Starting phenix.real_space_refine on Wed Mar 4 19:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_13546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_13546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_13546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_13546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnb_13546/03_2026/7pnb_13546.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.73, per 1000 atoms: 0.24 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: 2.21 Conformation dependent library (CDL) restraints added in 604.5 milliseconds 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: 0.54 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: 2.43 Time building geometry restraints manager: 2.55 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: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' selection = chain 't' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.113 16333 Z= 0.765 Angle : 2.026 21.586 22905 Z= 0.956 Chirality : 0.122 0.920 3240 Planarity : 0.028 0.308 2394 Dihedral : 18.905 116.601 9711 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.044 0.010 TYR F 89 PHE 0.041 0.011 PHE D 44 Details of bonding type rmsd covalent geometry : bond 0.01307 (16074) covalent geometry : angle 1.74589 (22149) hydrogen bonds : bond 0.14660 ( 450) hydrogen bonds : angle 8.83808 ( 1275) glycosidic custom : bond 0.01421 ( 45) glycosidic custom : angle 9.95793 ( 135) Misc. bond : bond 0.10510 ( 7) link_ALPHA1-4 : bond 0.03365 ( 45) link_ALPHA1-4 : angle 4.59179 ( 135) link_ALPHA1-6 : bond 0.00280 ( 36) link_ALPHA1-6 : angle 1.68717 ( 108) link_BETA1-4 : bond 0.01557 ( 81) link_BETA1-4 : angle 4.51231 ( 243) link_NAG-ASN : bond 0.03142 ( 45) link_NAG-ASN : angle 6.09617 ( 135) *********************** 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 : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.8640 (m-80) cc_final: 0.8297 (m-80) REVERT: A 87 ASN cc_start: 0.8783 (m-40) cc_final: 0.8580 (m110) REVERT: A 129 GLN cc_start: 0.8412 (tt0) cc_final: 0.8150 (tt0) REVERT: A 152 THR cc_start: 0.8561 (m) cc_final: 0.8254 (p) REVERT: B 102 TYR cc_start: 0.8575 (m-80) cc_final: 0.8177 (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: 0.8045 (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: 0.8493 (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: 0.8278 (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: 0.8216 (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: 0.8157 (mt0) REVERT: F 125 TYR cc_start: 0.8699 (m-80) cc_final: 0.8096 (m-80) REVERT: F 151 SER cc_start: 0.8431 (p) cc_final: 0.8223 (t) REVERT: F 164 SER cc_start: 0.8551 (m) cc_final: 0.8164 (p) REVERT: F 177 THR cc_start: 0.8356 (m) cc_final: 0.8153 (t) REVERT: F 178 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: G 58 SER cc_start: 0.8672 (m) cc_final: 0.8154 (p) REVERT: G 97 VAL cc_start: 0.8470 (t) cc_final: 0.8237 (m) REVERT: G 102 TYR cc_start: 0.8870 (m-80) cc_final: 0.8405 (m-80) REVERT: G 194 MET cc_start: 0.8422 (mtm) cc_final: 0.8177 (mtp) REVERT: G 195 THR cc_start: 0.8573 (p) cc_final: 0.8032 (t) REVERT: G 201 ILE cc_start: 0.8318 (mm) cc_final: 0.7986 (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: 0.8325 (m-40) REVERT: H 135 TYR cc_start: 0.8483 (m-80) cc_final: 0.8248 (m-10) REVERT: H 161 TYR cc_start: 0.8475 (m-80) cc_final: 0.7855 (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: 0.7132 (m-80) REVERT: I 161 TYR cc_start: 0.8249 (m-80) cc_final: 0.8037 (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: 0.0982 time to fit residues: 63.7678 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 : 0.517 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 120 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097702 restraints weight = 22199.125| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.26 r_work: 0.3040 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16333 Z= 0.190 Angle : 1.018 9.638 22905 Z= 0.410 Chirality : 0.053 0.282 3240 Planarity : 0.005 0.047 2394 Dihedral : 15.749 107.102 6910 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.42 % Allowed : 9.97 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.27 (0.18), residues: 711 loop : 0.18 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.032 0.002 TYR H 27 PHE 0.018 0.002 PHE F 90 Details of bonding type rmsd covalent geometry : bond 0.00404 (16074) covalent geometry : angle 0.90149 (22149) hydrogen bonds : bond 0.03118 ( 450) hydrogen bonds : angle 7.17657 ( 1275) glycosidic custom : bond 0.00495 ( 45) glycosidic custom : angle 3.27096 ( 135) Misc. bond : bond 0.00186 ( 7) link_ALPHA1-4 : bond 0.00964 ( 45) link_ALPHA1-4 : angle 2.61919 ( 135) link_ALPHA1-6 : bond 0.00608 ( 36) link_ALPHA1-6 : angle 1.40172 ( 108) link_BETA1-4 : bond 0.00442 ( 81) link_BETA1-4 : angle 2.38892 ( 243) link_NAG-ASN : bond 0.00456 ( 45) link_NAG-ASN : angle 3.63526 ( 135) *********************** 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 392 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 344 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 152 THR cc_start: 0.8361 (m) cc_final: 0.7899 (p) REVERT: A 181 ASP cc_start: 0.7967 (t0) cc_final: 0.7746 (t70) REVERT: B 67 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7422 (mm110) REVERT: B 93 MET cc_start: 0.8265 (mmm) cc_final: 0.7901 (mmm) REVERT: B 102 TYR cc_start: 0.8198 (m-80) cc_final: 0.7674 (m-80) REVERT: B 112 TYR cc_start: 0.8208 (p90) cc_final: 0.7404 (p90) REVERT: B 125 TYR cc_start: 0.8459 (m-80) cc_final: 0.7891 (m-80) REVERT: B 194 MET cc_start: 0.8365 (mtm) cc_final: 0.8038 (mtp) REVERT: C 58 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 93 MET cc_start: 0.8411 (mmp) cc_final: 0.7976 (mmm) REVERT: C 102 TYR cc_start: 0.8376 (m-80) cc_final: 0.7525 (m-80) REVERT: C 104 TYR cc_start: 0.8608 (p90) cc_final: 0.8392 (p90) REVERT: C 166 LEU cc_start: 0.8203 (tp) cc_final: 0.8000 (tt) REVERT: C 177 THR cc_start: 0.8387 (m) cc_final: 0.7953 (p) REVERT: C 181 ASP cc_start: 0.7738 (t0) cc_final: 0.7523 (t0) REVERT: C 194 MET cc_start: 0.8175 (mtm) cc_final: 0.7875 (mtm) REVERT: D 29 TYR cc_start: 0.8142 (m-80) cc_final: 0.7939 (m-80) REVERT: D 79 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8282 (m) REVERT: E 42 MET cc_start: 0.8425 (ptm) cc_final: 0.8115 (ptm) REVERT: E 46 ILE cc_start: 0.8459 (mt) cc_final: 0.8234 (mm) REVERT: E 58 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8316 (p) REVERT: E 69 SER cc_start: 0.8078 (t) cc_final: 0.7789 (m) REVERT: E 93 MET cc_start: 0.8191 (mmp) cc_final: 0.7864 (mmt) REVERT: E 125 TYR cc_start: 0.8468 (m-80) cc_final: 0.7289 (m-80) REVERT: F 25 VAL cc_start: 0.8535 (t) cc_final: 0.8228 (p) REVERT: F 29 TYR cc_start: 0.8140 (m-80) cc_final: 0.7760 (m-80) REVERT: F 38 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7578 (m) REVERT: F 102 TYR cc_start: 0.8393 (m-80) cc_final: 0.8156 (m-10) REVERT: F 125 TYR cc_start: 0.8837 (m-80) cc_final: 0.8288 (m-80) REVERT: F 177 THR cc_start: 0.8060 (m) cc_final: 0.7489 (p) REVERT: F 178 PRO cc_start: 0.8624 (Cg_exo) cc_final: 0.8386 (Cg_endo) REVERT: F 180 ASN cc_start: 0.7951 (p0) cc_final: 0.7652 (p0) REVERT: G 58 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8030 (p) REVERT: G 91 ASN cc_start: 0.8470 (t0) cc_final: 0.8242 (t0) REVERT: G 93 MET cc_start: 0.8325 (tpp) cc_final: 0.7780 (tpp) REVERT: G 102 TYR cc_start: 0.8374 (m-80) cc_final: 0.7760 (m-80) REVERT: G 152 THR cc_start: 0.8402 (m) cc_final: 0.8057 (p) REVERT: G 194 MET cc_start: 0.8323 (mtm) cc_final: 0.8087 (mtp) REVERT: H 27 TYR cc_start: 0.8531 (m-10) cc_final: 0.8297 (m-10) REVERT: H 38 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (m) REVERT: H 47 GLN cc_start: 0.8402 (mt0) cc_final: 0.7913 (mt0) REVERT: H 58 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7581 (m) REVERT: H 78 GLN cc_start: 0.7300 (tt0) cc_final: 0.6966 (tm-30) REVERT: H 130 GLN cc_start: 0.8276 (mp10) cc_final: 0.7980 (mp10) REVERT: H 148 THR cc_start: 0.8314 (p) cc_final: 0.7949 (p) REVERT: H 157 ASN cc_start: 0.7203 (m-40) cc_final: 0.6962 (m-40) REVERT: H 161 TYR cc_start: 0.8206 (m-80) cc_final: 0.7645 (m-80) REVERT: I 58 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7663 (m) REVERT: I 59 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7121 (m-40) REVERT: I 89 TYR cc_start: 0.7593 (m-80) cc_final: 0.7328 (m-80) REVERT: I 125 TYR cc_start: 0.7878 (m-80) cc_final: 0.7678 (m-10) REVERT: I 186 THR cc_start: 0.8296 (m) cc_final: 0.7854 (p) outliers start: 48 outliers final: 23 residues processed: 379 average time/residue: 0.0969 time to fit residues: 60.6806 Evaluate side-chains 359 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 58 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 58 SER Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 0.0020 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 120 GLN E 59 ASN E 120 GLN F 120 GLN F 132 GLN H 65 ASN H 132 GLN H 188 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097339 restraints weight = 22452.083| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.31 r_work: 0.3036 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16333 Z= 0.166 Angle : 0.924 9.565 22905 Z= 0.369 Chirality : 0.048 0.225 3240 Planarity : 0.005 0.048 2394 Dihedral : 13.233 106.264 6907 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.49 % Allowed : 13.18 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.12 (0.19), residues: 729 loop : 0.30 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR H 86 PHE 0.018 0.002 PHE D 92 Details of bonding type rmsd covalent geometry : bond 0.00366 (16074) covalent geometry : angle 0.83433 (22149) hydrogen bonds : bond 0.02732 ( 450) hydrogen bonds : angle 6.72815 ( 1275) glycosidic custom : bond 0.00283 ( 45) glycosidic custom : angle 2.80181 ( 135) Misc. bond : bond 0.00111 ( 7) link_ALPHA1-4 : bond 0.00798 ( 45) link_ALPHA1-4 : angle 2.34448 ( 135) link_ALPHA1-6 : bond 0.00643 ( 36) link_ALPHA1-6 : angle 1.35372 ( 108) link_BETA1-4 : bond 0.00327 ( 81) link_BETA1-4 : angle 2.09632 ( 243) link_NAG-ASN : bond 0.00336 ( 45) link_NAG-ASN : angle 2.81006 ( 135) *********************** 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 413 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.8434 (t) cc_final: 0.7906 (p) REVERT: A 130 GLN cc_start: 0.8556 (mp-120) cc_final: 0.8326 (mp10) REVERT: A 152 THR cc_start: 0.8375 (m) cc_final: 0.7935 (p) REVERT: B 67 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7395 (mm110) REVERT: B 102 TYR cc_start: 0.8191 (m-80) cc_final: 0.7689 (m-80) REVERT: B 125 TYR cc_start: 0.8452 (m-80) cc_final: 0.7681 (m-80) REVERT: B 194 MET cc_start: 0.8381 (mtm) cc_final: 0.8042 (mtp) REVERT: C 93 MET cc_start: 0.8398 (mmp) cc_final: 0.7970 (mmm) REVERT: C 102 TYR cc_start: 0.8415 (m-80) cc_final: 0.7577 (m-80) REVERT: C 181 ASP cc_start: 0.7827 (t0) cc_final: 0.7575 (t0) REVERT: C 194 MET cc_start: 0.8176 (mtm) cc_final: 0.7920 (mtm) REVERT: D 104 TYR cc_start: 0.8479 (p90) cc_final: 0.8238 (p90) REVERT: E 42 MET cc_start: 0.8332 (ptm) cc_final: 0.8077 (ptm) REVERT: E 69 SER cc_start: 0.8003 (t) cc_final: 0.7732 (m) REVERT: E 125 TYR cc_start: 0.8508 (m-80) cc_final: 0.7331 (m-80) REVERT: F 38 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7481 (m) REVERT: F 59 ASN cc_start: 0.8240 (t0) cc_final: 0.7846 (t0) REVERT: F 102 TYR cc_start: 0.8442 (m-80) cc_final: 0.8173 (m-10) REVERT: F 125 TYR cc_start: 0.8842 (m-80) cc_final: 0.8487 (m-80) REVERT: F 177 THR cc_start: 0.8080 (m) cc_final: 0.7486 (p) REVERT: F 178 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8325 (Cg_endo) REVERT: G 93 MET cc_start: 0.8270 (tpp) cc_final: 0.7742 (tpp) REVERT: G 102 TYR cc_start: 0.8374 (m-80) cc_final: 0.7759 (m-80) REVERT: G 152 THR cc_start: 0.8438 (m) cc_final: 0.8016 (p) REVERT: G 194 MET cc_start: 0.8323 (mtm) cc_final: 0.8079 (mtp) REVERT: G 195 THR cc_start: 0.8467 (p) cc_final: 0.7582 (t) REVERT: H 27 TYR cc_start: 0.8571 (m-10) cc_final: 0.8272 (m-10) REVERT: H 38 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (m) REVERT: H 47 GLN cc_start: 0.8422 (mt0) cc_final: 0.7991 (mt0) REVERT: H 58 SER cc_start: 0.7976 (m) cc_final: 0.7723 (m) REVERT: H 128 ASN cc_start: 0.7949 (t0) cc_final: 0.7699 (m-40) REVERT: H 129 GLN cc_start: 0.8149 (tt0) cc_final: 0.7889 (tt0) REVERT: H 130 GLN cc_start: 0.8191 (mp10) cc_final: 0.7914 (mp10) REVERT: H 148 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7855 (p) REVERT: H 164 SER cc_start: 0.8346 (m) cc_final: 0.8106 (m) REVERT: I 59 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: I 67 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6786 (mm-40) REVERT: I 78 GLN cc_start: 0.7314 (tt0) cc_final: 0.7050 (tt0) REVERT: I 89 TYR cc_start: 0.7625 (m-80) cc_final: 0.7374 (m-80) REVERT: I 125 TYR cc_start: 0.7872 (m-80) cc_final: 0.6531 (m-80) REVERT: I 186 THR cc_start: 0.8309 (m) cc_final: 0.7804 (p) outliers start: 49 outliers final: 33 residues processed: 388 average time/residue: 0.0962 time to fit residues: 61.6667 Evaluate side-chains 388 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 351 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 SER 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 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 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN C 47 GLN D 129 GLN E 120 GLN F 47 GLN F 120 GLN F 132 GLN G 87 ASN G 188 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096887 restraints weight = 22305.993| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.29 r_work: 0.3025 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 16333 Z= 0.203 Angle : 0.912 13.107 22905 Z= 0.369 Chirality : 0.048 0.406 3240 Planarity : 0.005 0.047 2394 Dihedral : 12.559 106.116 6906 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.12 (0.19), residues: 729 loop : 0.32 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR H 86 PHE 0.026 0.003 PHE A 90 Details of bonding type rmsd covalent geometry : bond 0.00456 (16074) covalent geometry : angle 0.81576 (22149) hydrogen bonds : bond 0.02876 ( 450) hydrogen bonds : angle 6.63455 ( 1275) glycosidic custom : bond 0.00254 ( 45) glycosidic custom : angle 2.70948 ( 135) Misc. bond : bond 0.00169 ( 7) link_ALPHA1-4 : bond 0.00817 ( 45) link_ALPHA1-4 : angle 2.57694 ( 135) link_ALPHA1-6 : bond 0.00552 ( 36) link_ALPHA1-6 : angle 1.45266 ( 108) link_BETA1-4 : bond 0.00283 ( 81) link_BETA1-4 : angle 2.08103 ( 243) link_NAG-ASN : bond 0.00340 ( 45) link_NAG-ASN : angle 2.92537 ( 135) *********************** 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 395 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.519 Fit side-chains REVERT: A 29 TYR cc_start: 0.8098 (m-80) cc_final: 0.7812 (m-80) REVERT: A 152 THR cc_start: 0.8365 (m) cc_final: 0.7926 (p) REVERT: B 65 ASN cc_start: 0.8235 (t0) cc_final: 0.8026 (t0) REVERT: B 67 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7431 (mm110) REVERT: B 93 MET cc_start: 0.8115 (mmm) cc_final: 0.7649 (mmm) REVERT: B 102 TYR cc_start: 0.8257 (m-80) cc_final: 0.7797 (m-80) REVERT: B 125 TYR cc_start: 0.8438 (m-80) cc_final: 0.7677 (m-80) REVERT: B 141 VAL cc_start: 0.8486 (t) cc_final: 0.8071 (m) REVERT: B 165 LEU cc_start: 0.8460 (tp) cc_final: 0.8179 (tt) REVERT: B 194 MET cc_start: 0.8416 (mtm) cc_final: 0.8129 (mtp) REVERT: C 93 MET cc_start: 0.8399 (mmp) cc_final: 0.8003 (mmm) REVERT: C 102 TYR cc_start: 0.8414 (m-80) cc_final: 0.7524 (m-80) REVERT: C 112 TYR cc_start: 0.8444 (p90) cc_final: 0.8103 (p90) REVERT: C 156 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 194 MET cc_start: 0.8179 (mtm) cc_final: 0.7871 (mtm) REVERT: D 104 TYR cc_start: 0.8426 (p90) cc_final: 0.8167 (p90) REVERT: E 125 TYR cc_start: 0.8517 (m-80) cc_final: 0.8265 (m-80) REVERT: F 38 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7422 (m) REVERT: F 59 ASN cc_start: 0.8231 (t0) cc_final: 0.7852 (t0) REVERT: F 102 TYR cc_start: 0.8423 (m-80) cc_final: 0.8156 (m-10) REVERT: F 125 TYR cc_start: 0.8878 (m-80) cc_final: 0.8678 (m-80) REVERT: F 177 THR cc_start: 0.8085 (m) cc_final: 0.7489 (p) REVERT: F 178 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8312 (t) cc_final: 0.7955 (m) REVERT: G 102 TYR cc_start: 0.8359 (m-80) cc_final: 0.7690 (m-80) REVERT: G 152 THR cc_start: 0.8433 (m) cc_final: 0.8002 (p) REVERT: G 194 MET cc_start: 0.8368 (mtm) cc_final: 0.8059 (mtp) REVERT: G 195 THR cc_start: 0.8457 (p) cc_final: 0.7503 (t) REVERT: H 27 TYR cc_start: 0.8550 (m-10) cc_final: 0.8215 (m-10) REVERT: H 38 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7792 (m) REVERT: H 47 GLN cc_start: 0.8441 (mt0) cc_final: 0.8050 (mt0) REVERT: H 58 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7773 (m) REVERT: H 128 ASN cc_start: 0.7942 (t0) cc_final: 0.7683 (m-40) REVERT: H 130 GLN cc_start: 0.8216 (mp10) cc_final: 0.7973 (mp10) REVERT: H 148 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7856 (p) REVERT: H 155 GLN cc_start: 0.8539 (tt0) cc_final: 0.8202 (tt0) REVERT: H 164 SER cc_start: 0.8387 (m) cc_final: 0.8142 (m) REVERT: I 51 ASN cc_start: 0.7914 (t0) cc_final: 0.7625 (t0) REVERT: I 58 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7759 (m) REVERT: I 59 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7190 (m-40) REVERT: I 67 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6738 (mm-40) REVERT: I 78 GLN cc_start: 0.7362 (tt0) cc_final: 0.7116 (tt0) REVERT: I 89 TYR cc_start: 0.7588 (m-80) cc_final: 0.7289 (m-80) REVERT: I 102 TYR cc_start: 0.8095 (m-80) cc_final: 0.7489 (m-80) REVERT: I 125 TYR cc_start: 0.7890 (m-80) cc_final: 0.6465 (m-80) outliers start: 52 outliers final: 38 residues processed: 368 average time/residue: 0.0947 time to fit residues: 57.7948 Evaluate side-chains 380 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain 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 D residue 156 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 GLN E 171 GLN F 120 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 = 0.3470 r_free = 0.3470 target = 0.116727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094648 restraints weight = 22436.943| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.33 r_work: 0.3022 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16333 Z= 0.211 Angle : 0.890 12.653 22905 Z= 0.363 Chirality : 0.047 0.370 3240 Planarity : 0.005 0.045 2394 Dihedral : 12.374 105.478 6906 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.34 % Allowed : 14.67 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.05 (0.19), residues: 729 loop : 0.30 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR H 135 PHE 0.024 0.003 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00477 (16074) covalent geometry : angle 0.79446 (22149) hydrogen bonds : bond 0.02918 ( 450) hydrogen bonds : angle 6.59242 ( 1275) glycosidic custom : bond 0.00240 ( 45) glycosidic custom : angle 2.61145 ( 135) Misc. bond : bond 0.00173 ( 7) link_ALPHA1-4 : bond 0.00778 ( 45) link_ALPHA1-4 : angle 2.55473 ( 135) link_ALPHA1-6 : bond 0.00532 ( 36) link_ALPHA1-6 : angle 1.46913 ( 108) link_BETA1-4 : bond 0.00241 ( 81) link_BETA1-4 : angle 2.01809 ( 243) link_NAG-ASN : bond 0.00394 ( 45) link_NAG-ASN : angle 2.90131 ( 135) *********************** 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 420 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 359 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8079 (m-80) cc_final: 0.7791 (m-80) REVERT: A 134 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 152 THR cc_start: 0.8345 (m) cc_final: 0.7934 (p) REVERT: B 58 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8305 (p) REVERT: B 67 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7361 (mm110) REVERT: B 102 TYR cc_start: 0.8297 (m-80) cc_final: 0.7814 (m-80) REVERT: B 125 TYR cc_start: 0.8423 (m-80) cc_final: 0.7645 (m-80) REVERT: B 141 VAL cc_start: 0.8502 (t) cc_final: 0.8092 (m) REVERT: B 165 LEU cc_start: 0.8441 (tp) cc_final: 0.8189 (tt) REVERT: B 194 MET cc_start: 0.8431 (mtm) cc_final: 0.8127 (mtp) REVERT: C 76 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8089 (p) REVERT: C 93 MET cc_start: 0.8394 (mmp) cc_final: 0.7938 (mmm) REVERT: C 102 TYR cc_start: 0.8419 (m-80) cc_final: 0.7542 (m-80) REVERT: C 112 TYR cc_start: 0.8437 (p90) cc_final: 0.8142 (p90) REVERT: C 156 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8212 (tt) REVERT: C 166 LEU cc_start: 0.8208 (tp) cc_final: 0.7996 (tt) REVERT: C 187 VAL cc_start: 0.8542 (t) cc_final: 0.8028 (p) REVERT: D 201 ILE cc_start: 0.8459 (mp) cc_final: 0.8254 (mm) REVERT: E 125 TYR cc_start: 0.8525 (m-80) cc_final: 0.8237 (m-80) REVERT: F 38 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7316 (m) REVERT: F 102 TYR cc_start: 0.8445 (m-80) cc_final: 0.8191 (m-10) REVERT: F 177 THR cc_start: 0.8096 (m) cc_final: 0.7500 (p) REVERT: F 178 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.8332 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8306 (t) cc_final: 0.7950 (m) REVERT: G 102 TYR cc_start: 0.8335 (m-80) cc_final: 0.7730 (m-80) REVERT: G 152 THR cc_start: 0.8436 (m) cc_final: 0.8148 (t) REVERT: G 194 MET cc_start: 0.8375 (mtm) cc_final: 0.8018 (mtp) REVERT: H 38 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7793 (m) REVERT: H 58 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7872 (m) REVERT: H 128 ASN cc_start: 0.7985 (t0) cc_final: 0.7750 (m-40) REVERT: H 130 GLN cc_start: 0.8216 (mp10) cc_final: 0.7986 (mp10) REVERT: H 148 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7754 (p) REVERT: H 155 GLN cc_start: 0.8584 (tt0) cc_final: 0.8333 (tt0) REVERT: I 51 ASN cc_start: 0.7967 (t0) cc_final: 0.7639 (t0) REVERT: I 58 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7799 (m) REVERT: I 59 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7193 (m-40) REVERT: I 67 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6893 (mm-40) REVERT: I 78 GLN cc_start: 0.7440 (tt0) cc_final: 0.7157 (tm-30) REVERT: I 89 TYR cc_start: 0.7577 (m-80) cc_final: 0.7259 (m-80) REVERT: I 102 TYR cc_start: 0.8102 (m-80) cc_final: 0.7489 (m-80) outliers start: 61 outliers final: 44 residues processed: 387 average time/residue: 0.0926 time to fit residues: 59.9723 Evaluate side-chains 402 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 134 VAL 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 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 69 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.0270 chunk 94 optimal weight: 0.0870 chunk 143 optimal weight: 0.0870 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 G 87 ASN H 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097618 restraints weight = 22164.807| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.30 r_work: 0.3049 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16333 Z= 0.140 Angle : 0.835 12.382 22905 Z= 0.339 Chirality : 0.046 0.351 3240 Planarity : 0.004 0.042 2394 Dihedral : 12.246 104.676 6906 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.99 % Allowed : 16.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.13 (0.19), residues: 729 loop : 0.42 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR H 86 PHE 0.018 0.002 PHE H 90 Details of bonding type rmsd covalent geometry : bond 0.00308 (16074) covalent geometry : angle 0.74518 (22149) hydrogen bonds : bond 0.02490 ( 450) hydrogen bonds : angle 6.37547 ( 1275) glycosidic custom : bond 0.00226 ( 45) glycosidic custom : angle 2.47946 ( 135) Misc. bond : bond 0.00072 ( 7) link_ALPHA1-4 : bond 0.00763 ( 45) link_ALPHA1-4 : angle 2.45863 ( 135) link_ALPHA1-6 : bond 0.00589 ( 36) link_ALPHA1-6 : angle 1.41258 ( 108) link_BETA1-4 : bond 0.00234 ( 81) link_BETA1-4 : angle 1.76321 ( 243) link_NAG-ASN : bond 0.00377 ( 45) link_NAG-ASN : angle 2.77544 ( 135) *********************** 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 397 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8093 (m-80) cc_final: 0.7862 (m-80) REVERT: A 65 ASN cc_start: 0.8138 (t0) cc_final: 0.7901 (t0) REVERT: A 152 THR cc_start: 0.8323 (m) cc_final: 0.7869 (p) REVERT: A 155 GLN cc_start: 0.8421 (tt0) cc_final: 0.8187 (tt0) REVERT: B 102 TYR cc_start: 0.8228 (m-80) cc_final: 0.7735 (m-80) REVERT: B 112 TYR cc_start: 0.8181 (p90) cc_final: 0.7093 (p90) REVERT: B 125 TYR cc_start: 0.8410 (m-80) cc_final: 0.7669 (m-80) REVERT: B 141 VAL cc_start: 0.8522 (t) cc_final: 0.8110 (m) REVERT: B 165 LEU cc_start: 0.8451 (tp) cc_final: 0.8180 (tt) REVERT: B 180 ASN cc_start: 0.8123 (p0) cc_final: 0.7874 (p0) REVERT: B 194 MET cc_start: 0.8402 (mtm) cc_final: 0.8090 (mtp) REVERT: C 76 THR cc_start: 0.8531 (m) cc_final: 0.8047 (p) REVERT: C 93 MET cc_start: 0.8345 (mmp) cc_final: 0.7921 (mmm) REVERT: C 102 TYR cc_start: 0.8413 (m-80) cc_final: 0.7550 (m-80) REVERT: C 112 TYR cc_start: 0.8424 (p90) cc_final: 0.8169 (p90) REVERT: C 125 TYR cc_start: 0.8383 (m-80) cc_final: 0.8148 (m-80) REVERT: C 152 THR cc_start: 0.8403 (m) cc_final: 0.8167 (p) REVERT: C 156 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8202 (tt) REVERT: C 166 LEU cc_start: 0.8234 (tp) cc_final: 0.7989 (tt) REVERT: C 187 VAL cc_start: 0.8506 (t) cc_final: 0.8033 (p) REVERT: F 38 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7223 (m) REVERT: F 93 MET cc_start: 0.7981 (mmm) cc_final: 0.7658 (mmm) REVERT: F 102 TYR cc_start: 0.8450 (m-80) cc_final: 0.8204 (m-10) REVERT: F 177 THR cc_start: 0.8077 (m) cc_final: 0.7476 (p) REVERT: F 178 PRO cc_start: 0.8552 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: G 58 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8146 (p) REVERT: G 102 TYR cc_start: 0.8346 (m-80) cc_final: 0.7692 (m-80) REVERT: G 152 THR cc_start: 0.8390 (m) cc_final: 0.7952 (p) REVERT: G 170 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: G 194 MET cc_start: 0.8363 (mtm) cc_final: 0.8031 (mtm) REVERT: H 38 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7689 (m) REVERT: H 58 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7828 (p) REVERT: H 128 ASN cc_start: 0.7934 (t0) cc_final: 0.7696 (m-40) REVERT: H 130 GLN cc_start: 0.8196 (mp10) cc_final: 0.7972 (mp10) REVERT: H 148 THR cc_start: 0.8104 (p) cc_final: 0.7887 (p) REVERT: H 155 GLN cc_start: 0.8530 (tt0) cc_final: 0.8274 (tt0) REVERT: I 51 ASN cc_start: 0.7948 (t0) cc_final: 0.7603 (t0) REVERT: I 58 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7776 (m) REVERT: I 59 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: I 67 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6742 (mm-40) REVERT: I 78 GLN cc_start: 0.7392 (tt0) cc_final: 0.7081 (tm-30) REVERT: I 89 TYR cc_start: 0.7519 (m-80) cc_final: 0.7215 (m-80) REVERT: I 102 TYR cc_start: 0.8096 (m-80) cc_final: 0.7503 (m-80) REVERT: I 125 TYR cc_start: 0.7935 (m-80) cc_final: 0.6427 (m-80) outliers start: 56 outliers final: 41 residues processed: 368 average time/residue: 0.0927 time to fit residues: 56.8342 Evaluate side-chains 374 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 58 SER 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 170 TYR Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 F 120 GLN F 129 GLN F 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092695 restraints weight = 23521.782| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.38 r_work: 0.2956 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16333 Z= 0.255 Angle : 0.917 12.707 22905 Z= 0.375 Chirality : 0.049 0.384 3240 Planarity : 0.005 0.044 2394 Dihedral : 12.195 104.685 6906 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.20 % Allowed : 16.45 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.05 (0.19), residues: 729 loop : 0.35 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR B 43 PHE 0.027 0.003 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00583 (16074) covalent geometry : angle 0.81045 (22149) hydrogen bonds : bond 0.03105 ( 450) hydrogen bonds : angle 6.56673 ( 1275) glycosidic custom : bond 0.00231 ( 45) glycosidic custom : angle 2.71703 ( 135) Misc. bond : bond 0.00212 ( 7) link_ALPHA1-4 : bond 0.00757 ( 45) link_ALPHA1-4 : angle 2.58906 ( 135) link_ALPHA1-6 : bond 0.00478 ( 36) link_ALPHA1-6 : angle 1.54617 ( 108) link_BETA1-4 : bond 0.00260 ( 81) link_BETA1-4 : angle 2.06744 ( 243) link_NAG-ASN : bond 0.00601 ( 45) link_NAG-ASN : angle 3.34370 ( 135) *********************** 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 397 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8108 (m-80) cc_final: 0.7878 (m-80) REVERT: A 65 ASN cc_start: 0.8134 (t0) cc_final: 0.7917 (t0) REVERT: A 134 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 152 THR cc_start: 0.8312 (m) cc_final: 0.7886 (p) REVERT: A 155 GLN cc_start: 0.8452 (tt0) cc_final: 0.8180 (tt0) REVERT: A 184 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 67 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7430 (mm110) REVERT: B 102 TYR cc_start: 0.8300 (m-80) cc_final: 0.7799 (m-80) REVERT: B 125 TYR cc_start: 0.8407 (m-80) cc_final: 0.7569 (m-80) REVERT: B 141 VAL cc_start: 0.8509 (t) cc_final: 0.8109 (m) REVERT: B 165 LEU cc_start: 0.8458 (tp) cc_final: 0.8191 (tt) REVERT: B 194 MET cc_start: 0.8416 (mtm) cc_final: 0.8105 (mtp) REVERT: C 37 ASN cc_start: 0.8271 (t0) cc_final: 0.8035 (t0) REVERT: C 76 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 93 MET cc_start: 0.8408 (mmp) cc_final: 0.7860 (mmm) REVERT: C 102 TYR cc_start: 0.8483 (m-80) cc_final: 0.7581 (m-80) REVERT: C 112 TYR cc_start: 0.8399 (p90) cc_final: 0.8156 (p90) REVERT: C 152 THR cc_start: 0.8401 (m) cc_final: 0.8174 (p) REVERT: C 156 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 166 LEU cc_start: 0.8168 (tp) cc_final: 0.7956 (tt) REVERT: C 187 VAL cc_start: 0.8519 (t) cc_final: 0.8047 (p) REVERT: D 59 ASN cc_start: 0.8265 (t0) cc_final: 0.7925 (t0) REVERT: D 201 ILE cc_start: 0.8497 (mp) cc_final: 0.8276 (mm) REVERT: F 38 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7270 (m) REVERT: F 102 TYR cc_start: 0.8505 (m-80) cc_final: 0.8255 (m-10) REVERT: F 152 THR cc_start: 0.8572 (m) cc_final: 0.8322 (t) REVERT: F 177 THR cc_start: 0.8081 (m) cc_final: 0.7477 (p) REVERT: F 178 PRO cc_start: 0.8546 (Cg_exo) cc_final: 0.8314 (Cg_endo) REVERT: G 58 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8274 (p) REVERT: G 97 VAL cc_start: 0.8296 (t) cc_final: 0.7919 (m) REVERT: G 102 TYR cc_start: 0.8331 (m-80) cc_final: 0.7666 (m-80) REVERT: G 152 THR cc_start: 0.8442 (m) cc_final: 0.8132 (t) REVERT: G 170 TYR cc_start: 0.8266 (m-10) cc_final: 0.8055 (m-80) REVERT: G 194 MET cc_start: 0.8386 (mtm) cc_final: 0.7872 (mtp) REVERT: H 38 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7824 (m) REVERT: H 58 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7820 (m) REVERT: H 128 ASN cc_start: 0.8058 (t0) cc_final: 0.7839 (m-40) REVERT: H 130 GLN cc_start: 0.8228 (mp10) cc_final: 0.7998 (mp10) REVERT: H 148 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7916 (p) REVERT: H 155 GLN cc_start: 0.8503 (tt0) cc_final: 0.8242 (tt0) REVERT: I 58 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7741 (m) REVERT: I 59 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7146 (m-40) REVERT: I 67 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6911 (mm-40) REVERT: I 78 GLN cc_start: 0.7510 (tt0) cc_final: 0.7159 (tm-30) REVERT: I 89 TYR cc_start: 0.7541 (m-80) cc_final: 0.7226 (m-80) REVERT: I 102 TYR cc_start: 0.8111 (m-80) cc_final: 0.7512 (m-80) outliers start: 59 outliers final: 42 residues processed: 366 average time/residue: 0.0942 time to fit residues: 57.6649 Evaluate side-chains 388 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 145 VAL 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 76 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 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 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 85 THR 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 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 I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 150 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 D 188 ASN E 30 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092887 restraints weight = 23645.106| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.39 r_work: 0.2957 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16333 Z= 0.246 Angle : 0.912 12.581 22905 Z= 0.373 Chirality : 0.048 0.350 3240 Planarity : 0.005 0.044 2394 Dihedral : 12.158 104.831 6905 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.99 % Allowed : 16.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.29 (0.19), residues: 792 loop : 0.57 (0.25), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR E 43 PHE 0.027 0.003 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00560 (16074) covalent geometry : angle 0.80713 (22149) hydrogen bonds : bond 0.03087 ( 450) hydrogen bonds : angle 6.59856 ( 1275) glycosidic custom : bond 0.00260 ( 45) glycosidic custom : angle 2.74448 ( 135) Misc. bond : bond 0.00212 ( 7) link_ALPHA1-4 : bond 0.00772 ( 45) link_ALPHA1-4 : angle 2.57927 ( 135) link_ALPHA1-6 : bond 0.00493 ( 36) link_ALPHA1-6 : angle 1.53152 ( 108) link_BETA1-4 : bond 0.00240 ( 81) link_BETA1-4 : angle 2.01385 ( 243) link_NAG-ASN : bond 0.00514 ( 45) link_NAG-ASN : angle 3.29459 ( 135) *********************** 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 390 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 334 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8139 (t0) cc_final: 0.7920 (t0) REVERT: A 120 GLN cc_start: 0.8523 (tt0) cc_final: 0.8317 (tt0) REVERT: A 134 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 152 THR cc_start: 0.8314 (m) cc_final: 0.7888 (p) REVERT: A 184 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 67 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7455 (mm110) REVERT: B 102 TYR cc_start: 0.8289 (m-80) cc_final: 0.7805 (m-80) REVERT: B 112 TYR cc_start: 0.8181 (p90) cc_final: 0.7038 (p90) REVERT: B 125 TYR cc_start: 0.8417 (m-80) cc_final: 0.7824 (m-80) REVERT: B 141 VAL cc_start: 0.8507 (t) cc_final: 0.8100 (m) REVERT: B 194 MET cc_start: 0.8420 (mtm) cc_final: 0.8129 (mtp) REVERT: C 58 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 76 THR cc_start: 0.8521 (m) cc_final: 0.8059 (p) REVERT: C 93 MET cc_start: 0.8387 (mmp) cc_final: 0.7786 (mmm) REVERT: C 102 TYR cc_start: 0.8462 (m-80) cc_final: 0.7544 (m-80) REVERT: C 112 TYR cc_start: 0.8398 (p90) cc_final: 0.8164 (p90) REVERT: C 152 THR cc_start: 0.8410 (m) cc_final: 0.8182 (p) REVERT: C 156 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8245 (tt) REVERT: C 166 LEU cc_start: 0.8206 (tp) cc_final: 0.7973 (tt) REVERT: C 187 VAL cc_start: 0.8511 (t) cc_final: 0.8090 (p) REVERT: D 59 ASN cc_start: 0.8240 (t0) cc_final: 0.7871 (t0) REVERT: E 125 TYR cc_start: 0.8528 (m-80) cc_final: 0.8234 (m-80) REVERT: F 38 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7278 (m) REVERT: F 51 ASN cc_start: 0.8397 (t0) cc_final: 0.7806 (t0) REVERT: F 102 TYR cc_start: 0.8475 (m-80) cc_final: 0.8239 (m-10) REVERT: F 152 THR cc_start: 0.8579 (m) cc_final: 0.8330 (t) REVERT: F 177 THR cc_start: 0.8092 (m) cc_final: 0.7492 (p) REVERT: F 178 PRO cc_start: 0.8555 (Cg_exo) cc_final: 0.8333 (Cg_endo) REVERT: G 58 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8205 (p) REVERT: G 97 VAL cc_start: 0.8316 (t) cc_final: 0.7974 (m) REVERT: G 102 TYR cc_start: 0.8306 (m-80) cc_final: 0.7661 (m-80) REVERT: G 152 THR cc_start: 0.8454 (m) cc_final: 0.8157 (t) REVERT: G 194 MET cc_start: 0.8379 (mtm) cc_final: 0.7879 (mtp) REVERT: H 38 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7726 (m) REVERT: H 128 ASN cc_start: 0.8045 (t0) cc_final: 0.7830 (m-40) REVERT: H 130 GLN cc_start: 0.8239 (mp10) cc_final: 0.8011 (mp10) REVERT: I 67 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6940 (mm-40) REVERT: I 78 GLN cc_start: 0.7499 (tt0) cc_final: 0.7145 (tm-30) REVERT: I 89 TYR cc_start: 0.7545 (m-80) cc_final: 0.7250 (m-80) REVERT: I 102 TYR cc_start: 0.8150 (m-80) cc_final: 0.7453 (m-80) outliers start: 56 outliers final: 43 residues processed: 361 average time/residue: 0.0923 time to fit residues: 55.4096 Evaluate side-chains 379 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 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 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR 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 I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.4980 chunk 56 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 D 188 ASN F 129 GLN ** G 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093768 restraints weight = 23637.205| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.38 r_work: 0.2969 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16333 Z= 0.182 Angle : 0.873 12.529 22905 Z= 0.355 Chirality : 0.047 0.344 3240 Planarity : 0.005 0.049 2394 Dihedral : 12.020 103.649 6903 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.92 % Allowed : 16.95 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1629 helix: None (None), residues: 0 sheet: -0.29 (0.19), residues: 792 loop : 0.65 (0.25), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR H 86 PHE 0.020 0.002 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00408 (16074) covalent geometry : angle 0.77099 (22149) hydrogen bonds : bond 0.02764 ( 450) hydrogen bonds : angle 6.47099 ( 1275) glycosidic custom : bond 0.00234 ( 45) glycosidic custom : angle 2.62902 ( 135) Misc. bond : bond 0.00133 ( 7) link_ALPHA1-4 : bond 0.00774 ( 45) link_ALPHA1-4 : angle 2.51863 ( 135) link_ALPHA1-6 : bond 0.00546 ( 36) link_ALPHA1-6 : angle 1.47087 ( 108) link_BETA1-4 : bond 0.00218 ( 81) link_BETA1-4 : angle 1.84891 ( 243) link_NAG-ASN : bond 0.00540 ( 45) link_NAG-ASN : angle 3.25693 ( 135) *********************** 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 390 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8143 (t0) cc_final: 0.7923 (t0) REVERT: A 120 GLN cc_start: 0.8506 (tt0) cc_final: 0.8301 (tt0) REVERT: A 134 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 152 THR cc_start: 0.8313 (m) cc_final: 0.7899 (p) REVERT: A 170 TYR cc_start: 0.8345 (m-80) cc_final: 0.7794 (m-80) REVERT: A 184 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 67 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7442 (mm110) REVERT: B 102 TYR cc_start: 0.8289 (m-80) cc_final: 0.7823 (m-80) REVERT: B 112 TYR cc_start: 0.8168 (p90) cc_final: 0.7003 (p90) REVERT: B 125 TYR cc_start: 0.8411 (m-80) cc_final: 0.7591 (m-80) REVERT: B 141 VAL cc_start: 0.8506 (t) cc_final: 0.8113 (m) REVERT: B 165 LEU cc_start: 0.8411 (tp) cc_final: 0.8146 (tt) REVERT: B 194 MET cc_start: 0.8399 (mtm) cc_final: 0.8104 (mtp) REVERT: C 58 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 76 THR cc_start: 0.8504 (m) cc_final: 0.8027 (p) REVERT: C 93 MET cc_start: 0.8351 (mmp) cc_final: 0.7767 (mmm) REVERT: C 102 TYR cc_start: 0.8461 (m-80) cc_final: 0.7563 (m-80) REVERT: C 112 TYR cc_start: 0.8397 (p90) cc_final: 0.8177 (p90) REVERT: C 125 TYR cc_start: 0.8404 (m-80) cc_final: 0.8096 (m-80) REVERT: C 152 THR cc_start: 0.8404 (m) cc_final: 0.8194 (p) REVERT: C 156 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8192 (tt) REVERT: C 166 LEU cc_start: 0.8210 (tp) cc_final: 0.7960 (tt) REVERT: C 187 VAL cc_start: 0.8493 (t) cc_final: 0.8082 (p) REVERT: D 59 ASN cc_start: 0.8236 (t0) cc_final: 0.7864 (t0) REVERT: E 125 TYR cc_start: 0.8520 (m-80) cc_final: 0.8217 (m-80) REVERT: F 38 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7267 (m) REVERT: F 51 ASN cc_start: 0.8371 (t0) cc_final: 0.7779 (t0) REVERT: F 102 TYR cc_start: 0.8497 (m-80) cc_final: 0.8230 (m-10) REVERT: F 152 THR cc_start: 0.8573 (m) cc_final: 0.8308 (t) REVERT: F 177 THR cc_start: 0.8092 (m) cc_final: 0.7498 (p) REVERT: F 178 PRO cc_start: 0.8554 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: G 58 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8254 (p) REVERT: G 97 VAL cc_start: 0.8286 (t) cc_final: 0.7960 (m) REVERT: G 102 TYR cc_start: 0.8303 (m-80) cc_final: 0.7629 (m-80) REVERT: G 152 THR cc_start: 0.8393 (m) cc_final: 0.8100 (t) REVERT: G 194 MET cc_start: 0.8368 (mtm) cc_final: 0.7752 (mtp) REVERT: H 38 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7668 (m) REVERT: H 128 ASN cc_start: 0.8067 (t0) cc_final: 0.7860 (m-40) REVERT: H 130 GLN cc_start: 0.8217 (mp10) cc_final: 0.8003 (mp10) REVERT: H 148 THR cc_start: 0.8332 (p) cc_final: 0.7876 (p) REVERT: I 67 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6809 (mm-40) REVERT: I 78 GLN cc_start: 0.7542 (tt0) cc_final: 0.6994 (tt0) REVERT: I 89 TYR cc_start: 0.7493 (m-80) cc_final: 0.7200 (m-80) REVERT: I 102 TYR cc_start: 0.8129 (m-80) cc_final: 0.7444 (m-80) outliers start: 55 outliers final: 45 residues processed: 362 average time/residue: 0.0900 time to fit residues: 54.4202 Evaluate side-chains 385 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 333 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 SER 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 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 144 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 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 I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN F 129 GLN ** G 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093066 restraints weight = 23545.547| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.38 r_work: 0.2958 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16333 Z= 0.249 Angle : 0.912 12.654 22905 Z= 0.373 Chirality : 0.049 0.578 3240 Planarity : 0.005 0.050 2394 Dihedral : 11.988 103.767 6903 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.13 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1629 helix: None (None), residues: 0 sheet: -0.32 (0.19), residues: 792 loop : 0.61 (0.25), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR B 43 PHE 0.026 0.003 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00569 (16074) covalent geometry : angle 0.80723 (22149) hydrogen bonds : bond 0.03065 ( 450) hydrogen bonds : angle 6.52724 ( 1275) glycosidic custom : bond 0.00255 ( 45) glycosidic custom : angle 2.76667 ( 135) Misc. bond : bond 0.00216 ( 7) link_ALPHA1-4 : bond 0.00767 ( 45) link_ALPHA1-4 : angle 2.57662 ( 135) link_ALPHA1-6 : bond 0.00486 ( 36) link_ALPHA1-6 : angle 1.54645 ( 108) link_BETA1-4 : bond 0.00253 ( 81) link_BETA1-4 : angle 1.96825 ( 243) link_NAG-ASN : bond 0.00619 ( 45) link_NAG-ASN : angle 3.34171 ( 135) ********************** 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 392 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8148 (t0) cc_final: 0.7920 (t0) REVERT: A 120 GLN cc_start: 0.8528 (tt0) cc_final: 0.8319 (tt0) REVERT: A 134 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 152 THR cc_start: 0.8307 (m) cc_final: 0.7888 (p) REVERT: A 184 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 67 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7431 (mm110) REVERT: B 102 TYR cc_start: 0.8308 (m-80) cc_final: 0.7876 (m-80) REVERT: B 112 TYR cc_start: 0.8180 (p90) cc_final: 0.7006 (p90) REVERT: B 125 TYR cc_start: 0.8416 (m-80) cc_final: 0.7595 (m-80) REVERT: B 141 VAL cc_start: 0.8516 (t) cc_final: 0.8116 (m) REVERT: B 165 LEU cc_start: 0.8433 (tp) cc_final: 0.8147 (tt) REVERT: B 194 MET cc_start: 0.8407 (mtm) cc_final: 0.8133 (mtp) REVERT: C 58 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8302 (p) REVERT: C 76 THR cc_start: 0.8516 (m) cc_final: 0.8046 (p) REVERT: C 93 MET cc_start: 0.8353 (mmp) cc_final: 0.7744 (mmm) REVERT: C 102 TYR cc_start: 0.8463 (m-80) cc_final: 0.7608 (m-80) REVERT: C 112 TYR cc_start: 0.8395 (p90) cc_final: 0.8175 (p90) REVERT: C 125 TYR cc_start: 0.8412 (m-80) cc_final: 0.8103 (m-80) REVERT: C 152 THR cc_start: 0.8402 (m) cc_final: 0.8193 (p) REVERT: C 156 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (tt) REVERT: C 166 LEU cc_start: 0.8203 (tp) cc_final: 0.7957 (tt) REVERT: C 187 VAL cc_start: 0.8511 (t) cc_final: 0.8104 (p) REVERT: E 125 TYR cc_start: 0.8523 (m-80) cc_final: 0.8228 (m-80) REVERT: F 102 TYR cc_start: 0.8494 (m-80) cc_final: 0.8248 (m-10) REVERT: F 152 THR cc_start: 0.8570 (m) cc_final: 0.8325 (t) REVERT: F 177 THR cc_start: 0.8093 (m) cc_final: 0.7490 (p) REVERT: F 178 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8327 (Cg_endo) REVERT: G 58 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8265 (p) REVERT: G 97 VAL cc_start: 0.8307 (t) cc_final: 0.7962 (m) REVERT: G 102 TYR cc_start: 0.8295 (m-80) cc_final: 0.7623 (m-80) REVERT: G 152 THR cc_start: 0.8454 (m) cc_final: 0.8160 (t) REVERT: G 194 MET cc_start: 0.8378 (mtm) cc_final: 0.7794 (mtp) REVERT: H 38 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7760 (m) REVERT: H 128 ASN cc_start: 0.8043 (t0) cc_final: 0.7828 (m-40) REVERT: H 130 GLN cc_start: 0.8235 (mp10) cc_final: 0.8022 (mp10) REVERT: H 148 THR cc_start: 0.8343 (p) cc_final: 0.7893 (p) REVERT: I 67 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6942 (mm-40) REVERT: I 78 GLN cc_start: 0.7520 (tt0) cc_final: 0.6965 (tt0) REVERT: I 89 TYR cc_start: 0.7514 (m-80) cc_final: 0.7215 (m-80) REVERT: I 102 TYR cc_start: 0.8141 (m-80) cc_final: 0.7458 (m-80) outliers start: 58 outliers final: 47 residues processed: 366 average time/residue: 0.0918 time to fit residues: 56.2580 Evaluate side-chains 387 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 156 ILE 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 34 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 73 SER 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 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 144 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN C 49 ASN F 129 GLN ** G 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093773 restraints weight = 23374.669| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.35 r_work: 0.2961 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16333 Z= 0.214 Angle : 0.913 15.916 22905 Z= 0.372 Chirality : 0.051 1.028 3240 Planarity : 0.005 0.051 2394 Dihedral : 11.941 103.203 6903 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.99 % Allowed : 17.24 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1629 helix: None (None), residues: 0 sheet: -0.35 (0.19), residues: 792 loop : 0.63 (0.25), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR H 86 PHE 0.023 0.003 PHE E 90 Details of bonding type rmsd covalent geometry : bond 0.00482 (16074) covalent geometry : angle 0.79983 (22149) hydrogen bonds : bond 0.02997 ( 450) hydrogen bonds : angle 6.53526 ( 1275) glycosidic custom : bond 0.00257 ( 45) glycosidic custom : angle 2.73484 ( 135) Misc. bond : bond 0.00174 ( 7) link_ALPHA1-4 : bond 0.00804 ( 45) link_ALPHA1-4 : angle 2.57304 ( 135) link_ALPHA1-6 : bond 0.00522 ( 36) link_ALPHA1-6 : angle 1.49733 ( 108) link_BETA1-4 : bond 0.00441 ( 81) link_BETA1-4 : angle 2.05505 ( 243) link_NAG-ASN : bond 0.00668 ( 45) link_NAG-ASN : angle 3.58829 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.08 seconds wall clock time: 63 minutes 7.80 seconds (3787.80 seconds total)