight = 40320.996| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.36 r_work: 0.2670 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22260 Z= 0.119 Angle : 0.604 10.427 30468 Z= 0.280 Chirality : 0.046 0.310 3798 Planarity : 0.003 0.042 3585 Dihedral : 9.835 65.357 5907 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.13 % Allowed : 17.29 % Favored : 80.57 % 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: 0.67 (0.18), residues: 756 loop : 0.06 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 35 HIS 0.002 0.001 HIS I 216 PHE 0.011 0.001 PHE G 53 TYR 0.015 0.001 TYR L 91 ARG 0.012 0.001 ARG G 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 63) link_NAG-ASN : angle 1.70922 ( 189) link_ALPHA1-6 : bond 0.00432 ( 12) link_ALPHA1-6 : angle 1.69339 ( 36) link_BETA1-4 : bond 0.00458 ( 69) link_BETA1-4 : angle 1.39896 ( 207) link_ALPHA1-2 : bond 0.00608 ( 3) link_ALPHA1-2 : angle 2.09061 ( 9) link_ALPHA1-3 : bond 0.01348 ( 12) link_ALPHA1-3 : angle 2.48247 ( 36) hydrogen bonds : bond 0.03726 ( 654) hydrogen bonds : angle 4.82231 ( 1764) SS BOND : bond 0.00171 ( 42) SS BOND : angle 0.83640 ( 84) covalent geometry : bond 0.00261 (22059) covalent geometry : angle 0.57077 (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 325 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7659 (mt-10) REVERT: G 103 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8734 (tt0) REVERT: G 151 ARG cc_start: 0.8482 (mtt-85) cc_final: 0.8262 (mtt-85) REVERT: A 519 PHE cc_start: 0.8558 (m-80) cc_final: 0.8345 (m-80) REVERT: A 621 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 500 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8414 (mtt90) REVERT: F 621 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7581 (mt-10) REVERT: H 72 ASP cc_start: 0.8018 (t70) cc_final: 0.7442 (t70) REVERT: H 77 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6931 (ttmm) REVERT: H 82 MET cc_start: 0.7716 (mtm) cc_final: 0.6717 (mpp) REVERT: L 4 MET cc_start: 0.7100 (mmm) cc_final: 0.6859 (mmm) REVERT: L 95 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8027 (mp10) REVERT: D 72 ASP cc_start: 0.7874 (t70) cc_final: 0.7438 (t70) REVERT: D 83 ARG cc_start: 0.8393 (mpt-90) cc_final: 0.7852 (mmt90) REVERT: D 100 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7386 (mpt) REVERT: E 46 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7176 (tp) REVERT: E 95 GLN cc_start: 0.8609 (mt0) cc_final: 0.8363 (mp10) REVERT: J 60 SER cc_start: 0.7341 (t) cc_final: 0.6936 (p) REVERT: J 72 ASP cc_start: 0.8160 (t70) cc_final: 0.7407 (t70) REVERT: J 77 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7217 (ttmm) outliers start: 46 outliers final: 19 residues processed: 306 average time/residue: 1.3118 time to fit residues: 464.3288 Evaluate side-chains 283 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 D residue 100 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 123 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 148 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.105859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061053 restraints weight = 40663.783| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.40 r_work: 0.2646 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22260 Z= 0.136 Angle : 0.603 9.585 30468 Z= 0.281 Chirality : 0.046 0.320 3798 Planarity : 0.003 0.030 3585 Dihedral : 8.472 56.474 5907 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.78 % Allowed : 16.88 % Favored : 80.34 % 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: 1.04 (0.17), residues: 2448 helix: 2.45 (0.26), residues: 420 sheet: 0.75 (0.18), residues: 780 loop : 0.11 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE G 53 TYR 0.009 0.001 TYR E 91 ARG 0.006 0.000 ARG G 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 63) link_NAG-ASN : angle 1.74526 ( 189) link_ALPHA1-6 : bond 0.00463 ( 12) link_ALPHA1-6 : angle 1.71394 ( 36) link_BETA1-4 : bond 0.00426 ( 69) link_BETA1-4 : angle 1.44401 ( 207) link_ALPHA1-2 : bond 0.00615 ( 3) link_ALPHA1-2 : angle 2.04260 ( 9) link_ALPHA1-3 : bond 0.01386 ( 12) link_ALPHA1-3 : angle 2.48468 ( 36) hydrogen bonds : bond 0.03839 ( 654) hydrogen bonds : angle 4.73355 ( 1764) SS BOND : bond 0.00321 ( 42) SS BOND : angle 0.79361 ( 84) covalent geometry : bond 0.00307 (22059) covalent geometry : angle 0.56846 (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 335 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 3.262 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8440 (tmt170) REVERT: B 621 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7632 (mt-10) REVERT: G 500 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8579 (mtp-110) REVERT: A 519 PHE cc_start: 0.8520 (m-80) cc_final: 0.8319 (m-80) REVERT: A 621 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 155 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8233 (mttp) REVERT: C 500 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8385 (mtt90) REVERT: F 621 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7570 (mt-10) REVERT: I 155 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8275 (mttp) REVERT: H 72 ASP cc_start: 0.8238 (t70) cc_final: 0.7165 (t70) REVERT: H 74 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7982 (mp0) REVERT: H 77 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7541 (ttmm) REVERT: H 83 ARG cc_start: 0.8493 (mpt-90) cc_final: 0.8284 (mtp-110) REVERT: L 4 MET cc_start: 0.7146 (mmm) cc_final: 0.6845 (mmm) REVERT: L 95 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8028 (mp10) REVERT: D 72 ASP cc_start: 0.8138 (t70) cc_final: 0.7206 (t70) REVERT: D 74 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7934 (mp0) REVERT: D 77 LYS cc_start: 0.7686 (ttmm) cc_final: 0.6918 (ttmm) REVERT: D 100 MET cc_start: 0.7730 (mtt) cc_final: 0.7431 (mpt) REVERT: E 95 GLN cc_start: 0.8596 (mt0) cc_final: 0.8325 (mp10) REVERT: J 30 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8781 (pttt) REVERT: J 59 TYR cc_start: 0.7487 (m-80) cc_final: 0.7251 (m-80) REVERT: J 60 SER cc_start: 0.7447 (t) cc_final: 0.7069 (p) REVERT: J 72 ASP cc_start: 0.8222 (t70) cc_final: 0.7391 (t70) REVERT: J 77 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7145 (ttmm) REVERT: K 33 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7868 (tm) REVERT: K 34 ASN cc_start: 0.8850 (m-40) cc_final: 0.8527 (m110) REVERT: K 36 TYR cc_start: 0.7700 (m-80) cc_final: 0.7415 (m-80) outliers start: 60 outliers final: 28 residues processed: 312 average time/residue: 1.7269 time to fit residues: 621.1445 Evaluate side-chains 296 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 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 84 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN L 34 ASN E 24 GLN E 38 GLN K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058455 restraints weight = 40902.247| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.41 r_work: 0.2583 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 22260 Z= 0.259 Angle : 0.688 10.406 30468 Z= 0.321 Chirality : 0.049 0.298 3798 Planarity : 0.004 0.036 3585 Dihedral : 8.167 55.333 5907 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 17.06 % Favored : 80.11 % 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: 0.87 (0.17), residues: 2448 helix: 2.12 (0.26), residues: 423 sheet: 0.64 (0.18), residues: 765 loop : 0.09 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 35 HIS 0.004 0.001 HIS D 35 PHE 0.014 0.002 PHE G 353 TYR 0.016 0.002 TYR L 91 ARG 0.014 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 63) link_NAG-ASN : angle 2.05405 ( 189) link_ALPHA1-6 : bond 0.00393 ( 12) link_ALPHA1-6 : angle 1.67713 ( 36) link_BETA1-4 : bond 0.00425 ( 69) link_BETA1-4 : angle 1.62466 ( 207) link_ALPHA1-2 : bond 0.00559 ( 3) link_ALPHA1-2 : angle 1.98247 ( 9) link_ALPHA1-3 : bond 0.01191 ( 12) link_ALPHA1-3 : angle 2.38721 ( 36) hydrogen bonds : bond 0.04837 ( 654) hydrogen bonds : angle 4.88196 ( 1764) SS BOND : bond 0.00211 ( 42) SS BOND : angle 0.89368 ( 84) covalent geometry : bond 0.00604 (22059) covalent geometry : angle 0.65054 (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 336 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7380 (tmt90) REVERT: B 621 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7730 (mt-10) REVERT: G 504 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7150 (mmt90) REVERT: A 621 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 155 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8276 (mttp) REVERT: F 621 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7600 (mt-10) REVERT: I 155 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: I 302 MET cc_start: 0.9230 (mmt) cc_final: 0.8976 (mmt) REVERT: I 432 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: H 72 ASP cc_start: 0.8202 (t70) cc_final: 0.7420 (t70) REVERT: L 4 MET cc_start: 0.7480 (mmm) cc_final: 0.6906 (mmm) REVERT: D 59 TYR cc_start: 0.7721 (m-80) cc_final: 0.7512 (m-80) REVERT: D 72 ASP cc_start: 0.8139 (t70) cc_final: 0.7410 (t70) REVERT: D 100 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7511 (mpt) REVERT: E 35 TRP cc_start: 0.8149 (m100) cc_final: 0.7869 (m100) REVERT: E 95 GLN cc_start: 0.8638 (mt0) cc_final: 0.8376 (mp10) REVERT: J 72 ASP cc_start: 0.8221 (t70) cc_final: 0.7361 (t70) REVERT: J 77 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7045 (ttmm) REVERT: K 33 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7850 (tm) REVERT: K 34 ASN cc_start: 0.8869 (m-40) cc_final: 0.8639 (m110) REVERT: K 106 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6531 (tp) outliers start: 61 outliers final: 34 residues processed: 313 average time/residue: 1.3231 time to fit residues: 476.8188 Evaluate side-chains 301 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 210 PHE 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 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 25 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 20 LEU 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 D residue 84 THR Chi-restraints excluded: chain D residue 100 MET 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 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 24 GLN 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 106 ILE 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: 2.9990 chunk 91 optimal weight: 0.7980 chunk 212 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 157 optimal weight: 0.3980 chunk 189 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN E 24 GLN J 76 ASN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059619 restraints weight = 40627.387| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.41 r_work: 0.2666 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22260 Z= 0.124 Angle : 0.625 12.204 30468 Z= 0.289 Chirality : 0.046 0.307 3798 Planarity : 0.003 0.044 3585 Dihedral : 7.545 54.547 5907 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.13 % Allowed : 18.08 % Favored : 79.79 % 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: 1.00 (0.17), residues: 2448 helix: 2.27 (0.26), residues: 423 sheet: 0.70 (0.18), residues: 780 loop : 0.16 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 35 HIS 0.003 0.001 HIS I 72 PHE 0.011 0.001 PHE G 53 TYR 0.013 0.001 TYR L 91 ARG 0.012 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 63) link_NAG-ASN : angle 1.81557 ( 189) link_ALPHA1-6 : bond 0.00493 ( 12) link_ALPHA1-6 : angle 1.58359 ( 36) link_BETA1-4 : bond 0.00401 ( 69) link_BETA1-4 : angle 1.43717 ( 207) link_ALPHA1-2 : bond 0.00579 ( 3) link_ALPHA1-2 : angle 1.98248 ( 9) link_ALPHA1-3 : bond 0.01337 ( 12) link_ALPHA1-3 : angle 2.49458 ( 36) hydrogen bonds : bond 0.03923 ( 654) hydrogen bonds : angle 4.77290 ( 1764) SS BOND : bond 0.00279 ( 42) SS BOND : angle 1.29482 ( 84) covalent geometry : bond 0.00273 (22059) covalent geometry : angle 0.58868 (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 317 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7783 (mt-10) REVERT: G 210 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6848 (m-10) REVERT: G 500 ARG cc_start: 0.8910 (mtp-110) cc_final: 0.8710 (mtp-110) REVERT: G 504 ARG cc_start: 0.7370 (mmm160) cc_final: 0.7125 (mmt90) REVERT: A 621 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 117 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8620 (mtmt) REVERT: C 155 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8388 (mttp) REVERT: C 500 ARG cc_start: 0.8894 (mtp-110) cc_final: 0.8447 (mtt90) REVERT: F 621 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7702 (mt-10) REVERT: I 155 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: I 302 MET cc_start: 0.9249 (mmt) cc_final: 0.8932 (mmt) REVERT: H 72 ASP cc_start: 0.8374 (t70) cc_final: 0.7544 (t70) REVERT: L 4 MET cc_start: 0.7496 (mmm) cc_final: 0.6784 (mmm) REVERT: L 95 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7955 (mp10) REVERT: D 72 ASP cc_start: 0.8298 (t70) cc_final: 0.7446 (t70) REVERT: D 77 LYS cc_start: 0.7716 (ttmm) cc_final: 0.6926 (ttmm) REVERT: D 100 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (mpt) REVERT: E 36 TYR cc_start: 0.8204 (m-80) cc_final: 0.7604 (m-80) REVERT: E 95 GLN cc_start: 0.8651 (mt0) cc_final: 0.8363 (mp10) REVERT: J 72 ASP cc_start: 0.8372 (t70) cc_final: 0.7483 (t70) REVERT: J 77 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7286 (ttmm) REVERT: K 33 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7992 (tm) outliers start: 46 outliers final: 27 residues processed: 300 average time/residue: 1.2636 time to fit residues: 435.2400 Evaluate side-chains 292 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 100 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 30 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 chunk 192 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 109 optimal weight: 0.0020 chunk 107 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN E 38 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058068 restraints weight = 40911.117| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.49 r_work: 0.2653 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22260 Z= 0.157 Angle : 0.634 12.634 30468 Z= 0.292 Chirality : 0.046 0.296 3798 Planarity : 0.003 0.040 3585 Dihedral : 7.188 54.454 5907 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 17.94 % Favored : 80.02 % 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: 0.92 (0.17), residues: 2448 helix: 2.26 (0.26), residues: 423 sheet: 0.61 (0.18), residues: 747 loop : 0.13 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.024 0.001 PHE E 62 TYR 0.013 0.001 TYR L 91 ARG 0.009 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 63) link_NAG-ASN : angle 1.82445 ( 189) link_ALPHA1-6 : bond 0.00450 ( 12) link_ALPHA1-6 : angle 1.56739 ( 36) link_BETA1-4 : bond 0.00405 ( 69) link_BETA1-4 : angle 1.49484 ( 207) link_ALPHA1-2 : bond 0.00555 ( 3) link_ALPHA1-2 : angle 1.95954 ( 9) link_ALPHA1-3 : bond 0.01339 ( 12) link_ALPHA1-3 : angle 2.44058 ( 36) hydrogen bonds : bond 0.04035 ( 654) hydrogen bonds : angle 4.72917 ( 1764) SS BOND : bond 0.00218 ( 42) SS BOND : angle 1.09693 ( 84) covalent geometry : bond 0.00358 (22059) covalent geometry : angle 0.59897 (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 316 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 210 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6905 (m-10) REVERT: G 504 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7272 (mmt90) REVERT: A 621 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 117 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (mtmt) REVERT: C 155 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8419 (mttp) REVERT: C 500 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8481 (mtt90) REVERT: F 621 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7763 (mt-10) REVERT: I 155 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8444 (mttp) REVERT: I 302 MET cc_start: 0.9264 (mmt) cc_final: 0.8955 (mmt) REVERT: H 72 ASP cc_start: 0.8346 (t70) cc_final: 0.7547 (t70) REVERT: H 77 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7374 (ttmm) REVERT: L 4 MET cc_start: 0.7538 (mmm) cc_final: 0.6768 (mmm) REVERT: D 72 ASP cc_start: 0.8320 (t70) cc_final: 0.7480 (t70) REVERT: D 77 LYS cc_start: 0.7766 (ttmm) cc_final: 0.6938 (ttmm) REVERT: D 100 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7578 (mpt) REVERT: E 95 GLN cc_start: 0.8658 (mt0) cc_final: 0.8361 (mp10) REVERT: J 72 ASP cc_start: 0.8389 (t70) cc_final: 0.7484 (t70) REVERT: J 82 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8305 (ptp90) REVERT: K 33 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (tm) outliers start: 44 outliers final: 31 residues processed: 299 average time/residue: 1.4911 time to fit residues: 519.7208 Evaluate side-chains 300 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 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 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 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU 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 100 MET 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 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: 3.9990 chunk 8 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060635 restraints weight = 40868.254| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.40 r_work: 0.2638 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2118 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= 0.123 Angle : 0.621 13.308 30468 Z= 0.285 Chirality : 0.045 0.291 3798 Planarity : 0.003 0.058 3585 Dihedral : 6.846 54.185 5907 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.99 % Allowed : 18.36 % 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: 0.97 (0.17), residues: 2448 helix: 2.31 (0.26), residues: 423 sheet: 0.65 (0.19), residues: 747 loop : 0.15 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.026 0.001 PHE E 62 TYR 0.015 0.001 TYR D 90 ARG 0.013 0.000 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 63) link_NAG-ASN : angle 1.73735 ( 189) link_ALPHA1-6 : bond 0.00467 ( 12) link_ALPHA1-6 : angle 1.51674 ( 36) link_BETA1-4 : bond 0.00410 ( 69) link_BETA1-4 : angle 1.44879 ( 207) link_ALPHA1-2 : bond 0.00554 ( 3) link_ALPHA1-2 : angle 1.93625 ( 9) link_ALPHA1-3 : bond 0.01341 ( 12) link_ALPHA1-3 : angle 2.42729 ( 36) hydrogen bonds : bond 0.03782 ( 654) hydrogen bonds : angle 4.70352 ( 1764) SS BOND : bond 0.00225 ( 42) SS BOND : angle 0.91644 ( 84) covalent geometry : bond 0.00274 (22059) covalent geometry : angle 0.58773 (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 314 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7704 (mt-10) REVERT: G 207 LYS cc_start: 0.8754 (mppt) cc_final: 0.8427 (mmpt) REVERT: G 210 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: G 504 ARG cc_start: 0.7402 (mmm160) cc_final: 0.7164 (mmt90) REVERT: A 621 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 117 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8528 (mtmt) REVERT: C 155 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8230 (mttp) REVERT: C 207 LYS cc_start: 0.8810 (mppt) cc_final: 0.8459 (mmpt) REVERT: C 500 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8355 (mtt90) REVERT: C 504 ARG cc_start: 0.7389 (mmm160) cc_final: 0.7133 (mmt90) REVERT: F 621 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7627 (mt-10) REVERT: I 155 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: I 207 LYS cc_start: 0.8812 (mppt) cc_final: 0.8459 (mmpt) REVERT: I 302 MET cc_start: 0.9160 (mmt) cc_final: 0.8881 (mmt) REVERT: H 72 ASP cc_start: 0.8259 (t70) cc_final: 0.7402 (t70) REVERT: H 77 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7164 (ttmm) REVERT: L 4 MET cc_start: 0.7448 (mmm) cc_final: 0.6710 (mmm) REVERT: L 95 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7912 (mp10) REVERT: D 72 ASP cc_start: 0.8196 (t70) cc_final: 0.7374 (t70) REVERT: D 77 LYS cc_start: 0.7649 (ttmm) cc_final: 0.6954 (ttmm) REVERT: D 82 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7142 (mpt) REVERT: E 4 MET cc_start: 0.6684 (mmm) cc_final: 0.6467 (mmm) REVERT: E 95 GLN cc_start: 0.8612 (mt0) cc_final: 0.8314 (mp10) REVERT: J 3 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7971 (tm-30) REVERT: J 72 ASP cc_start: 0.8315 (t70) cc_final: 0.7330 (t70) REVERT: J 77 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7129 (ttmm) REVERT: K 33 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7944 (tm) outliers start: 43 outliers final: 27 residues processed: 298 average time/residue: 1.2223 time to fit residues: 421.1670 Evaluate side-chains 294 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 LEU 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 117 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER 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 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 MET 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 84 THR Chi-restraints excluded: chain K residue 24 GLN 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: 2.9990 chunk 82 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN J 76 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059173 restraints weight = 41043.376| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.40 r_work: 0.2658 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22260 Z= 0.165 Angle : 0.642 13.097 30468 Z= 0.295 Chirality : 0.046 0.279 3798 Planarity : 0.003 0.041 3585 Dihedral : 6.786 54.379 5907 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 18.59 % Favored : 79.32 % 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: 0.91 (0.17), residues: 2448 helix: 2.02 (0.26), residues: 441 sheet: 0.64 (0.19), residues: 741 loop : 0.17 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.024 0.001 PHE E 62 TYR 0.017 0.001 TYR D 90 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 63) link_NAG-ASN : angle 1.80922 ( 189) link_ALPHA1-6 : bond 0.00406 ( 12) link_ALPHA1-6 : angle 1.54132 ( 36) link_BETA1-4 : bond 0.00415 ( 69) link_BETA1-4 : angle 1.51381 ( 207) link_ALPHA1-2 : bond 0.00524 ( 3) link_ALPHA1-2 : angle 1.91466 ( 9) link_ALPHA1-3 : bond 0.01308 ( 12) link_ALPHA1-3 : angle 2.37566 ( 36) hydrogen bonds : bond 0.04067 ( 654) hydrogen bonds : angle 4.70278 ( 1764) SS BOND : bond 0.00238 ( 42) SS BOND : angle 1.16290 ( 84) covalent geometry : bond 0.00379 (22059) covalent geometry : angle 0.60729 (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 311 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7828 (mt-10) REVERT: G 210 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: A 621 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 117 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8588 (mtmt) REVERT: C 155 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8384 (mttp) REVERT: C 500 ARG cc_start: 0.8903 (mtp-110) cc_final: 0.8448 (mtt90) REVERT: C 504 ARG cc_start: 0.7474 (mmm160) cc_final: 0.7222 (mmt90) REVERT: F 621 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7743 (mt-10) REVERT: I 155 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8419 (mttp) REVERT: I 302 MET cc_start: 0.9248 (mmt) cc_final: 0.8986 (mmt) REVERT: H 72 ASP cc_start: 0.8326 (t70) cc_final: 0.7513 (t70) REVERT: H 77 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7290 (ttmm) REVERT: D 59 TYR cc_start: 0.7842 (m-80) cc_final: 0.7638 (m-80) REVERT: D 72 ASP cc_start: 0.8325 (t70) cc_final: 0.7504 (t70) REVERT: D 77 LYS cc_start: 0.7780 (ttmm) cc_final: 0.6982 (ttmm) REVERT: D 82 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7201 (mpt) REVERT: E 4 MET cc_start: 0.6992 (mmm) cc_final: 0.6502 (mmm) REVERT: E 95 GLN cc_start: 0.8654 (mt0) cc_final: 0.8357 (mp10) REVERT: J 72 ASP cc_start: 0.8401 (t70) cc_final: 0.7417 (t70) REVERT: J 77 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7237 (ttmm) REVERT: K 33 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8001 (tm) outliers start: 45 outliers final: 30 residues processed: 291 average time/residue: 1.2297 time to fit residues: 412.6913 Evaluate side-chains 300 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 75 VAL 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 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 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 LEU 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 82 MET Chi-restraints excluded: chain E residue 5 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 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: 0.6980 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN E 24 GLN K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060326 restraints weight = 40759.812| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.37 r_work: 0.2631 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22260 Z= 0.134 Angle : 0.634 13.307 30468 Z= 0.292 Chirality : 0.045 0.276 3798 Planarity : 0.004 0.065 3585 Dihedral : 6.676 57.402 5907 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 18.73 % Favored : 79.37 % 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: 0.91 (0.17), residues: 2448 helix: 2.04 (0.26), residues: 441 sheet: 0.61 (0.18), residues: 747 loop : 0.18 (0.18), residues: 1260 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 0.025 0.001 PHE E 62 TYR 0.014 0.001 TYR D 90 ARG 0.016 0.000 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 63) link_NAG-ASN : angle 1.77318 ( 189) link_ALPHA1-6 : bond 0.00413 ( 12) link_ALPHA1-6 : angle 1.51756 ( 36) link_BETA1-4 : bond 0.00402 ( 69) link_BETA1-4 : angle 1.48636 ( 207) link_ALPHA1-2 : bond 0.00521 ( 3) link_ALPHA1-2 : angle 1.90728 ( 9) link_ALPHA1-3 : bond 0.01292 ( 12) link_ALPHA1-3 : angle 2.37535 ( 36) hydrogen bonds : bond 0.03888 ( 654) hydrogen bonds : angle 4.68925 ( 1764) SS BOND : bond 0.00216 ( 42) SS BOND : angle 0.98357 ( 84) covalent geometry : bond 0.00303 (22059) covalent geometry : angle 0.60056 (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 309 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7719 (mt-10) REVERT: G 207 LYS cc_start: 0.8746 (mppt) cc_final: 0.8406 (mmpt) REVERT: G 210 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: A 621 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 117 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (mtmt) REVERT: C 155 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8228 (mttp) REVERT: C 207 LYS cc_start: 0.8823 (mppt) cc_final: 0.8455 (mmpt) REVERT: C 500 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8347 (mtt90) REVERT: C 504 ARG cc_start: 0.7440 (mmm160) cc_final: 0.7144 (mmt90) REVERT: F 621 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7637 (mt-10) REVERT: I 155 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8257 (mttp) REVERT: I 207 LYS cc_start: 0.8815 (mppt) cc_final: 0.8464 (mmpt) REVERT: I 210 PHE cc_start: 0.8259 (p90) cc_final: 0.6885 (m-10) REVERT: I 302 MET cc_start: 0.9171 (mmt) cc_final: 0.8885 (mmt) REVERT: H 72 ASP cc_start: 0.8253 (t70) cc_final: 0.7434 (t70) REVERT: H 77 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7144 (ttmm) REVERT: D 36 TRP cc_start: 0.8216 (m100) cc_final: 0.7815 (m100) REVERT: D 59 TYR cc_start: 0.7729 (m-80) cc_final: 0.7527 (m-80) REVERT: D 72 ASP cc_start: 0.8205 (t70) cc_final: 0.7386 (t70) REVERT: D 77 LYS cc_start: 0.7658 (ttmm) cc_final: 0.6868 (ttmm) REVERT: D 82 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7194 (mpt) REVERT: E 4 MET cc_start: 0.6749 (mmm) cc_final: 0.6254 (mmm) REVERT: E 95 GLN cc_start: 0.8611 (mt0) cc_final: 0.8299 (mp10) REVERT: J 72 ASP cc_start: 0.8267 (t70) cc_final: 0.7287 (t70) REVERT: J 77 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7091 (ttmm) REVERT: K 33 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7970 (tm) outliers start: 41 outliers final: 27 residues processed: 290 average time/residue: 1.2390 time to fit residues: 415.9921 Evaluate side-chains 297 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 75 VAL 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 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 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 47 LEU 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 D residue 82 MET 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 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: 0.6980 chunk 71 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060528 restraints weight = 40694.941| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.40 r_work: 0.2637 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22260 Z= 0.130 Angle : 0.619 13.154 30468 Z= 0.286 Chirality : 0.044 0.264 3798 Planarity : 0.004 0.060 3585 Dihedral : 6.454 58.683 5907 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.67 % Allowed : 18.96 % Favored : 79.37 % 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: 2.06 (0.26), residues: 441 sheet: 0.64 (0.18), residues: 747 loop : 0.18 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP K 35 HIS 0.003 0.001 HIS I 72 PHE 0.023 0.001 PHE E 62 TYR 0.013 0.001 TYR D 90 ARG 0.015 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 63) link_NAG-ASN : angle 1.72607 ( 189) link_ALPHA1-6 : bond 0.00379 ( 12) link_ALPHA1-6 : angle 1.50334 ( 36) link_BETA1-4 : bond 0.00408 ( 69) link_BETA1-4 : angle 1.46917 ( 207) link_ALPHA1-2 : bond 0.00497 ( 3) link_ALPHA1-2 : angle 1.87626 ( 9) link_ALPHA1-3 : bond 0.01227 ( 12) link_ALPHA1-3 : angle 2.33285 ( 36) hydrogen bonds : bond 0.03783 ( 654) hydrogen bonds : angle 4.65823 ( 1764) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.95074 ( 84) covalent geometry : bond 0.00294 (22059) covalent geometry : angle 0.58590 (29907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30627.34 seconds wall clock time: 534 minutes 13.12 seconds (32053.12 seconds total)