Starting phenix.real_space_refine on Sat May 17 15:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnb_13546/05_2025/7pnb_13546.cif" } resolution = 3.46 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= 0.015 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 81 5.16 5 C 9819 2.51 5 N 2061 2.21 5 O 3753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15714 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "U" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Z" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "e" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "g" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "j" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "o" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "r" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "s" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "t" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "w" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "y" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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 Time building chain proxies: 10.70, per 1000 atoms: 0.68 Number of scatterers: 15714 At special positions: 0 Unit cell: (75.384, 74.337, 343.416, 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 81 16.00 O 3753 8.00 N 2061 7.00 C 9819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=7, symmetry=0 Links applied ?1-3 " NAG 0 2 " - " YZT 0 3 " " NAG 1 2 " - " YZT 1 3 " " NAG J 2 " - " YZT J 3 " " NAG K 2 " - " YZT K 3 " " NAG L 2 " - " YZT L 3 " " NAG M 2 " - " YZT M 3 " " NAG N 2 " - " YZT N 3 " " NAG O 2 " - " YZT O 3 " " NAG P 2 " - " YZT P 3 " " NAG Q 2 " - " YZT Q 3 " " NAG R 2 " - " YZT R 3 " " NAG S 2 " - " YZT S 3 " " NAG T 2 " - " YZT T 3 " " NAG U 2 " - " YZT U 3 " " NAG V 2 " - " YZT V 3 " " NAG W 2 " - " YZT W 3 " " NAG X 2 " - " YZT X 3 " " NAG Y 2 " - " YZT Y 3 " " NAG Z 2 " - " YZT Z 3 " " NAG a 2 " - " YZT a 3 " " NAG b 2 " - " YZT b 3 " " NAG c 2 " - " YZT c 3 " " NAG d 2 " - " YZT d 3 " " NAG e 2 " - " YZT e 3 " " NAG f 2 " - " YZT f 3 " " NAG g 2 " - " YZT g 3 " " NAG h 2 " - " YZT h 3 " " NAG i 2 " - " YZT i 3 " " NAG j 2 " - " YZT j 3 " " NAG k 2 " - " YZT k 3 " " NAG l 2 " - " YZT l 3 " " NAG m 2 " - " YZT m 3 " " NAG n 2 " - " YZT n 3 " " NAG o 2 " - " YZT o 3 " " NAG p 2 " - " YZT p 3 " " NAG q 2 " - " YZT q 3 " " NAG r 2 " - " YZT r 3 " " NAG s 2 " - " YZT s 3 " " NAG t 2 " - " YZT t 3 " " NAG u 2 " - " YZT u 3 " " NAG v 2 " - " YZT v 3 " " NAG w 2 " - " YZT w 3 " " NAG x 2 " - " YZT x 3 " " NAG y 2 " - " YZT y 3 " " NAG z 2 " - " YZT z 3 " ALPHA1-4 " NAG 0 2 " - " MAN 0 5 " " NAG 1 2 " - " MAN 1 5 " " NAG J 2 " - " MAN J 5 " " NAG K 2 " - " MAN K 4 " " NAG L 2 " - " MAN L 5 " " NAG M 2 " - " MAN M 5 " " NAG N 2 " - " MAN N 5 " " NAG O 2 " - " MAN O 5 " " NAG P 2 " - " MAN P 4 " " NAG Q 2 " - " MAN Q 5 " " NAG R 2 " - " MAN R 5 " " NAG S 2 " - " MAN S 5 " " NAG T 2 " - " MAN T 5 " " NAG U 2 " - " MAN U 4 " " NAG V 2 " - " MAN V 5 " " NAG W 2 " - " MAN W 5 " " NAG X 2 " - " MAN X 5 " " NAG Y 2 " - " MAN Y 5 " " NAG Z 2 " - " MAN Z 4 " " NAG a 2 " - " MAN a 5 " " NAG b 2 " - " MAN b 5 " " NAG c 2 " - " MAN c 5 " " NAG d 2 " - " MAN d 5 " " NAG e 2 " - " MAN e 4 " " NAG f 2 " - " MAN f 5 " " NAG g 2 " - " MAN g 5 " " NAG h 2 " - " MAN h 5 " " NAG i 2 " - " MAN i 5 " " NAG j 2 " - " MAN j 4 " " NAG k 2 " - " MAN k 5 " " NAG l 2 " - " MAN l 5 " " NAG m 2 " - " MAN m 5 " " NAG n 2 " - " MAN n 5 " " NAG o 2 " - " MAN o 4 " " NAG p 2 " - " MAN p 5 " " NAG q 2 " - " MAN q 5 " " NAG r 2 " - " MAN r 5 " " NAG s 2 " - " MAN s 5 " " NAG t 2 " - " MAN t 4 " " NAG u 2 " - " MAN u 5 " " NAG v 2 " - " MAN v 5 " " NAG w 2 " - " MAN w 5 " " NAG x 2 " - " MAN x 5 " " NAG y 2 " - " MAN y 4 " " NAG z 2 " - " MAN z 5 " ALPHA1-6 " NAG 0 2 " - " MAN 0 6 " " NAG 1 2 " - " MAN 1 6 " " NAG J 2 " - " MAN J 6 " " NAG L 2 " - " MAN L 6 " " NAG M 2 " - " MAN M 6 " " NAG N 2 " - " MAN N 6 " " NAG O 2 " - " MAN O 6 " " NAG Q 2 " - " MAN Q 6 " " NAG R 2 " - " MAN R 6 " " NAG S 2 " - " MAN S 6 " " NAG T 2 " - " MAN T 6 " " NAG V 2 " - " MAN V 6 " " NAG W 2 " - " MAN W 6 " " NAG X 2 " - " MAN X 6 " " NAG Y 2 " - " MAN Y 6 " " NAG a 2 " - " MAN a 6 " " NAG b 2 " - " MAN b 6 " " NAG c 2 " - " MAN c 6 " " NAG d 2 " - " MAN d 6 " " NAG f 2 " - " MAN f 6 " " NAG g 2 " - " MAN g 6 " " NAG h 2 " - " MAN h 6 " " NAG i 2 " - " MAN i 6 " " NAG k 2 " - " MAN k 6 " " NAG l 2 " - " MAN l 6 " " NAG m 2 " - " MAN m 6 " " NAG n 2 " - " MAN n 6 " " NAG p 2 " - " MAN p 6 " " NAG q 2 " - " MAN q 6 " " NAG r 2 " - " MAN r 6 " " NAG s 2 " - " MAN s 6 " " NAG u 2 " - " MAN u 6 " " NAG v 2 " - " MAN v 6 " " NAG w 2 " - " MAN w 6 " " NAG x 2 " - " MAN x 6 " " NAG z 2 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " YZT 0 3 " - " BGC 0 4 " " NAG 1 1 " - " NAG 1 2 " " YZT 1 3 " - " BGC 1 4 " " NAG J 1 " - " NAG J 2 " " YZT J 3 " - " BGC J 4 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " YZT L 3 " - " BGC L 4 " " NAG M 1 " - " NAG M 2 " " YZT M 3 " - " BGC M 4 " " NAG N 1 " - " NAG N 2 " " YZT N 3 " - " BGC N 4 " " NAG O 1 " - " NAG O 2 " " YZT O 3 " - " BGC O 4 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " YZT Q 3 " - " BGC Q 4 " " NAG R 1 " - " NAG R 2 " " YZT R 3 " - " BGC R 4 " " NAG S 1 " - " NAG S 2 " " YZT S 3 " - " BGC S 4 " " NAG T 1 " - " NAG T 2 " " YZT T 3 " - " BGC T 4 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " YZT V 3 " - " BGC V 4 " " NAG W 1 " - " NAG W 2 " " YZT W 3 " - " BGC W 4 " " NAG X 1 " - " NAG X 2 " " YZT X 3 " - " BGC X 4 " " NAG Y 1 " - " NAG Y 2 " " YZT Y 3 " - " BGC Y 4 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " YZT a 3 " - " BGC a 4 " " NAG b 1 " - " NAG b 2 " " YZT b 3 " - " BGC b 4 " " NAG c 1 " - " NAG c 2 " " YZT c 3 " - " BGC c 4 " " NAG d 1 " - " NAG d 2 " " YZT d 3 " - " BGC d 4 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " YZT f 3 " - " BGC f 4 " " NAG g 1 " - " NAG g 2 " " YZT g 3 " - " BGC g 4 " " NAG h 1 " - " NAG h 2 " " YZT h 3 " - " BGC h 4 " " NAG i 1 " - " NAG i 2 " " YZT i 3 " - " BGC i 4 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " YZT k 3 " - " BGC k 4 " " NAG l 1 " - " NAG l 2 " " YZT l 3 " - " BGC l 4 " " NAG m 1 " - " NAG m 2 " " YZT m 3 " - " BGC m 4 " " NAG n 1 " - " NAG n 2 " " YZT n 3 " - " BGC n 4 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " YZT p 3 " - " BGC p 4 " " NAG q 1 " - " NAG q 2 " " YZT q 3 " - " BGC q 4 " " NAG r 1 " - " NAG r 2 " " YZT r 3 " - " BGC r 4 " " NAG s 1 " - " NAG s 2 " " YZT s 3 " - " BGC s 4 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " YZT u 3 " - " BGC u 4 " " NAG v 1 " - " NAG v 2 " " YZT v 3 " - " BGC v 4 " " NAG w 1 " - " NAG w 2 " " YZT w 3 " - " BGC w 4 " " NAG x 1 " - " NAG x 2 " " YZT x 3 " - " BGC x 4 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " YZT z 3 " - " BGC z 4 " NAG-ASN " NAG 0 1 " - " ASN I 146 " " NAG 1 1 " - " ASN I 121 " " NAG J 1 " - " ASN A 56 " " NAG K 1 " - " ASN A 80 " " NAG L 1 " - " ASN A 83 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 121 " " NAG O 1 " - " ASN B 56 " " NAG P 1 " - " ASN B 80 " " NAG Q 1 " - " ASN B 83 " " NAG R 1 " - " ASN B 146 " " NAG S 1 " - " ASN B 121 " " NAG T 1 " - " ASN C 56 " " NAG U 1 " - " ASN C 80 " " NAG V 1 " - " ASN C 83 " " NAG W 1 " - " ASN C 146 " " NAG X 1 " - " ASN C 121 " " NAG Y 1 " - " ASN D 56 " " NAG Z 1 " - " ASN D 80 " " NAG a 1 " - " ASN D 83 " " NAG b 1 " - " ASN D 146 " " NAG c 1 " - " ASN D 121 " " NAG d 1 " - " ASN E 56 " " NAG e 1 " - " ASN E 80 " " NAG f 1 " - " ASN E 83 " " NAG g 1 " - " ASN E 146 " " NAG h 1 " - " ASN E 121 " " NAG i 1 " - " ASN F 56 " " NAG j 1 " - " ASN F 80 " " NAG k 1 " - " ASN F 83 " " NAG l 1 " - " ASN F 146 " " NAG m 1 " - " ASN F 121 " " NAG n 1 " - " ASN G 56 " " NAG o 1 " - " ASN G 80 " " NAG p 1 " - " ASN G 83 " " NAG q 1 " - " ASN G 146 " " NAG r 1 " - " ASN G 121 " " NAG s 1 " - " ASN H 56 " " NAG t 1 " - " ASN H 80 " " NAG u 1 " - " ASN H 83 " " NAG v 1 " - " ASN H 146 " " NAG w 1 " - " ASN H 121 " " NAG x 1 " - " ASN I 56 " " NAG y 1 " - " ASN I 80 " " NAG z 1 " - " ASN I 83 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3042 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 4.7% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.519A pdb=" N GLY A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.524A pdb=" N GLY B 50 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.866A pdb=" N SER B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.528A pdb=" N GLY C 50 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.866A pdb=" N SER C 73 " --> pdb=" O SER C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.527A pdb=" N GLY D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.864A pdb=" N SER D 73 " --> pdb=" O SER D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.527A pdb=" N GLY E 50 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.865A pdb=" N SER E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'F' and resid 47 through 51 removed outlier: 3.524A pdb=" N GLY F 50 " --> pdb=" O GLN F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 73 removed outlier: 3.863A pdb=" N SER F 73 " --> pdb=" O SER F 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 73' Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.524A pdb=" N GLY G 50 " --> pdb=" O GLN G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.525A pdb=" N GLY H 50 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'I' and resid 47 through 51 removed outlier: 3.524A pdb=" N GLY I 50 " --> pdb=" O GLN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 73 removed outlier: 3.860A pdb=" N SER I 73 " --> pdb=" O SER I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.272A pdb=" N PHE B 75 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR C 34 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 77 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLY C 36 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 79 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.410A pdb=" N ALA A 122 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 141 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN A 120 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY A 159 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 95 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR A 161 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET A 93 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 163 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN C 37 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B 181 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU B 182 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 112 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 184 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR B 110 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 186 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 108 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN B 188 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.325A pdb=" N PHE A 75 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 34 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA A 77 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY B 36 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 79 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN B 37 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 181 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 182 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR A 112 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 184 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR A 110 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 186 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 108 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 188 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.284A pdb=" N PHE C 75 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR D 34 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 77 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY D 36 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 79 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.405A pdb=" N ALA B 122 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 141 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN B 120 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY B 159 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 95 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR B 161 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET B 93 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 163 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN D 37 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP C 181 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU C 182 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR C 112 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 184 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR C 110 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 186 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 108 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 188 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.255A pdb=" N PHE D 75 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR E 34 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 77 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY E 36 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 79 " --> pdb=" O GLY E 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.405A pdb=" N ALA C 122 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 141 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN C 120 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY C 159 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU C 95 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 161 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET C 93 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 163 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN E 37 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP D 181 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU D 182 " --> pdb=" O TYR D 112 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR D 112 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR D 184 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR D 110 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR D 186 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 108 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 188 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 45 removed outlier: 6.298A pdb=" N PHE E 75 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR F 34 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA E 77 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY F 36 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL E 79 " --> pdb=" O GLY F 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 144 through 145 removed outlier: 6.401A pdb=" N ALA D 122 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 141 " --> pdb=" O GLN D 120 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN D 120 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY D 159 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU D 95 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR D 161 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET D 93 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 163 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN F 37 " --> pdb=" O ASP E 181 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP E 181 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU E 182 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR E 112 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR E 184 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR E 110 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR E 186 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL E 108 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN E 188 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.294A pdb=" N PHE F 75 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR G 34 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA F 77 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY G 36 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL F 79 " --> pdb=" O GLY G 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.401A pdb=" N ALA E 122 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL E 141 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLN E 120 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY E 159 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU E 95 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR E 161 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET E 93 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL E 163 " --> pdb=" O ASN E 91 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN G 37 " --> pdb=" O ASP F 181 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP F 181 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU F 182 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR F 112 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 184 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR F 110 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR F 186 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 108 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN F 188 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.212A pdb=" N PHE G 75 " --> pdb=" O GLN H 32 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR H 34 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA G 77 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY H 36 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 79 " --> pdb=" O GLY H 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 144 through 145 removed outlier: 6.405A pdb=" N ALA F 122 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL F 141 " --> pdb=" O GLN F 120 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN F 120 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY F 159 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 95 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR F 161 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET F 93 " --> pdb=" O TYR F 161 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL F 163 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN H 37 " --> pdb=" O ASP G 181 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP G 181 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU G 182 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR G 112 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR G 184 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 110 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR G 186 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL G 108 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN G 188 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.311A pdb=" N PHE H 75 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR I 34 " --> pdb=" O PHE H 75 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA H 77 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY I 36 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL H 79 " --> pdb=" O GLY I 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 144 through 145 removed outlier: 6.406A pdb=" N ALA G 122 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL G 141 " --> pdb=" O GLN G 120 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN G 120 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY G 159 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU G 95 " --> pdb=" O GLY G 159 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR G 161 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET G 93 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL G 163 " --> pdb=" O ASN G 91 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN I 37 " --> pdb=" O ASP H 181 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP H 181 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU H 182 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR H 112 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR H 184 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR H 110 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR H 186 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 108 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN H 188 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 42 through 45 removed outlier: 6.203A pdb=" N VAL H 163 " --> pdb=" O ASN H 91 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET H 93 " --> pdb=" O TYR H 161 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR H 161 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU H 95 " --> pdb=" O GLY H 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY H 159 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN H 120 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 141 " --> pdb=" O GLN H 120 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA H 122 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 45 removed outlier: 6.211A pdb=" N VAL I 163 " --> pdb=" O ASN I 91 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET I 93 " --> pdb=" O TYR I 161 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR I 161 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU I 95 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY I 159 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN I 120 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL I 141 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA I 122 " --> pdb=" O LEU I 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 64 through 68 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 156 removed outlier: 6.705A pdb=" N ASN I 188 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL I 108 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR I 186 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR I 110 " --> pdb=" O THR I 184 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR I 184 " --> pdb=" O TYR I 110 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1275 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: 4.39 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: 1.21 - 1.33: 2834 1.33 - 1.46: 5681 1.46 - 1.58: 7441 1.58 - 1.71: 1 1.71 - 1.83: 117 Bond restraints: 16074 Sorted by residual: bond pdb=" S6 YZT d 3 " pdb="O2S6 YZT d 3 " ideal model delta sigma weight residual 1.477 1.585 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" S6 YZT Y 3 " pdb="O2S6 YZT Y 3 " ideal model delta sigma weight residual 1.477 1.572 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" S6 YZT W 3 " pdb="O2S6 YZT W 3 " ideal model delta sigma weight residual 1.477 1.570 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" S6 YZT i 3 " pdb="O2S6 YZT i 3 " ideal model delta sigma weight residual 1.477 1.569 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" S6 YZT q 3 " pdb="O2S6 YZT q 3 " ideal model delta sigma weight residual 1.477 1.569 -0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 16069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 19243 2.44 - 4.87: 2515 4.87 - 7.31: 334 7.31 - 9.74: 30 9.74 - 12.18: 27 Bond angle restraints: 22149 Sorted by residual: angle pdb=" C ASN B 57 " pdb=" CA ASN B 57 " pdb=" CB ASN B 57 " ideal model delta sigma weight residual 112.44 100.26 12.18 1.72e+00 3.38e-01 5.01e+01 angle pdb=" C ASN A 57 " pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta sigma weight residual 112.44 100.26 12.18 1.72e+00 3.38e-01 5.01e+01 angle pdb=" CA ASN G 146 " pdb=" CB ASN G 146 " pdb=" CG ASN G 146 " ideal model delta sigma weight residual 112.60 119.65 -7.05 1.00e+00 1.00e+00 4.97e+01 angle pdb=" C ASN C 57 " pdb=" CA ASN C 57 " pdb=" CB ASN C 57 " ideal model delta sigma weight residual 112.44 100.32 12.12 1.72e+00 3.38e-01 4.96e+01 angle pdb=" CA ASN E 146 " pdb=" CB ASN E 146 " pdb=" CG ASN E 146 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.00e+00 1.00e+00 4.92e+01 ... (remaining 22144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.32: 11891 23.32 - 46.64: 458 46.64 - 69.96: 170 69.96 - 93.28: 189 93.28 - 116.60: 45 Dihedral angle restraints: 12753 sinusoidal: 7920 harmonic: 4833 Sorted by residual: dihedral pdb=" C ASN A 57 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta harmonic sigma weight residual -122.60 -108.46 -14.14 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" C ASN B 57 " pdb=" N ASN B 57 " pdb=" CA ASN B 57 " pdb=" CB ASN B 57 " ideal model delta harmonic sigma weight residual -122.60 -108.53 -14.07 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C ASN C 57 " pdb=" N ASN C 57 " pdb=" CA ASN C 57 " pdb=" CB ASN C 57 " ideal model delta harmonic sigma weight residual -122.60 -108.64 -13.96 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 12750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 2936 0.184 - 0.368: 279 0.368 - 0.552: 16 0.552 - 0.736: 0 0.736 - 0.920: 9 Chirality restraints: 3240 Sorted by residual: chirality pdb=" C1 MAN e 4 " pdb=" O4 NAG e 2 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.12e+03 chirality pdb=" C1 MAN U 4 " pdb=" O4 NAG U 2 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 chirality pdb=" C1 MAN Z 4 " pdb=" O4 NAG Z 2 " pdb=" C2 MAN Z 4 " pdb=" O5 MAN Z 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 ... (remaining 3237 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " -0.364 2.00e-02 2.50e+03 3.08e-01 1.18e+03 pdb=" C7 NAG U 1 " 0.093 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.359 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG j 1 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG y 1 " -0.357 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG y 1 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG y 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG y 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG y 1 " -0.118 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4823 2.84 - 3.36: 13833 3.36 - 3.87: 27361 3.87 - 4.39: 30758 4.39 - 4.90: 51959 Nonbonded interactions: 128734 Sorted by model distance: nonbonded pdb=" O TYR B 170 " pdb=" OG1 THR B 173 " model vdw 2.330 3.040 nonbonded pdb=" O TYR C 170 " pdb=" OG1 THR C 173 " model vdw 2.330 3.040 nonbonded pdb=" O TYR F 170 " pdb=" OG1 THR F 173 " model vdw 2.331 3.040 nonbonded pdb=" O TYR D 170 " pdb=" OG1 THR D 173 " model vdw 2.331 3.040 nonbonded pdb=" O TYR E 170 " pdb=" OG1 THR E 173 " model vdw 2.331 3.040 ... (remaining 128729 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: 0.11 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' selection = chain 't' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.920 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.013 0.113 16333 Z= 0.765 Angle : 2.026 21.586 22905 Z= 0.956 Chirality : 0.122 0.920 3240 Planarity : 0.028 0.308 2394 Dihedral : 18.905 116.601 9711 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.56 % Allowed : 3.21 % Favored : 94.23 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.58 (0.19), residues: 639 loop : -0.24 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.011 PHE D 44 TYR 0.044 0.010 TYR F 89 Details of bonding type rmsd link_NAG-ASN : bond 0.03142 ( 45) link_NAG-ASN : angle 6.09617 ( 135) link_ALPHA1-4 : bond 0.03365 ( 45) link_ALPHA1-4 : angle 4.59179 ( 135) link_ALPHA1-6 : bond 0.00280 ( 36) link_ALPHA1-6 : angle 1.68717 ( 108) link_BETA1-4 : bond 0.01557 ( 81) link_BETA1-4 : angle 4.51231 ( 243) hydrogen bonds : bond 0.14660 ( 450) hydrogen bonds : angle 8.83808 ( 1275) glycosidic custom : bond 0.01421 ( 45) glycosidic custom : angle 9.95793 ( 135) covalent geometry : bond 0.01307 (16074) covalent geometry : angle 1.74589 (22149) Misc. bond : bond 0.10510 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.8640 (m-80) cc_final: 0.8295 (m-80) REVERT: A 87 ASN cc_start: 0.8783 (m-40) cc_final: 0.8581 (m110) REVERT: A 129 GLN cc_start: 0.8412 (tt0) cc_final: 0.8156 (tt0) REVERT: A 152 THR cc_start: 0.8561 (m) cc_final: 0.8249 (p) REVERT: B 102 TYR cc_start: 0.8575 (m-80) cc_final: 0.8176 (m-80) REVERT: B 125 TYR cc_start: 0.8443 (m-80) cc_final: 0.7776 (m-80) REVERT: B 128 ASN cc_start: 0.8471 (t0) cc_final: 0.8243 (t0) REVERT: B 165 LEU cc_start: 0.8658 (tp) cc_final: 0.8437 (tt) REVERT: B 194 MET cc_start: 0.8270 (mtm) cc_final: 0.8044 (mtp) REVERT: B 201 ILE cc_start: 0.8496 (mm) cc_final: 0.8268 (mm) REVERT: C 76 THR cc_start: 0.8824 (m) cc_final: 0.8492 (p) REVERT: C 93 MET cc_start: 0.8618 (mmp) cc_final: 0.8139 (tpp) REVERT: C 102 TYR cc_start: 0.8729 (m-80) cc_final: 0.8112 (m-80) REVERT: C 104 TYR cc_start: 0.8709 (p90) cc_final: 0.8356 (p90) REVERT: C 177 THR cc_start: 0.8481 (m) cc_final: 0.8277 (p) REVERT: C 194 MET cc_start: 0.8186 (mtm) cc_final: 0.7928 (mtp) REVERT: E 69 SER cc_start: 0.8483 (t) cc_final: 0.8263 (m) REVERT: E 80 ASN cc_start: 0.8514 (m-40) cc_final: 0.8214 (m-40) REVERT: E 125 TYR cc_start: 0.8405 (m-80) cc_final: 0.7551 (m-80) REVERT: E 129 GLN cc_start: 0.8629 (tt0) cc_final: 0.8156 (mt0) REVERT: F 125 TYR cc_start: 0.8699 (m-80) cc_final: 0.8095 (m-80) REVERT: F 151 SER cc_start: 0.8431 (p) cc_final: 0.8226 (t) REVERT: F 164 SER cc_start: 0.8551 (m) cc_final: 0.8163 (p) REVERT: F 177 THR cc_start: 0.8356 (m) cc_final: 0.8154 (t) REVERT: F 178 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8470 (t) cc_final: 0.8252 (m) REVERT: G 102 TYR cc_start: 0.8870 (m-80) cc_final: 0.8406 (m-80) REVERT: G 194 MET cc_start: 0.8422 (mtm) cc_final: 0.8175 (mtp) REVERT: G 195 THR cc_start: 0.8573 (p) cc_final: 0.8031 (t) REVERT: G 201 ILE cc_start: 0.8318 (mm) cc_final: 0.7987 (mt) REVERT: H 86 TYR cc_start: 0.8623 (m-80) cc_final: 0.8411 (m-80) REVERT: H 128 ASN cc_start: 0.8527 (t0) cc_final: 0.8327 (m-40) REVERT: H 161 TYR cc_start: 0.8475 (m-80) cc_final: 0.7856 (m-80) REVERT: I 59 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: I 89 TYR cc_start: 0.7652 (m-80) cc_final: 0.7419 (m-80) REVERT: I 102 TYR cc_start: 0.8580 (m-80) cc_final: 0.8144 (m-10) REVERT: I 125 TYR cc_start: 0.8243 (m-80) cc_final: 0.7131 (m-80) REVERT: I 161 TYR cc_start: 0.8249 (m-80) cc_final: 0.8036 (m-80) REVERT: I 186 THR cc_start: 0.8488 (m) cc_final: 0.8254 (p) outliers start: 36 outliers final: 5 residues processed: 396 average time/residue: 0.2104 time to fit residues: 134.0869 Evaluate side-chains 301 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 295 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain I residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 59 ASN A 129 GLN B 37 ASN B 59 ASN B 87 ASN B 188 ASN C 37 ASN D 37 ASN E 37 ASN E 120 GLN E 129 GLN F 37 ASN F 59 ASN F 120 GLN F 132 GLN G 37 ASN G 87 ASN G 171 GLN H 67 GLN H 78 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096689 restraints weight = 22145.133| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.27 r_work: 0.3024 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16333 Z= 0.222 Angle : 1.039 9.402 22905 Z= 0.419 Chirality : 0.053 0.259 3240 Planarity : 0.005 0.046 2394 Dihedral : 15.800 107.098 6910 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.28 % Allowed : 9.97 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 711 loop : 0.15 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE F 90 TYR 0.030 0.002 TYR H 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 45) link_NAG-ASN : angle 3.65236 ( 135) link_ALPHA1-4 : bond 0.00945 ( 45) link_ALPHA1-4 : angle 2.57054 ( 135) link_ALPHA1-6 : bond 0.00590 ( 36) link_ALPHA1-6 : angle 1.44759 ( 108) link_BETA1-4 : bond 0.00409 ( 81) link_BETA1-4 : angle 2.41437 ( 243) hydrogen bonds : bond 0.03273 ( 450) hydrogen bonds : angle 7.22442 ( 1275) glycosidic custom : bond 0.00566 ( 45) glycosidic custom : angle 3.30866 ( 135) covalent geometry : bond 0.00486 (16074) covalent geometry : angle 0.92383 (22149) Misc. bond : bond 0.00309 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8513 (mp10) cc_final: 0.7949 (mp10) REVERT: A 152 THR cc_start: 0.8285 (m) cc_final: 0.7824 (p) REVERT: A 181 ASP cc_start: 0.7994 (t0) cc_final: 0.7773 (t70) REVERT: B 67 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7370 (mm-40) REVERT: B 93 MET cc_start: 0.8247 (mmm) cc_final: 0.7905 (mmm) REVERT: B 102 TYR cc_start: 0.8217 (m-80) cc_final: 0.7681 (m-80) REVERT: B 112 TYR cc_start: 0.8205 (p90) cc_final: 0.7395 (p90) REVERT: B 125 TYR cc_start: 0.8459 (m-80) cc_final: 0.7855 (m-80) REVERT: B 194 MET cc_start: 0.8383 (mtm) cc_final: 0.8033 (mtp) REVERT: C 58 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7960 (p) REVERT: C 93 MET cc_start: 0.8375 (mmp) cc_final: 0.7893 (mmm) REVERT: C 102 TYR cc_start: 0.8417 (m-80) cc_final: 0.7588 (m-80) REVERT: C 177 THR cc_start: 0.8389 (m) cc_final: 0.7947 (p) REVERT: C 181 ASP cc_start: 0.7752 (t0) cc_final: 0.7535 (t0) REVERT: C 201 ILE cc_start: 0.8325 (mm) cc_final: 0.8095 (mm) REVERT: D 79 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8291 (m) REVERT: E 42 MET cc_start: 0.8431 (ptm) cc_final: 0.8158 (ptm) REVERT: E 69 SER cc_start: 0.8084 (t) cc_final: 0.7777 (m) REVERT: E 125 TYR cc_start: 0.8478 (m-80) cc_final: 0.7301 (m-80) REVERT: F 29 TYR cc_start: 0.8177 (m-80) cc_final: 0.7953 (m-80) REVERT: F 38 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7560 (m) REVERT: F 102 TYR cc_start: 0.8404 (m-80) cc_final: 0.8150 (m-10) REVERT: F 125 TYR cc_start: 0.8844 (m-80) cc_final: 0.8612 (m-80) REVERT: F 177 THR cc_start: 0.8078 (m) cc_final: 0.7507 (p) REVERT: F 178 PRO cc_start: 0.8647 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: F 180 ASN cc_start: 0.7972 (p0) cc_final: 0.7679 (p0) REVERT: G 91 ASN cc_start: 0.8475 (t0) cc_final: 0.8249 (t0) REVERT: G 93 MET cc_start: 0.8355 (tpp) cc_final: 0.7957 (tpp) REVERT: G 97 VAL cc_start: 0.8257 (t) cc_final: 0.7887 (m) REVERT: G 102 TYR cc_start: 0.8389 (m-80) cc_final: 0.7700 (m-80) REVERT: G 194 MET cc_start: 0.8332 (mtm) cc_final: 0.8047 (mtp) REVERT: G 195 THR cc_start: 0.8465 (p) cc_final: 0.7565 (t) REVERT: H 38 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7931 (m) REVERT: H 47 GLN cc_start: 0.8416 (mt0) cc_final: 0.7940 (mt0) REVERT: H 58 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7607 (m) REVERT: H 78 GLN cc_start: 0.7310 (tt0) cc_final: 0.6974 (tm-30) REVERT: H 129 GLN cc_start: 0.8107 (tt0) cc_final: 0.7893 (tt0) REVERT: H 130 GLN cc_start: 0.8254 (mp10) cc_final: 0.7984 (mp10) REVERT: H 142 ASN cc_start: 0.8787 (m-40) cc_final: 0.8583 (m-40) REVERT: H 148 THR cc_start: 0.8303 (p) cc_final: 0.7933 (p) REVERT: H 152 THR cc_start: 0.8255 (p) cc_final: 0.8053 (p) REVERT: H 157 ASN cc_start: 0.7206 (m-40) cc_final: 0.6965 (m-40) REVERT: H 161 TYR cc_start: 0.8214 (m-80) cc_final: 0.7655 (m-80) REVERT: I 58 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7664 (m) REVERT: I 59 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7119 (m-40) REVERT: I 89 TYR cc_start: 0.7608 (m-80) cc_final: 0.7355 (m-80) REVERT: I 125 TYR cc_start: 0.7862 (m-80) cc_final: 0.7660 (m-10) REVERT: I 186 THR cc_start: 0.8296 (m) cc_final: 0.7819 (p) outliers start: 46 outliers final: 24 residues processed: 382 average time/residue: 0.2050 time to fit residues: 128.9211 Evaluate side-chains 355 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 120 GLN E 59 ASN E 120 GLN F 120 GLN F 132 GLN G 171 GLN H 59 ASN H 65 ASN H 188 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096201 restraints weight = 22107.301| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.31 r_work: 0.3021 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16333 Z= 0.193 Angle : 0.947 9.568 22905 Z= 0.380 Chirality : 0.048 0.200 3240 Planarity : 0.005 0.047 2394 Dihedral : 13.291 106.871 6907 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.42 % Allowed : 13.11 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.22 (0.19), residues: 711 loop : 0.24 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE E 90 TYR 0.026 0.002 TYR H 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 45) link_NAG-ASN : angle 2.89023 ( 135) link_ALPHA1-4 : bond 0.00811 ( 45) link_ALPHA1-4 : angle 2.39809 ( 135) link_ALPHA1-6 : bond 0.00622 ( 36) link_ALPHA1-6 : angle 1.39301 ( 108) link_BETA1-4 : bond 0.00313 ( 81) link_BETA1-4 : angle 2.17489 ( 243) hydrogen bonds : bond 0.02917 ( 450) hydrogen bonds : angle 6.81259 ( 1275) glycosidic custom : bond 0.00291 ( 45) glycosidic custom : angle 2.89172 ( 135) covalent geometry : bond 0.00429 (16074) covalent geometry : angle 0.85377 (22149) Misc. bond : bond 0.00187 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8102 (m-80) cc_final: 0.7815 (m-80) REVERT: A 130 GLN cc_start: 0.8542 (mp10) cc_final: 0.8015 (mp10) REVERT: A 152 THR cc_start: 0.8309 (m) cc_final: 0.7868 (p) REVERT: B 67 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7400 (mm110) REVERT: B 93 MET cc_start: 0.8176 (mmm) cc_final: 0.7739 (mmm) REVERT: B 102 TYR cc_start: 0.8251 (m-80) cc_final: 0.7775 (m-80) REVERT: B 125 TYR cc_start: 0.8448 (m-80) cc_final: 0.7700 (m-80) REVERT: B 165 LEU cc_start: 0.8469 (tp) cc_final: 0.8171 (tt) REVERT: B 194 MET cc_start: 0.8419 (mtm) cc_final: 0.8092 (mtp) REVERT: C 93 MET cc_start: 0.8394 (mmp) cc_final: 0.8001 (mmm) REVERT: C 102 TYR cc_start: 0.8411 (m-80) cc_final: 0.7504 (m-80) REVERT: C 112 TYR cc_start: 0.8449 (p90) cc_final: 0.7969 (p90) REVERT: C 194 MET cc_start: 0.8160 (mtm) cc_final: 0.7803 (mtp) REVERT: E 42 MET cc_start: 0.8324 (ptm) cc_final: 0.8109 (ptm) REVERT: E 69 SER cc_start: 0.7959 (t) cc_final: 0.7716 (m) REVERT: E 125 TYR cc_start: 0.8502 (m-80) cc_final: 0.8285 (m-80) REVERT: F 38 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7472 (m) REVERT: F 59 ASN cc_start: 0.8276 (t0) cc_final: 0.7889 (t0) REVERT: F 102 TYR cc_start: 0.8399 (m-80) cc_final: 0.8130 (m-10) REVERT: F 177 THR cc_start: 0.8088 (m) cc_final: 0.7498 (p) REVERT: F 178 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8267 (t) cc_final: 0.7890 (m) REVERT: G 102 TYR cc_start: 0.8379 (m-80) cc_final: 0.7727 (m-80) REVERT: G 152 THR cc_start: 0.8456 (m) cc_final: 0.8058 (p) REVERT: G 194 MET cc_start: 0.8346 (mtm) cc_final: 0.8068 (mtp) REVERT: G 195 THR cc_start: 0.8473 (p) cc_final: 0.7579 (t) REVERT: H 38 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7783 (m) REVERT: H 47 GLN cc_start: 0.8453 (mt0) cc_final: 0.8009 (mt0) REVERT: H 58 SER cc_start: 0.7978 (m) cc_final: 0.7669 (m) REVERT: H 128 ASN cc_start: 0.8015 (t0) cc_final: 0.7773 (m-40) REVERT: H 129 GLN cc_start: 0.8243 (tt0) cc_final: 0.7887 (tt0) REVERT: H 130 GLN cc_start: 0.8218 (mp10) cc_final: 0.7972 (mp10) REVERT: H 148 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (p) REVERT: H 164 SER cc_start: 0.8387 (m) cc_final: 0.8180 (m) REVERT: I 59 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7153 (m-40) REVERT: I 89 TYR cc_start: 0.7648 (m-80) cc_final: 0.7363 (m-80) REVERT: I 105 LEU cc_start: 0.7783 (tp) cc_final: 0.7435 (tp) REVERT: I 125 TYR cc_start: 0.7914 (m-80) cc_final: 0.6529 (m-80) outliers start: 48 outliers final: 32 residues processed: 368 average time/residue: 0.2008 time to fit residues: 121.2543 Evaluate side-chains 368 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 27 optimal weight: 0.0060 chunk 112 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN E 129 GLN F 47 GLN F 132 GLN G 87 ASN H 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097971 restraints weight = 22087.116| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.28 r_work: 0.3041 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16333 Z= 0.156 Angle : 0.886 13.182 22905 Z= 0.356 Chirality : 0.047 0.400 3240 Planarity : 0.005 0.047 2394 Dihedral : 12.598 106.106 6906 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.35 % Allowed : 15.17 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.12 (0.19), residues: 729 loop : 0.35 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE A 90 TYR 0.022 0.002 TYR H 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 45) link_NAG-ASN : angle 2.96138 ( 135) link_ALPHA1-4 : bond 0.00798 ( 45) link_ALPHA1-4 : angle 2.50483 ( 135) link_ALPHA1-6 : bond 0.00588 ( 36) link_ALPHA1-6 : angle 1.41656 ( 108) link_BETA1-4 : bond 0.00272 ( 81) link_BETA1-4 : angle 1.96900 ( 243) hydrogen bonds : bond 0.02609 ( 450) hydrogen bonds : angle 6.57126 ( 1275) glycosidic custom : bond 0.00241 ( 45) glycosidic custom : angle 2.59214 ( 135) covalent geometry : bond 0.00343 (16074) covalent geometry : angle 0.79177 (22149) Misc. bond : bond 0.00106 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8103 (m-80) cc_final: 0.7855 (m-80) REVERT: A 130 GLN cc_start: 0.8498 (mp10) cc_final: 0.8246 (mp10) REVERT: A 152 THR cc_start: 0.8267 (m) cc_final: 0.7817 (p) REVERT: B 67 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7347 (mm110) REVERT: B 102 TYR cc_start: 0.8198 (m-80) cc_final: 0.7695 (m-80) REVERT: B 125 TYR cc_start: 0.8433 (m-80) cc_final: 0.7669 (m-80) REVERT: B 141 VAL cc_start: 0.8473 (t) cc_final: 0.8070 (m) REVERT: B 165 LEU cc_start: 0.8462 (tp) cc_final: 0.8168 (tt) REVERT: B 180 ASN cc_start: 0.8089 (p0) cc_final: 0.7889 (p0) REVERT: B 194 MET cc_start: 0.8409 (mtm) cc_final: 0.8086 (mtp) REVERT: C 29 TYR cc_start: 0.8272 (m-80) cc_final: 0.7734 (m-80) REVERT: C 93 MET cc_start: 0.8396 (mmp) cc_final: 0.7740 (mmm) REVERT: C 102 TYR cc_start: 0.8414 (m-80) cc_final: 0.7473 (m-80) REVERT: C 112 TYR cc_start: 0.8434 (p90) cc_final: 0.8104 (p90) REVERT: C 156 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8219 (tt) REVERT: E 125 TYR cc_start: 0.8519 (m-80) cc_final: 0.8263 (m-80) REVERT: E 126 ILE cc_start: 0.8427 (mt) cc_final: 0.8188 (mt) REVERT: F 38 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7411 (m) REVERT: F 102 TYR cc_start: 0.8425 (m-80) cc_final: 0.8187 (m-10) REVERT: F 177 THR cc_start: 0.8076 (m) cc_final: 0.7477 (p) REVERT: F 178 PRO cc_start: 0.8546 (Cg_exo) cc_final: 0.8289 (Cg_endo) REVERT: G 102 TYR cc_start: 0.8348 (m-80) cc_final: 0.7681 (m-80) REVERT: G 152 THR cc_start: 0.8447 (m) cc_final: 0.8062 (p) REVERT: G 194 MET cc_start: 0.8346 (mtm) cc_final: 0.8017 (mtm) REVERT: G 195 THR cc_start: 0.8448 (p) cc_final: 0.7465 (t) REVERT: H 38 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7652 (m) REVERT: H 47 GLN cc_start: 0.8400 (mt0) cc_final: 0.7991 (mt0) REVERT: H 58 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7697 (m) REVERT: H 128 ASN cc_start: 0.7987 (t0) cc_final: 0.7735 (m-40) REVERT: H 130 GLN cc_start: 0.8228 (mp10) cc_final: 0.7979 (mp10) REVERT: H 148 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7788 (p) REVERT: I 58 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7741 (m) REVERT: I 59 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: I 67 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6751 (mm-40) REVERT: I 78 GLN cc_start: 0.7366 (tt0) cc_final: 0.7110 (tt0) REVERT: I 89 TYR cc_start: 0.7564 (m-80) cc_final: 0.7285 (m-80) REVERT: I 102 TYR cc_start: 0.8133 (m-80) cc_final: 0.7518 (m-80) REVERT: I 125 TYR cc_start: 0.7898 (m-80) cc_final: 0.6550 (m-80) outliers start: 47 outliers final: 34 residues processed: 374 average time/residue: 0.2036 time to fit residues: 125.7646 Evaluate side-chains 374 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN F 120 GLN F 129 GLN F 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096404 restraints weight = 22384.253| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.30 r_work: 0.3022 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16333 Z= 0.217 Angle : 0.903 12.686 22905 Z= 0.367 Chirality : 0.048 0.364 3240 Planarity : 0.005 0.045 2394 Dihedral : 12.392 105.487 6906 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.20 % Allowed : 15.38 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.06 (0.19), residues: 729 loop : 0.32 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE E 90 TYR 0.025 0.002 TYR H 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 45) link_NAG-ASN : angle 3.00075 ( 135) link_ALPHA1-4 : bond 0.00770 ( 45) link_ALPHA1-4 : angle 2.56162 ( 135) link_ALPHA1-6 : bond 0.00530 ( 36) link_ALPHA1-6 : angle 1.47714 ( 108) link_BETA1-4 : bond 0.00257 ( 81) link_BETA1-4 : angle 2.03510 ( 243) hydrogen bonds : bond 0.02932 ( 450) hydrogen bonds : angle 6.58629 ( 1275) glycosidic custom : bond 0.00223 ( 45) glycosidic custom : angle 2.62194 ( 135) covalent geometry : bond 0.00496 (16074) covalent geometry : angle 0.80686 (22149) Misc. bond : bond 0.00179 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8097 (m-80) cc_final: 0.7813 (m-80) REVERT: A 65 ASN cc_start: 0.8138 (t0) cc_final: 0.7929 (t0) REVERT: A 130 GLN cc_start: 0.8517 (mp10) cc_final: 0.8228 (mp10) REVERT: A 152 THR cc_start: 0.8305 (m) cc_final: 0.7880 (p) REVERT: B 67 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7407 (mm110) REVERT: B 102 TYR cc_start: 0.8280 (m-80) cc_final: 0.7799 (m-80) REVERT: B 125 TYR cc_start: 0.8419 (m-80) cc_final: 0.7655 (m-80) REVERT: B 141 VAL cc_start: 0.8517 (t) cc_final: 0.8104 (m) REVERT: B 165 LEU cc_start: 0.8450 (tp) cc_final: 0.8189 (tt) REVERT: B 194 MET cc_start: 0.8418 (mtm) cc_final: 0.8116 (mtp) REVERT: C 76 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8070 (p) REVERT: C 93 MET cc_start: 0.8408 (mmp) cc_final: 0.7938 (mmm) REVERT: C 102 TYR cc_start: 0.8426 (m-80) cc_final: 0.7554 (m-80) REVERT: C 112 TYR cc_start: 0.8443 (p90) cc_final: 0.8135 (p90) REVERT: C 156 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8220 (tt) REVERT: C 187 VAL cc_start: 0.8557 (t) cc_final: 0.8035 (p) REVERT: C 194 MET cc_start: 0.8151 (mtm) cc_final: 0.7740 (mtp) REVERT: E 42 MET cc_start: 0.8396 (ptm) cc_final: 0.8190 (ptm) REVERT: E 125 TYR cc_start: 0.8512 (m-80) cc_final: 0.8262 (m-80) REVERT: F 38 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7326 (m) REVERT: F 102 TYR cc_start: 0.8436 (m-80) cc_final: 0.8186 (m-10) REVERT: F 177 THR cc_start: 0.8088 (m) cc_final: 0.7480 (p) REVERT: F 178 PRO cc_start: 0.8584 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8306 (t) cc_final: 0.7905 (m) REVERT: G 102 TYR cc_start: 0.8331 (m-80) cc_final: 0.7733 (m-80) REVERT: G 152 THR cc_start: 0.8459 (m) cc_final: 0.8056 (p) REVERT: G 195 THR cc_start: 0.8468 (p) cc_final: 0.7451 (t) REVERT: H 38 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (m) REVERT: H 58 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7830 (m) REVERT: H 128 ASN cc_start: 0.8014 (t0) cc_final: 0.7796 (m-40) REVERT: H 130 GLN cc_start: 0.8216 (mp10) cc_final: 0.7980 (mp10) REVERT: H 148 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7767 (p) REVERT: I 28 TYR cc_start: 0.8559 (m-80) cc_final: 0.8108 (m-80) REVERT: I 51 ASN cc_start: 0.7934 (t0) cc_final: 0.7660 (t0) REVERT: I 58 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7785 (m) REVERT: I 59 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7206 (m-40) REVERT: I 67 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6890 (mm-40) REVERT: I 78 GLN cc_start: 0.7420 (tt0) cc_final: 0.7140 (tm-30) REVERT: I 89 TYR cc_start: 0.7586 (m-80) cc_final: 0.7257 (m-80) REVERT: I 102 TYR cc_start: 0.8115 (m-80) cc_final: 0.7574 (m-80) REVERT: I 105 LEU cc_start: 0.7788 (tp) cc_final: 0.7450 (tp) REVERT: I 125 TYR cc_start: 0.7979 (m-80) cc_final: 0.6534 (m-80) outliers start: 59 outliers final: 45 residues processed: 379 average time/residue: 0.1973 time to fit residues: 122.0517 Evaluate side-chains 402 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 58 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 140 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 49 ASN F 129 GLN H 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097590 restraints weight = 22231.556| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.29 r_work: 0.3045 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16333 Z= 0.158 Angle : 0.849 12.404 22905 Z= 0.344 Chirality : 0.046 0.352 3240 Planarity : 0.005 0.047 2394 Dihedral : 12.272 105.012 6906 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.77 % Allowed : 16.45 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.09 (0.19), residues: 729 loop : 0.41 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE H 90 TYR 0.018 0.002 TYR H 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 45) link_NAG-ASN : angle 2.90467 ( 135) link_ALPHA1-4 : bond 0.00779 ( 45) link_ALPHA1-4 : angle 2.47954 ( 135) link_ALPHA1-6 : bond 0.00572 ( 36) link_ALPHA1-6 : angle 1.42236 ( 108) link_BETA1-4 : bond 0.00229 ( 81) link_BETA1-4 : angle 1.82059 ( 243) hydrogen bonds : bond 0.02569 ( 450) hydrogen bonds : angle 6.39252 ( 1275) glycosidic custom : bond 0.00229 ( 45) glycosidic custom : angle 2.49831 ( 135) covalent geometry : bond 0.00352 (16074) covalent geometry : angle 0.75607 (22149) Misc. bond : bond 0.00113 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8088 (m-80) cc_final: 0.7859 (m-80) REVERT: A 65 ASN cc_start: 0.8161 (t0) cc_final: 0.7929 (t0) REVERT: A 130 GLN cc_start: 0.8511 (mp10) cc_final: 0.8215 (mp10) REVERT: A 152 THR cc_start: 0.8279 (m) cc_final: 0.7835 (p) REVERT: B 102 TYR cc_start: 0.8260 (m-80) cc_final: 0.7761 (m-80) REVERT: B 112 TYR cc_start: 0.8183 (p90) cc_final: 0.7094 (p90) REVERT: B 125 TYR cc_start: 0.8407 (m-80) cc_final: 0.7662 (m-80) REVERT: B 141 VAL cc_start: 0.8529 (t) cc_final: 0.8103 (m) REVERT: B 165 LEU cc_start: 0.8455 (tp) cc_final: 0.8202 (tt) REVERT: B 194 MET cc_start: 0.8401 (mtm) cc_final: 0.8081 (mtp) REVERT: C 76 THR cc_start: 0.8516 (m) cc_final: 0.8046 (p) REVERT: C 93 MET cc_start: 0.8398 (mmp) cc_final: 0.7979 (mmm) REVERT: C 102 TYR cc_start: 0.8415 (m-80) cc_final: 0.7550 (m-80) REVERT: C 112 TYR cc_start: 0.8429 (p90) cc_final: 0.8174 (p90) REVERT: C 152 THR cc_start: 0.8419 (m) cc_final: 0.8174 (p) REVERT: C 156 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8207 (tt) REVERT: C 166 LEU cc_start: 0.8189 (tp) cc_final: 0.7944 (tt) REVERT: C 187 VAL cc_start: 0.8518 (t) cc_final: 0.8035 (p) REVERT: C 194 MET cc_start: 0.8124 (mtm) cc_final: 0.7740 (mtp) REVERT: F 38 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7257 (m) REVERT: F 93 MET cc_start: 0.7999 (mmm) cc_final: 0.7770 (mmm) REVERT: F 102 TYR cc_start: 0.8446 (m-80) cc_final: 0.8203 (m-10) REVERT: F 177 THR cc_start: 0.8080 (m) cc_final: 0.7479 (p) REVERT: F 178 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: G 102 TYR cc_start: 0.8322 (m-80) cc_final: 0.7686 (m-80) REVERT: G 152 THR cc_start: 0.8458 (m) cc_final: 0.8060 (p) REVERT: H 38 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7651 (m) REVERT: H 58 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7779 (m) REVERT: H 128 ASN cc_start: 0.7977 (t0) cc_final: 0.7740 (m-40) REVERT: H 130 GLN cc_start: 0.8208 (mp10) cc_final: 0.7975 (mp10) REVERT: H 148 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7885 (p) REVERT: H 155 GLN cc_start: 0.8543 (tt0) cc_final: 0.8284 (tt0) REVERT: I 28 TYR cc_start: 0.8533 (m-80) cc_final: 0.8091 (m-80) REVERT: I 51 ASN cc_start: 0.7931 (t0) cc_final: 0.7630 (t0) REVERT: I 58 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7765 (m) REVERT: I 59 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7193 (m-40) REVERT: I 67 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6752 (mm-40) REVERT: I 78 GLN cc_start: 0.7456 (tt0) cc_final: 0.7153 (tm-30) REVERT: I 89 TYR cc_start: 0.7525 (m-80) cc_final: 0.7200 (m-80) REVERT: I 102 TYR cc_start: 0.8103 (m-80) cc_final: 0.7523 (m-80) REVERT: I 125 TYR cc_start: 0.7951 (m-80) cc_final: 0.6430 (m-80) outliers start: 53 outliers final: 42 residues processed: 371 average time/residue: 0.1995 time to fit residues: 123.2224 Evaluate side-chains 389 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN E 171 GLN F 129 GLN F 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093237 restraints weight = 23699.901| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.39 r_work: 0.2964 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16333 Z= 0.224 Angle : 0.889 12.783 22905 Z= 0.363 Chirality : 0.047 0.343 3240 Planarity : 0.005 0.047 2394 Dihedral : 12.190 104.519 6906 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.85 % Allowed : 17.17 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.01 (0.19), residues: 729 loop : 0.37 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE H 189 TYR 0.019 0.002 TYR A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 45) link_NAG-ASN : angle 3.16172 ( 135) link_ALPHA1-4 : bond 0.00763 ( 45) link_ALPHA1-4 : angle 2.54334 ( 135) link_ALPHA1-6 : bond 0.00509 ( 36) link_ALPHA1-6 : angle 1.50494 ( 108) link_BETA1-4 : bond 0.00234 ( 81) link_BETA1-4 : angle 1.95399 ( 243) hydrogen bonds : bond 0.02956 ( 450) hydrogen bonds : angle 6.48634 ( 1275) glycosidic custom : bond 0.00212 ( 45) glycosidic custom : angle 2.62804 ( 135) covalent geometry : bond 0.00509 (16074) covalent geometry : angle 0.78831 (22149) Misc. bond : bond 0.00189 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8105 (m-80) cc_final: 0.7875 (m-80) REVERT: A 65 ASN cc_start: 0.8149 (t0) cc_final: 0.7926 (t0) REVERT: A 130 GLN cc_start: 0.8541 (mp10) cc_final: 0.8216 (mp10) REVERT: A 152 THR cc_start: 0.8261 (m) cc_final: 0.7834 (p) REVERT: B 67 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7403 (mm110) REVERT: B 102 TYR cc_start: 0.8307 (m-80) cc_final: 0.7816 (m-80) REVERT: B 112 TYR cc_start: 0.8208 (p90) cc_final: 0.7047 (p90) REVERT: B 125 TYR cc_start: 0.8400 (m-80) cc_final: 0.7574 (m-80) REVERT: B 141 VAL cc_start: 0.8515 (t) cc_final: 0.8108 (m) REVERT: B 165 LEU cc_start: 0.8460 (tp) cc_final: 0.8187 (tt) REVERT: B 194 MET cc_start: 0.8414 (mtm) cc_final: 0.8108 (mtp) REVERT: C 76 THR cc_start: 0.8501 (m) cc_final: 0.8024 (p) REVERT: C 93 MET cc_start: 0.8395 (mmp) cc_final: 0.7858 (mmm) REVERT: C 102 TYR cc_start: 0.8483 (m-80) cc_final: 0.7580 (m-80) REVERT: C 112 TYR cc_start: 0.8418 (p90) cc_final: 0.8176 (p90) REVERT: C 152 THR cc_start: 0.8418 (m) cc_final: 0.8185 (p) REVERT: C 156 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (tt) REVERT: C 187 VAL cc_start: 0.8526 (t) cc_final: 0.8041 (p) REVERT: C 194 MET cc_start: 0.8179 (mtm) cc_final: 0.7789 (mtp) REVERT: D 201 ILE cc_start: 0.8481 (mp) cc_final: 0.8267 (mm) REVERT: E 42 MET cc_start: 0.8441 (ptm) cc_final: 0.8239 (ptm) REVERT: F 93 MET cc_start: 0.8068 (mmm) cc_final: 0.7833 (mmm) REVERT: F 102 TYR cc_start: 0.8498 (m-80) cc_final: 0.8255 (m-10) REVERT: F 152 THR cc_start: 0.8522 (m) cc_final: 0.8246 (t) REVERT: F 177 THR cc_start: 0.8066 (m) cc_final: 0.7463 (p) REVERT: F 178 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8301 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8290 (t) cc_final: 0.7898 (m) REVERT: G 102 TYR cc_start: 0.8296 (m-80) cc_final: 0.7638 (m-80) REVERT: G 152 THR cc_start: 0.8441 (m) cc_final: 0.8034 (p) REVERT: H 38 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7773 (m) REVERT: H 58 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7865 (m) REVERT: H 128 ASN cc_start: 0.8077 (t0) cc_final: 0.7875 (m-40) REVERT: H 130 GLN cc_start: 0.8235 (mp10) cc_final: 0.7985 (mp10) REVERT: H 148 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7895 (p) REVERT: H 155 GLN cc_start: 0.8521 (tt0) cc_final: 0.8272 (tt0) REVERT: I 28 TYR cc_start: 0.8553 (m-80) cc_final: 0.8082 (m-80) REVERT: I 58 SER cc_start: 0.8215 (m) cc_final: 0.7792 (m) REVERT: I 59 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: I 67 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6892 (mm-40) REVERT: I 78 GLN cc_start: 0.7518 (tt0) cc_final: 0.7162 (tm-30) REVERT: I 89 TYR cc_start: 0.7527 (m-80) cc_final: 0.7217 (m-80) REVERT: I 102 TYR cc_start: 0.8151 (m-80) cc_final: 0.7544 (m-80) outliers start: 54 outliers final: 39 residues processed: 365 average time/residue: 0.1983 time to fit residues: 120.6440 Evaluate side-chains 390 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 161 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN E 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093828 restraints weight = 23469.027| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.38 r_work: 0.2978 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16333 Z= 0.186 Angle : 0.862 12.598 22905 Z= 0.351 Chirality : 0.047 0.347 3240 Planarity : 0.005 0.046 2394 Dihedral : 12.093 103.968 6905 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.99 % Allowed : 17.24 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.04 (0.19), residues: 729 loop : 0.41 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE E 75 TYR 0.020 0.002 TYR A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 45) link_NAG-ASN : angle 3.09001 ( 135) link_ALPHA1-4 : bond 0.00778 ( 45) link_ALPHA1-4 : angle 2.50842 ( 135) link_ALPHA1-6 : bond 0.00550 ( 36) link_ALPHA1-6 : angle 1.46406 ( 108) link_BETA1-4 : bond 0.00212 ( 81) link_BETA1-4 : angle 1.81614 ( 243) hydrogen bonds : bond 0.02734 ( 450) hydrogen bonds : angle 6.41756 ( 1275) glycosidic custom : bond 0.00227 ( 45) glycosidic custom : angle 2.58869 ( 135) covalent geometry : bond 0.00420 (16074) covalent geometry : angle 0.76461 (22149) Misc. bond : bond 0.00139 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 354 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8128 (t0) cc_final: 0.7900 (t0) REVERT: A 130 GLN cc_start: 0.8537 (mp10) cc_final: 0.8214 (mp10) REVERT: A 152 THR cc_start: 0.8257 (m) cc_final: 0.7826 (p) REVERT: A 184 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 67 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7366 (mm110) REVERT: B 102 TYR cc_start: 0.8284 (m-80) cc_final: 0.7811 (m-80) REVERT: B 112 TYR cc_start: 0.8201 (p90) cc_final: 0.7088 (p90) REVERT: B 125 TYR cc_start: 0.8399 (m-80) cc_final: 0.7584 (m-80) REVERT: B 141 VAL cc_start: 0.8512 (t) cc_final: 0.8113 (m) REVERT: B 165 LEU cc_start: 0.8469 (tp) cc_final: 0.8188 (tt) REVERT: B 194 MET cc_start: 0.8392 (mtm) cc_final: 0.8093 (mtp) REVERT: C 76 THR cc_start: 0.8501 (m) cc_final: 0.8027 (p) REVERT: C 93 MET cc_start: 0.8365 (mmp) cc_final: 0.7836 (mmm) REVERT: C 102 TYR cc_start: 0.8448 (m-80) cc_final: 0.7552 (m-80) REVERT: C 112 TYR cc_start: 0.8408 (p90) cc_final: 0.8175 (p90) REVERT: C 152 THR cc_start: 0.8425 (m) cc_final: 0.8201 (p) REVERT: C 156 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (tt) REVERT: C 187 VAL cc_start: 0.8495 (t) cc_final: 0.8061 (p) REVERT: C 194 MET cc_start: 0.8206 (mtm) cc_final: 0.7838 (mtp) REVERT: E 42 MET cc_start: 0.8429 (ptm) cc_final: 0.8206 (ptm) REVERT: F 38 VAL cc_start: 0.7777 (p) cc_final: 0.7175 (m) REVERT: F 51 ASN cc_start: 0.8390 (t0) cc_final: 0.7774 (t0) REVERT: F 102 TYR cc_start: 0.8484 (m-80) cc_final: 0.8222 (m-10) REVERT: F 152 THR cc_start: 0.8515 (m) cc_final: 0.8241 (t) REVERT: F 177 THR cc_start: 0.8072 (m) cc_final: 0.7471 (p) REVERT: F 178 PRO cc_start: 0.8529 (Cg_exo) cc_final: 0.8291 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8268 (t) cc_final: 0.7910 (m) REVERT: G 102 TYR cc_start: 0.8302 (m-80) cc_final: 0.7614 (m-80) REVERT: G 152 THR cc_start: 0.8440 (m) cc_final: 0.8040 (p) REVERT: G 194 MET cc_start: 0.8301 (mtm) cc_final: 0.7714 (mtp) REVERT: H 38 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7602 (m) REVERT: H 58 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7827 (m) REVERT: H 128 ASN cc_start: 0.8053 (t0) cc_final: 0.7852 (m-40) REVERT: H 130 GLN cc_start: 0.8247 (mp10) cc_final: 0.8002 (mp10) REVERT: H 148 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7879 (p) REVERT: I 28 TYR cc_start: 0.8572 (m-80) cc_final: 0.8089 (m-80) REVERT: I 58 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7588 (p) REVERT: I 67 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6776 (mm-40) REVERT: I 78 GLN cc_start: 0.7534 (tt0) cc_final: 0.7167 (tm-30) REVERT: I 89 TYR cc_start: 0.7496 (m-80) cc_final: 0.7194 (m-80) REVERT: I 102 TYR cc_start: 0.8133 (m-80) cc_final: 0.7537 (m-80) outliers start: 56 outliers final: 44 residues processed: 376 average time/residue: 0.1963 time to fit residues: 120.6836 Evaluate side-chains 403 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 157 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN E 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094912 restraints weight = 23412.140| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.38 r_work: 0.2990 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16333 Z= 0.151 Angle : 0.836 12.445 22905 Z= 0.339 Chirality : 0.046 0.350 3240 Planarity : 0.005 0.045 2394 Dihedral : 11.915 102.890 6903 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.56 % Allowed : 17.59 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.02 (0.19), residues: 729 loop : 0.50 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE E 75 TYR 0.019 0.001 TYR A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 45) link_NAG-ASN : angle 3.04205 ( 135) link_ALPHA1-4 : bond 0.00770 ( 45) link_ALPHA1-4 : angle 2.46258 ( 135) link_ALPHA1-6 : bond 0.00582 ( 36) link_ALPHA1-6 : angle 1.42266 ( 108) link_BETA1-4 : bond 0.00209 ( 81) link_BETA1-4 : angle 1.71225 ( 243) hydrogen bonds : bond 0.02538 ( 450) hydrogen bonds : angle 6.27253 ( 1275) glycosidic custom : bond 0.00199 ( 45) glycosidic custom : angle 2.51473 ( 135) covalent geometry : bond 0.00336 (16074) covalent geometry : angle 0.74033 (22149) Misc. bond : bond 0.00092 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8108 (t0) cc_final: 0.7882 (t0) REVERT: A 130 GLN cc_start: 0.8522 (mp10) cc_final: 0.8197 (mp10) REVERT: A 152 THR cc_start: 0.8202 (m) cc_final: 0.7763 (p) REVERT: A 170 TYR cc_start: 0.8347 (m-80) cc_final: 0.7736 (m-80) REVERT: A 184 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 102 TYR cc_start: 0.8285 (m-80) cc_final: 0.7788 (m-80) REVERT: B 112 TYR cc_start: 0.8185 (p90) cc_final: 0.7056 (p90) REVERT: B 125 TYR cc_start: 0.8407 (m-80) cc_final: 0.7598 (m-80) REVERT: B 141 VAL cc_start: 0.8500 (t) cc_final: 0.8093 (m) REVERT: B 165 LEU cc_start: 0.8465 (tp) cc_final: 0.8183 (tt) REVERT: B 194 MET cc_start: 0.8365 (mtm) cc_final: 0.8068 (mtp) REVERT: C 32 GLN cc_start: 0.8194 (tt0) cc_final: 0.7970 (tt0) REVERT: C 58 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 76 THR cc_start: 0.8463 (m) cc_final: 0.7985 (p) REVERT: C 78 GLN cc_start: 0.8011 (tt0) cc_final: 0.7776 (tt0) REVERT: C 93 MET cc_start: 0.8364 (mmp) cc_final: 0.7856 (mmm) REVERT: C 102 TYR cc_start: 0.8447 (m-80) cc_final: 0.7545 (m-80) REVERT: C 112 TYR cc_start: 0.8400 (p90) cc_final: 0.8167 (p90) REVERT: C 152 THR cc_start: 0.8433 (m) cc_final: 0.8216 (p) REVERT: C 156 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8163 (tt) REVERT: C 187 VAL cc_start: 0.8487 (t) cc_final: 0.8075 (p) REVERT: C 194 MET cc_start: 0.8198 (mtm) cc_final: 0.7835 (mtp) REVERT: E 42 MET cc_start: 0.8494 (ptm) cc_final: 0.8257 (ptm) REVERT: F 38 VAL cc_start: 0.7743 (p) cc_final: 0.7156 (m) REVERT: F 51 ASN cc_start: 0.8324 (t0) cc_final: 0.7731 (t0) REVERT: F 102 TYR cc_start: 0.8509 (m-80) cc_final: 0.8240 (m-10) REVERT: F 152 THR cc_start: 0.8501 (m) cc_final: 0.8228 (t) REVERT: F 177 THR cc_start: 0.8073 (m) cc_final: 0.7475 (p) REVERT: F 178 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: G 42 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8066 (ptm) REVERT: G 102 TYR cc_start: 0.8281 (m-80) cc_final: 0.7581 (m-80) REVERT: G 152 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.7985 (p) REVERT: G 194 MET cc_start: 0.8284 (mtm) cc_final: 0.7679 (mtp) REVERT: H 38 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7515 (m) REVERT: H 58 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7810 (p) REVERT: H 128 ASN cc_start: 0.8025 (t0) cc_final: 0.7805 (m-40) REVERT: H 130 GLN cc_start: 0.8249 (mp10) cc_final: 0.8008 (mp10) REVERT: H 148 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7822 (p) REVERT: H 155 GLN cc_start: 0.8485 (tt0) cc_final: 0.8234 (tt0) REVERT: I 28 TYR cc_start: 0.8562 (m-80) cc_final: 0.8089 (m-80) REVERT: I 59 ASN cc_start: 0.7483 (t0) cc_final: 0.7211 (m-40) REVERT: I 67 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6735 (mm-40) REVERT: I 78 GLN cc_start: 0.7556 (tt0) cc_final: 0.6996 (tt0) REVERT: I 89 TYR cc_start: 0.7477 (m-80) cc_final: 0.7208 (m-80) REVERT: I 102 TYR cc_start: 0.8124 (m-80) cc_final: 0.7454 (m-80) outliers start: 50 outliers final: 38 residues processed: 373 average time/residue: 0.2025 time to fit residues: 123.5721 Evaluate side-chains 393 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 108 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 120 GLN E 128 ASN E 129 GLN H 120 GLN H 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094223 restraints weight = 23625.427| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.38 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16333 Z= 0.178 Angle : 0.859 12.441 22905 Z= 0.349 Chirality : 0.047 0.397 3240 Planarity : 0.005 0.045 2394 Dihedral : 11.795 102.083 6903 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.49 % Allowed : 17.66 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.01 (0.19), residues: 729 loop : 0.48 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE E 75 TYR 0.020 0.002 TYR A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 45) link_NAG-ASN : angle 3.22823 ( 135) link_ALPHA1-4 : bond 0.00764 ( 45) link_ALPHA1-4 : angle 2.50167 ( 135) link_ALPHA1-6 : bond 0.00545 ( 36) link_ALPHA1-6 : angle 1.46473 ( 108) link_BETA1-4 : bond 0.00210 ( 81) link_BETA1-4 : angle 1.77568 ( 243) hydrogen bonds : bond 0.02695 ( 450) hydrogen bonds : angle 6.30171 ( 1275) glycosidic custom : bond 0.00204 ( 45) glycosidic custom : angle 2.59878 ( 135) covalent geometry : bond 0.00401 (16074) covalent geometry : angle 0.75825 (22149) Misc. bond : bond 0.00143 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8115 (t0) cc_final: 0.7887 (t0) REVERT: A 130 GLN cc_start: 0.8520 (mp10) cc_final: 0.8199 (mp10) REVERT: A 152 THR cc_start: 0.8184 (m) cc_final: 0.7753 (p) REVERT: A 170 TYR cc_start: 0.8348 (m-80) cc_final: 0.7731 (m-80) REVERT: A 184 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 67 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7319 (mm110) REVERT: B 102 TYR cc_start: 0.8304 (m-80) cc_final: 0.7806 (m-80) REVERT: B 112 TYR cc_start: 0.8158 (p90) cc_final: 0.7083 (p90) REVERT: B 125 TYR cc_start: 0.8409 (m-80) cc_final: 0.7606 (m-80) REVERT: B 141 VAL cc_start: 0.8515 (t) cc_final: 0.8103 (m) REVERT: B 165 LEU cc_start: 0.8468 (tp) cc_final: 0.8192 (tt) REVERT: B 194 MET cc_start: 0.8386 (mtm) cc_final: 0.8081 (mtp) REVERT: C 32 GLN cc_start: 0.8200 (tt0) cc_final: 0.7994 (tt0) REVERT: C 76 THR cc_start: 0.8490 (m) cc_final: 0.8006 (p) REVERT: C 78 GLN cc_start: 0.8015 (tt0) cc_final: 0.7778 (tt0) REVERT: C 93 MET cc_start: 0.8379 (mmp) cc_final: 0.7814 (mmm) REVERT: C 102 TYR cc_start: 0.8437 (m-80) cc_final: 0.7552 (m-80) REVERT: C 112 TYR cc_start: 0.8395 (p90) cc_final: 0.8162 (p90) REVERT: C 152 THR cc_start: 0.8416 (m) cc_final: 0.8212 (p) REVERT: C 156 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8209 (tt) REVERT: C 187 VAL cc_start: 0.8513 (t) cc_final: 0.8093 (p) REVERT: C 194 MET cc_start: 0.8164 (mtm) cc_final: 0.7800 (mtp) REVERT: E 42 MET cc_start: 0.8379 (ptm) cc_final: 0.8129 (ptm) REVERT: F 38 VAL cc_start: 0.7770 (p) cc_final: 0.7173 (m) REVERT: F 51 ASN cc_start: 0.8360 (t0) cc_final: 0.7754 (t0) REVERT: F 102 TYR cc_start: 0.8500 (m-80) cc_final: 0.8238 (m-10) REVERT: F 152 THR cc_start: 0.8501 (m) cc_final: 0.8236 (t) REVERT: F 177 THR cc_start: 0.8073 (m) cc_final: 0.7475 (p) REVERT: F 178 PRO cc_start: 0.8514 (Cg_exo) cc_final: 0.8272 (Cg_endo) REVERT: G 42 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8051 (ptm) REVERT: G 97 VAL cc_start: 0.8258 (t) cc_final: 0.7846 (m) REVERT: G 102 TYR cc_start: 0.8273 (m-80) cc_final: 0.7616 (m-80) REVERT: G 152 THR cc_start: 0.8439 (m) cc_final: 0.8052 (p) REVERT: G 170 TYR cc_start: 0.8144 (m-10) cc_final: 0.7918 (m-80) REVERT: G 194 MET cc_start: 0.8274 (mtm) cc_final: 0.7652 (mtp) REVERT: H 38 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7611 (m) REVERT: H 58 SER cc_start: 0.8073 (m) cc_final: 0.7814 (p) REVERT: H 128 ASN cc_start: 0.8053 (t0) cc_final: 0.7837 (m-40) REVERT: H 130 GLN cc_start: 0.8235 (mp10) cc_final: 0.7996 (mp10) REVERT: H 148 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7844 (p) REVERT: H 155 GLN cc_start: 0.8484 (tt0) cc_final: 0.8227 (tt0) REVERT: I 28 TYR cc_start: 0.8562 (m-80) cc_final: 0.8070 (m-80) REVERT: I 51 ASN cc_start: 0.7946 (t0) cc_final: 0.7567 (t0) REVERT: I 59 ASN cc_start: 0.7456 (t0) cc_final: 0.7219 (m-40) REVERT: I 67 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6751 (mm-40) REVERT: I 78 GLN cc_start: 0.7564 (tt0) cc_final: 0.6997 (tt0) REVERT: I 89 TYR cc_start: 0.7479 (m-80) cc_final: 0.7208 (m-80) REVERT: I 102 TYR cc_start: 0.8160 (m-80) cc_final: 0.7467 (m-80) outliers start: 49 outliers final: 41 residues processed: 377 average time/residue: 0.2023 time to fit residues: 126.2906 Evaluate side-chains 397 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.7544 > 50: distance: 8 - 14: 6.214 distance: 14 - 15: 7.732 distance: 14 - 162: 7.456 distance: 15 - 16: 3.955 distance: 15 - 18: 9.833 distance: 16 - 17: 14.721 distance: 16 - 26: 6.129 distance: 17 - 159: 12.851 distance: 18 - 19: 11.182 distance: 19 - 20: 11.769 distance: 19 - 21: 14.729 distance: 20 - 22: 8.326 distance: 21 - 23: 6.342 distance: 22 - 24: 11.217 distance: 24 - 25: 7.473 distance: 26 - 27: 4.894 distance: 27 - 28: 5.845 distance: 27 - 30: 6.425 distance: 28 - 29: 14.390 distance: 28 - 37: 3.868 distance: 30 - 31: 9.820 distance: 31 - 32: 4.781 distance: 31 - 33: 6.273 distance: 33 - 35: 3.086 distance: 34 - 36: 3.135 distance: 35 - 36: 7.517 distance: 37 - 38: 11.800 distance: 37 - 150: 10.567 distance: 38 - 39: 8.318 distance: 38 - 41: 15.593 distance: 39 - 40: 4.551 distance: 40 - 147: 12.262 distance: 43 - 46: 3.231 distance: 44 - 45: 5.781 distance: 44 - 50: 6.518 distance: 46 - 48: 4.920 distance: 47 - 49: 8.259 distance: 50 - 51: 4.189 distance: 51 - 52: 19.697 distance: 51 - 54: 11.984 distance: 52 - 53: 11.744 distance: 52 - 59: 10.191 distance: 54 - 55: 3.998 distance: 55 - 56: 11.531 distance: 56 - 57: 6.825 distance: 56 - 58: 15.532 distance: 59 - 60: 6.775 distance: 59 - 65: 6.141 distance: 60 - 61: 10.144 distance: 60 - 63: 8.415 distance: 61 - 62: 11.790 distance: 61 - 66: 6.603 distance: 62 - 78: 31.849 distance: 63 - 64: 10.718 distance: 64 - 65: 3.579 distance: 66 - 67: 19.651 distance: 67 - 68: 8.410 distance: 67 - 70: 18.037 distance: 68 - 69: 23.446 distance: 68 - 74: 21.809 distance: 70 - 71: 28.220 distance: 71 - 72: 8.925 distance: 71 - 73: 11.463 distance: 74 - 75: 22.880 distance: 75 - 76: 28.926 distance: 76 - 77: 32.524 distance: 76 - 78: 22.862 distance: 78 - 79: 14.914 distance: 79 - 80: 12.455 distance: 79 - 82: 10.084 distance: 80 - 81: 19.621 distance: 80 - 86: 10.320 distance: 82 - 83: 16.951 distance: 83 - 84: 6.189 distance: 83 - 85: 15.723 distance: 86 - 87: 6.240 distance: 87 - 88: 10.065 distance: 87 - 90: 9.133 distance: 88 - 89: 21.720 distance: 88 - 91: 6.624