Starting phenix.real_space_refine on Tue Dec 31 13:51:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnb_13546/12_2024/7pnb_13546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnb_13546/12_2024/7pnb_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_13546/12_2024/7pnb_13546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnb_13546/12_2024/7pnb_13546.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnb_13546/12_2024/7pnb_13546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnb_13546/12_2024/7pnb_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.48, per 1000 atoms: 0.67 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: 9.45 Conformation dependent library (CDL) restraints added in 1.7 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: 2.15 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: 4.83 Time building geometry restraints manager: 9.43 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: 0.00 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.360 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- 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 0.108 16074 Z= 0.760 Angle : 1.746 12.180 22149 Z= 0.901 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 *********************** 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 : 1.538 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: 0.2188 time to fit residues: 139.2724 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 : 1.574 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 16074 Z= 0.308 Angle : 0.924 9.121 22149 Z= 0.390 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 *********************** 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 : 1.485 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8741 (mp10) cc_final: 0.8418 (mp10) REVERT: A 152 THR cc_start: 0.8595 (m) cc_final: 0.8285 (p) REVERT: B 67 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8158 (mm-40) REVERT: B 93 MET cc_start: 0.8351 (mmm) cc_final: 0.8070 (mmm) REVERT: B 102 TYR cc_start: 0.8627 (m-80) cc_final: 0.8248 (m-80) REVERT: B 112 TYR cc_start: 0.8518 (p90) cc_final: 0.7891 (p90) REVERT: B 125 TYR cc_start: 0.8513 (m-80) cc_final: 0.7860 (m-80) REVERT: B 194 MET cc_start: 0.8406 (mtm) cc_final: 0.8109 (mtp) REVERT: C 58 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (p) REVERT: C 93 MET cc_start: 0.8483 (mmp) cc_final: 0.8090 (mmm) REVERT: C 102 TYR cc_start: 0.8783 (m-80) cc_final: 0.8160 (m-80) REVERT: C 177 THR cc_start: 0.8525 (m) cc_final: 0.8203 (p) REVERT: D 29 TYR cc_start: 0.8362 (m-80) cc_final: 0.8139 (m-80) REVERT: D 79 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8444 (m) REVERT: E 125 TYR cc_start: 0.8497 (m-80) cc_final: 0.7475 (m-80) REVERT: F 29 TYR cc_start: 0.8392 (m-80) cc_final: 0.8156 (m-80) REVERT: F 38 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7655 (m) REVERT: F 125 TYR cc_start: 0.8835 (m-80) cc_final: 0.8598 (m-80) REVERT: F 177 THR cc_start: 0.8374 (m) cc_final: 0.8020 (p) REVERT: F 178 PRO cc_start: 0.8800 (Cg_exo) cc_final: 0.8600 (Cg_endo) REVERT: F 180 ASN cc_start: 0.8477 (p0) cc_final: 0.8262 (p0) REVERT: G 91 ASN cc_start: 0.8674 (t0) cc_final: 0.8450 (t0) REVERT: G 93 MET cc_start: 0.8594 (tpp) cc_final: 0.8362 (tpp) REVERT: G 97 VAL cc_start: 0.8345 (t) cc_final: 0.8053 (m) REVERT: G 102 TYR cc_start: 0.8884 (m-80) cc_final: 0.8355 (m-80) REVERT: G 194 MET cc_start: 0.8344 (mtm) cc_final: 0.8079 (mtp) REVERT: G 195 THR cc_start: 0.8643 (p) cc_final: 0.8069 (t) REVERT: H 47 GLN cc_start: 0.8427 (mt0) cc_final: 0.8082 (mt0) REVERT: H 58 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7885 (m) REVERT: H 78 GLN cc_start: 0.8060 (tt0) cc_final: 0.7761 (tm-30) REVERT: H 148 THR cc_start: 0.8091 (p) cc_final: 0.7795 (p) REVERT: H 157 ASN cc_start: 0.8008 (m-40) cc_final: 0.7730 (m-40) REVERT: H 161 TYR cc_start: 0.8518 (m-80) cc_final: 0.7966 (m-80) REVERT: I 58 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (m) REVERT: I 186 THR cc_start: 0.8517 (m) cc_final: 0.8135 (p) outliers start: 46 outliers final: 24 residues processed: 382 average time/residue: 0.2189 time to fit residues: 135.2780 Evaluate side-chains 358 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 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 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 81 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 118 optimal weight: 0.0030 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 87 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16074 Z= 0.196 Angle : 0.825 9.702 22149 Z= 0.342 Chirality : 0.047 0.210 3240 Planarity : 0.005 0.047 2394 Dihedral : 13.226 106.707 6905 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.13 % Allowed : 13.03 % Favored : 83.83 % 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: 0.16 (0.19), residues: 729 loop : 0.31 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE H 90 TYR 0.031 0.002 TYR H 27 *********************** 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 395 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 351 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8710 (mp10) cc_final: 0.8407 (mp10) REVERT: A 152 THR cc_start: 0.8550 (m) cc_final: 0.8241 (p) REVERT: B 67 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 93 MET cc_start: 0.8231 (mmm) cc_final: 0.7877 (mmm) REVERT: B 102 TYR cc_start: 0.8588 (m-80) cc_final: 0.8229 (m-80) REVERT: B 125 TYR cc_start: 0.8489 (m-80) cc_final: 0.7709 (m-80) REVERT: B 194 MET cc_start: 0.8398 (mtm) cc_final: 0.8134 (mtp) REVERT: C 93 MET cc_start: 0.8538 (mmp) cc_final: 0.8017 (mmm) REVERT: C 102 TYR cc_start: 0.8786 (m-80) cc_final: 0.8082 (m-80) REVERT: C 194 MET cc_start: 0.8258 (mtm) cc_final: 0.7949 (mtm) REVERT: E 112 TYR cc_start: 0.8749 (p90) cc_final: 0.8480 (p90) REVERT: E 125 TYR cc_start: 0.8509 (m-80) cc_final: 0.7409 (m-80) REVERT: F 25 VAL cc_start: 0.8518 (t) cc_final: 0.8240 (p) REVERT: F 38 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7559 (m) REVERT: F 59 ASN cc_start: 0.8755 (t0) cc_final: 0.8447 (t0) REVERT: F 102 TYR cc_start: 0.8739 (m-10) cc_final: 0.8531 (m-10) REVERT: F 125 TYR cc_start: 0.8813 (m-80) cc_final: 0.8499 (m-80) REVERT: F 177 THR cc_start: 0.8375 (m) cc_final: 0.8007 (p) REVERT: G 93 MET cc_start: 0.8681 (tpp) cc_final: 0.8327 (tpp) REVERT: G 102 TYR cc_start: 0.8877 (m-80) cc_final: 0.8379 (m-80) REVERT: G 152 THR cc_start: 0.8620 (m) cc_final: 0.8310 (p) REVERT: G 194 MET cc_start: 0.8297 (mtm) cc_final: 0.8037 (mtp) REVERT: G 195 THR cc_start: 0.8653 (p) cc_final: 0.8064 (t) REVERT: H 27 TYR cc_start: 0.8606 (m-10) cc_final: 0.8404 (m-10) REVERT: H 47 GLN cc_start: 0.8387 (mt0) cc_final: 0.8063 (mt0) REVERT: H 58 SER cc_start: 0.8154 (m) cc_final: 0.7935 (m) REVERT: H 148 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7707 (p) REVERT: I 67 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7758 (mm-40) REVERT: I 186 THR cc_start: 0.8509 (m) cc_final: 0.8108 (p) outliers start: 44 outliers final: 29 residues processed: 373 average time/residue: 0.2260 time to fit residues: 138.1732 Evaluate side-chains 362 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 331 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 SER 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 C residue 197 SER 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 E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 184 THR 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 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 145 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 87 ASN C 47 GLN D 129 GLN F 120 GLN F 132 GLN H 120 GLN H 155 GLN H 188 ASN I 78 GLN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16074 Z= 0.346 Angle : 0.839 9.599 22149 Z= 0.357 Chirality : 0.049 0.422 3240 Planarity : 0.005 0.047 2394 Dihedral : 12.561 106.086 6904 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.70 % Allowed : 15.10 % Favored : 81.20 % 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: 0.31 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.27 (0.19), residues: 711 loop : 0.30 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.003 PHE A 90 TYR 0.023 0.002 TYR F 102 *********************** 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: 52 poor density : 344 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8292 (m-80) cc_final: 0.8006 (m-80) REVERT: A 152 THR cc_start: 0.8592 (m) cc_final: 0.8300 (p) REVERT: B 37 ASN cc_start: 0.8512 (t0) cc_final: 0.8286 (t0) REVERT: B 67 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8233 (mm110) REVERT: B 93 MET cc_start: 0.8274 (mmm) cc_final: 0.7899 (mmm) REVERT: B 102 TYR cc_start: 0.8656 (m-80) cc_final: 0.8302 (m-80) REVERT: B 125 TYR cc_start: 0.8485 (m-80) cc_final: 0.7658 (m-80) REVERT: B 141 VAL cc_start: 0.8566 (t) cc_final: 0.8196 (m) REVERT: B 165 LEU cc_start: 0.8593 (tp) cc_final: 0.8357 (tt) REVERT: B 194 MET cc_start: 0.8470 (mtm) cc_final: 0.8197 (mtp) REVERT: C 93 MET cc_start: 0.8510 (mmp) cc_final: 0.8184 (mmm) REVERT: C 102 TYR cc_start: 0.8790 (m-80) cc_final: 0.8084 (m-80) REVERT: C 112 TYR cc_start: 0.8669 (p90) cc_final: 0.8466 (p90) REVERT: C 125 TYR cc_start: 0.8481 (m-80) cc_final: 0.8070 (m-80) REVERT: C 156 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8311 (tt) REVERT: C 194 MET cc_start: 0.8281 (mtm) cc_final: 0.7929 (mtp) REVERT: E 125 TYR cc_start: 0.8546 (m-80) cc_final: 0.8303 (m-80) REVERT: F 38 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7504 (m) REVERT: F 59 ASN cc_start: 0.8656 (t0) cc_final: 0.8392 (t0) REVERT: F 177 THR cc_start: 0.8394 (m) cc_final: 0.8010 (p) REVERT: G 97 VAL cc_start: 0.8337 (t) cc_final: 0.7996 (m) REVERT: G 102 TYR cc_start: 0.8844 (m-80) cc_final: 0.8305 (m-80) REVERT: G 152 THR cc_start: 0.8603 (m) cc_final: 0.8280 (p) REVERT: G 194 MET cc_start: 0.8327 (mtm) cc_final: 0.7981 (mtp) REVERT: G 195 THR cc_start: 0.8624 (p) cc_final: 0.8000 (t) REVERT: H 47 GLN cc_start: 0.8441 (mt0) cc_final: 0.8120 (mt0) REVERT: H 58 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8053 (m) REVERT: I 58 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.7907 (m) REVERT: I 67 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7829 (mm-40) REVERT: I 105 LEU cc_start: 0.7902 (tp) cc_final: 0.7661 (tp) outliers start: 52 outliers final: 43 residues processed: 371 average time/residue: 0.2139 time to fit residues: 128.4275 Evaluate side-chains 384 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL 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 123 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 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 E residue 192 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 58 SER Chi-restraints excluded: chain H residue 129 GLN 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 123 THR 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 130 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 GLN F 120 GLN F 129 GLN F 132 GLN F 171 GLN I 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16074 Z= 0.262 Angle : 0.780 9.203 22149 Z= 0.331 Chirality : 0.047 0.375 3240 Planarity : 0.005 0.045 2394 Dihedral : 12.362 105.679 6904 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.56 % Allowed : 15.74 % Favored : 80.70 % 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: 0.21 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.09 (0.19), residues: 729 loop : 0.34 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE E 75 TYR 0.024 0.002 TYR H 27 *********************** 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 401 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8288 (m-80) cc_final: 0.8062 (m-80) REVERT: A 152 THR cc_start: 0.8584 (m) cc_final: 0.8293 (p) REVERT: B 67 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8223 (mm110) REVERT: B 102 TYR cc_start: 0.8652 (m-80) cc_final: 0.8328 (m-80) REVERT: B 125 TYR cc_start: 0.8474 (m-80) cc_final: 0.7665 (m-80) REVERT: B 141 VAL cc_start: 0.8570 (t) cc_final: 0.8200 (m) REVERT: B 165 LEU cc_start: 0.8590 (tp) cc_final: 0.8362 (tt) REVERT: B 194 MET cc_start: 0.8458 (mtm) cc_final: 0.8197 (mtp) REVERT: C 76 THR cc_start: 0.8804 (m) cc_final: 0.8430 (p) REVERT: C 93 MET cc_start: 0.8476 (mmp) cc_final: 0.8147 (mmm) REVERT: C 102 TYR cc_start: 0.8789 (m-80) cc_final: 0.8037 (m-80) REVERT: C 125 TYR cc_start: 0.8448 (m-80) cc_final: 0.7987 (m-80) REVERT: C 156 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8311 (tt) REVERT: C 187 VAL cc_start: 0.8584 (t) cc_final: 0.8249 (p) REVERT: C 194 MET cc_start: 0.8265 (mtm) cc_final: 0.7882 (mtp) REVERT: E 125 TYR cc_start: 0.8543 (m-80) cc_final: 0.8252 (m-80) REVERT: F 38 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7414 (m) REVERT: F 51 ASN cc_start: 0.8579 (t0) cc_final: 0.8053 (t0) REVERT: F 93 MET cc_start: 0.8183 (mmm) cc_final: 0.7960 (mmm) REVERT: F 177 THR cc_start: 0.8402 (m) cc_final: 0.8014 (p) REVERT: G 97 VAL cc_start: 0.8353 (t) cc_final: 0.8074 (m) REVERT: G 102 TYR cc_start: 0.8837 (m-80) cc_final: 0.8337 (m-80) REVERT: G 152 THR cc_start: 0.8614 (m) cc_final: 0.8299 (p) REVERT: G 194 MET cc_start: 0.8300 (mtm) cc_final: 0.7961 (mtm) REVERT: H 58 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8066 (m) REVERT: I 58 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7868 (m) REVERT: I 67 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7818 (mm-40) REVERT: I 78 GLN cc_start: 0.7910 (tt0) cc_final: 0.7608 (tm-30) REVERT: I 102 TYR cc_start: 0.8542 (m-80) cc_final: 0.8148 (m-80) REVERT: I 123 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7858 (t) outliers start: 50 outliers final: 38 residues processed: 374 average time/residue: 0.2344 time to fit residues: 145.1130 Evaluate side-chains 380 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 337 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 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 D residue 26 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 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 192 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 H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN 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 79 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN D 129 GLN E 171 GLN F 120 GLN F 129 GLN F 132 GLN H 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16074 Z= 0.287 Angle : 0.785 9.318 22149 Z= 0.335 Chirality : 0.047 0.346 3240 Planarity : 0.005 0.042 2394 Dihedral : 12.255 105.029 6904 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.49 % Allowed : 16.60 % Favored : 79.91 % 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: 0.21 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.07 (0.19), residues: 729 loop : 0.37 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.003 PHE E 90 TYR 0.019 0.002 TYR H 86 *********************** 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 399 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 THR cc_start: 0.8579 (m) cc_final: 0.8287 (p) REVERT: B 102 TYR cc_start: 0.8650 (m-80) cc_final: 0.8323 (m-80) REVERT: B 125 TYR cc_start: 0.8469 (m-80) cc_final: 0.7654 (m-80) REVERT: B 141 VAL cc_start: 0.8608 (t) cc_final: 0.8235 (m) REVERT: B 165 LEU cc_start: 0.8581 (tp) cc_final: 0.8367 (tt) REVERT: B 194 MET cc_start: 0.8464 (mtm) cc_final: 0.8219 (mtp) REVERT: C 76 THR cc_start: 0.8799 (m) cc_final: 0.8427 (p) REVERT: C 93 MET cc_start: 0.8492 (mmp) cc_final: 0.8084 (mmm) REVERT: C 102 TYR cc_start: 0.8806 (m-80) cc_final: 0.8103 (m-80) REVERT: C 156 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8235 (tt) REVERT: C 187 VAL cc_start: 0.8590 (t) cc_final: 0.8260 (p) REVERT: C 194 MET cc_start: 0.8270 (mtm) cc_final: 0.7886 (mtp) REVERT: F 177 THR cc_start: 0.8414 (m) cc_final: 0.8026 (p) REVERT: G 97 VAL cc_start: 0.8355 (t) cc_final: 0.8062 (m) REVERT: G 102 TYR cc_start: 0.8816 (m-80) cc_final: 0.8305 (m-80) REVERT: G 152 THR cc_start: 0.8610 (m) cc_final: 0.8287 (p) REVERT: H 58 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (m) REVERT: I 58 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7909 (m) REVERT: I 67 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7820 (mm-40) outliers start: 49 outliers final: 40 residues processed: 373 average time/residue: 0.2118 time to fit residues: 128.1153 Evaluate side-chains 379 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 336 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 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 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 34 THR 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 129 GLN Chi-restraints excluded: chain H residue 145 VAL 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 79 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 155 GLN C 49 ASN D 129 GLN D 188 ASN E 30 GLN F 129 GLN F 132 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16074 Z= 0.309 Angle : 0.788 9.357 22149 Z= 0.338 Chirality : 0.048 0.387 3240 Planarity : 0.005 0.041 2394 Dihedral : 12.195 104.654 6903 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.70 % Allowed : 16.88 % Favored : 79.42 % 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 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.05 (0.19), residues: 729 loop : 0.37 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE E 90 TYR 0.018 0.002 TYR H 86 *********************** 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 402 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 THR cc_start: 0.8576 (m) cc_final: 0.8289 (p) REVERT: A 184 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 102 TYR cc_start: 0.8670 (m-80) cc_final: 0.8334 (m-80) REVERT: B 112 TYR cc_start: 0.8541 (p90) cc_final: 0.7703 (p90) REVERT: B 125 TYR cc_start: 0.8472 (m-80) cc_final: 0.7649 (m-80) REVERT: B 141 VAL cc_start: 0.8615 (t) cc_final: 0.8245 (m) REVERT: B 165 LEU cc_start: 0.8581 (tp) cc_final: 0.8368 (tt) REVERT: B 194 MET cc_start: 0.8470 (mtm) cc_final: 0.8210 (mtp) REVERT: C 76 THR cc_start: 0.8803 (m) cc_final: 0.8435 (p) REVERT: C 93 MET cc_start: 0.8485 (mmp) cc_final: 0.8074 (mmm) REVERT: C 102 TYR cc_start: 0.8794 (m-80) cc_final: 0.8038 (m-80) REVERT: C 156 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8289 (tt) REVERT: C 187 VAL cc_start: 0.8585 (t) cc_final: 0.8292 (p) REVERT: C 194 MET cc_start: 0.8285 (mtm) cc_final: 0.7905 (mtp) REVERT: F 51 ASN cc_start: 0.8562 (t0) cc_final: 0.8080 (t0) REVERT: F 177 THR cc_start: 0.8418 (m) cc_final: 0.8033 (p) REVERT: G 97 VAL cc_start: 0.8352 (t) cc_final: 0.8059 (m) REVERT: G 102 TYR cc_start: 0.8805 (m-80) cc_final: 0.8282 (m-80) REVERT: G 152 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8281 (p) REVERT: I 67 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7822 (mm-40) REVERT: I 78 GLN cc_start: 0.7927 (tt0) cc_final: 0.7561 (tm-30) outliers start: 52 outliers final: 44 residues processed: 374 average time/residue: 0.2076 time to fit residues: 126.6522 Evaluate side-chains 394 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 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 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 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 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 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 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL 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 123 THR 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 96 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 99 optimal weight: 0.1980 chunk 106 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN C 49 ASN D 129 GLN F 129 GLN F 132 GLN F 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16074 Z= 0.199 Angle : 0.746 9.153 22149 Z= 0.318 Chirality : 0.046 0.356 3240 Planarity : 0.004 0.041 2394 Dihedral : 12.080 103.725 6903 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.49 % Allowed : 17.45 % Favored : 79.06 % 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: 0.27 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.04 (0.19), residues: 729 loop : 0.48 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE H 90 TYR 0.020 0.001 TYR I 102 *********************** 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 380 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 152 THR cc_start: 0.8539 (m) cc_final: 0.8241 (p) REVERT: A 184 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 102 TYR cc_start: 0.8657 (m-80) cc_final: 0.8308 (m-80) REVERT: B 112 TYR cc_start: 0.8533 (p90) cc_final: 0.7687 (p90) REVERT: B 125 TYR cc_start: 0.8461 (m-80) cc_final: 0.7658 (m-80) REVERT: B 141 VAL cc_start: 0.8614 (t) cc_final: 0.8257 (m) REVERT: B 165 LEU cc_start: 0.8578 (tp) cc_final: 0.8354 (tt) REVERT: B 194 MET cc_start: 0.8453 (mtm) cc_final: 0.8187 (mtp) REVERT: C 76 THR cc_start: 0.8780 (m) cc_final: 0.8403 (p) REVERT: C 93 MET cc_start: 0.8455 (mmp) cc_final: 0.8089 (mmm) REVERT: C 102 TYR cc_start: 0.8782 (m-80) cc_final: 0.8035 (m-80) REVERT: C 125 TYR cc_start: 0.8417 (m-80) cc_final: 0.8165 (m-80) REVERT: C 156 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 187 VAL cc_start: 0.8566 (t) cc_final: 0.8279 (p) REVERT: C 194 MET cc_start: 0.8276 (mtm) cc_final: 0.7910 (mtp) REVERT: F 38 VAL cc_start: 0.7619 (p) cc_final: 0.7204 (m) REVERT: F 51 ASN cc_start: 0.8539 (t0) cc_final: 0.8055 (t0) REVERT: F 177 THR cc_start: 0.8418 (m) cc_final: 0.8036 (p) REVERT: G 102 TYR cc_start: 0.8795 (m-80) cc_final: 0.8257 (m-80) REVERT: G 152 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8295 (p) REVERT: G 194 MET cc_start: 0.8246 (mtm) cc_final: 0.7762 (mtp) REVERT: H 58 SER cc_start: 0.8354 (m) cc_final: 0.8073 (p) REVERT: I 51 ASN cc_start: 0.7789 (t0) cc_final: 0.7530 (t0) REVERT: I 58 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7956 (m) REVERT: I 67 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7727 (mm-40) REVERT: I 78 GLN cc_start: 0.7976 (tt0) cc_final: 0.7622 (tm-30) REVERT: I 125 TYR cc_start: 0.8278 (m-10) cc_final: 0.7576 (m-80) outliers start: 49 outliers final: 39 residues processed: 357 average time/residue: 0.2122 time to fit residues: 124.0481 Evaluate side-chains 368 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 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 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 98 SER Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL 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 123 THR 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 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 145 optimal weight: 0.2980 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN F 120 GLN F 129 GLN F 132 GLN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16074 Z= 0.269 Angle : 0.770 9.297 22149 Z= 0.330 Chirality : 0.048 0.343 3240 Planarity : 0.005 0.041 2394 Dihedral : 11.948 102.986 6903 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.49 % Allowed : 17.59 % Favored : 78.92 % 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: 0.02 (0.19), residues: 729 loop : 0.46 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE F 90 TYR 0.018 0.002 TYR I 102 *********************** 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 368 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 319 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 THR cc_start: 0.8539 (m) cc_final: 0.8248 (p) REVERT: A 184 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8471 (p) REVERT: B 102 TYR cc_start: 0.8660 (m-80) cc_final: 0.8304 (m-80) REVERT: B 112 TYR cc_start: 0.8519 (p90) cc_final: 0.7625 (p90) REVERT: B 125 TYR cc_start: 0.8467 (m-80) cc_final: 0.7648 (m-80) REVERT: B 141 VAL cc_start: 0.8634 (t) cc_final: 0.8265 (m) REVERT: B 165 LEU cc_start: 0.8580 (tp) cc_final: 0.8362 (tt) REVERT: B 194 MET cc_start: 0.8451 (mtm) cc_final: 0.8181 (mtp) REVERT: C 93 MET cc_start: 0.8458 (mmp) cc_final: 0.8055 (mmm) REVERT: C 102 TYR cc_start: 0.8806 (m-80) cc_final: 0.8109 (m-80) REVERT: C 156 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8227 (tt) REVERT: C 187 VAL cc_start: 0.8582 (t) cc_final: 0.8302 (p) REVERT: C 194 MET cc_start: 0.8286 (mtm) cc_final: 0.7910 (mtp) REVERT: F 38 VAL cc_start: 0.7663 (p) cc_final: 0.7224 (m) REVERT: F 51 ASN cc_start: 0.8584 (t0) cc_final: 0.8074 (t0) REVERT: F 177 THR cc_start: 0.8421 (m) cc_final: 0.8038 (p) REVERT: G 97 VAL cc_start: 0.8334 (t) cc_final: 0.8023 (m) REVERT: G 102 TYR cc_start: 0.8783 (m-80) cc_final: 0.8216 (m-80) REVERT: G 152 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8291 (p) REVERT: G 194 MET cc_start: 0.8244 (mtm) cc_final: 0.7702 (mtp) REVERT: I 58 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7897 (m) REVERT: I 67 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7731 (mm-40) REVERT: I 78 GLN cc_start: 0.8002 (tt0) cc_final: 0.7643 (tm-30) outliers start: 49 outliers final: 41 residues processed: 343 average time/residue: 0.2132 time to fit residues: 119.3586 Evaluate side-chains 360 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 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 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 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 98 SER Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL 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 H residue 188 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 79 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 F 129 GLN H 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16074 Z= 0.281 Angle : 0.773 9.244 22149 Z= 0.332 Chirality : 0.048 0.344 3240 Planarity : 0.005 0.042 2394 Dihedral : 11.902 102.642 6903 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.42 % Allowed : 17.74 % 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: 0.23 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.02 (0.19), residues: 729 loop : 0.44 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE H 189 TYR 0.018 0.002 TYR H 86 ********************** 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 372 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 THR cc_start: 0.8534 (m) cc_final: 0.8244 (p) REVERT: A 184 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8455 (p) REVERT: B 102 TYR cc_start: 0.8673 (m-80) cc_final: 0.8306 (m-80) REVERT: B 112 TYR cc_start: 0.8522 (p90) cc_final: 0.7692 (p90) REVERT: B 125 TYR cc_start: 0.8468 (m-80) cc_final: 0.7643 (m-80) REVERT: B 141 VAL cc_start: 0.8635 (t) cc_final: 0.8268 (m) REVERT: B 165 LEU cc_start: 0.8575 (tp) cc_final: 0.8374 (tt) REVERT: B 194 MET cc_start: 0.8450 (mtm) cc_final: 0.8175 (mtp) REVERT: C 93 MET cc_start: 0.8458 (mmp) cc_final: 0.8053 (mmm) REVERT: C 102 TYR cc_start: 0.8804 (m-80) cc_final: 0.8106 (m-80) REVERT: C 156 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8230 (tt) REVERT: C 187 VAL cc_start: 0.8577 (t) cc_final: 0.8292 (p) REVERT: C 194 MET cc_start: 0.8291 (mtm) cc_final: 0.7919 (mtp) REVERT: F 38 VAL cc_start: 0.7668 (p) cc_final: 0.7225 (m) REVERT: F 51 ASN cc_start: 0.8567 (t0) cc_final: 0.8065 (t0) REVERT: F 177 THR cc_start: 0.8428 (m) cc_final: 0.8045 (p) REVERT: G 97 VAL cc_start: 0.8335 (t) cc_final: 0.8035 (m) REVERT: G 102 TYR cc_start: 0.8779 (m-80) cc_final: 0.8215 (m-80) REVERT: G 152 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8290 (p) REVERT: G 194 MET cc_start: 0.8243 (mtm) cc_final: 0.7701 (mtp) REVERT: I 67 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7734 (mm-40) REVERT: I 78 GLN cc_start: 0.8024 (tt0) cc_final: 0.7665 (tm-30) outliers start: 48 outliers final: 43 residues processed: 348 average time/residue: 0.2405 time to fit residues: 136.9195 Evaluate side-chains 367 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 124 LEU Chi-restraints excluded: chain C residue 138 LYS 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 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 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 197 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE 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 H residue 188 ASN Chi-restraints excluded: chain I residue 79 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 53 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 116 ASN E 129 GLN F 129 GLN H 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093966 restraints weight = 23544.447| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.37 r_work: 0.2968 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 0.039 16074 Z= 0.288 Angle : 0.777 9.242 22149 Z= 0.334 Chirality : 0.048 0.344 3240 Planarity : 0.005 0.042 2394 Dihedral : 11.844 102.385 6903 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.49 % Allowed : 17.59 % Favored : 78.92 % 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 (0.23), residues: 1629 helix: None (None), residues: 0 sheet: -0.13 (0.19), residues: 774 loop : 0.65 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE E 90 TYR 0.021 0.002 TYR F 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.55 seconds wall clock time: 67 minutes 40.47 seconds (4060.47 seconds total)