Starting phenix.real_space_refine on Fri Jul 3 19:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnb_13546/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnb_13546/07_2026/7pnb_13546.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 3.66, per 1000 atoms: 0.23 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: 2.90 Conformation dependent library (CDL) restraints added in 613.2 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: 0.58 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: 2.74 Time building geometry restraints manager: 3.32 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 - 13.82: 6973 13.82 - 27.65: 612 27.65 - 41.47: 83 41.47 - 55.30: 78 55.30 - 69.12: 39 Dihedral angle restraints: 7785 sinusoidal: 2952 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 7782 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: 0.05 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: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 12.991 69.121 4743 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/Z covalent geometry : bond 0.01307 / 0.73 (16074) covalent geometry : angle 1.74589 / 0.90 (22149) hydrogen bonds : bond 0.14660 / 9.85 ( 450) hydrogen bonds : angle 8.83808 / 6.18 ( 1275) glycosidic custom : bond 0.01421 / 0.88 ( 45) glycosidic custom : angle 9.95793 / 7.23 ( 135) Misc. bond : bond 0.10510 / 5.48 ( 7) link_ALPHA1-4 : bond 0.03365 / 2.15 ( 45) link_ALPHA1-4 : angle 4.59179 / 3.04 ( 135) link_ALPHA1-6 : bond 0.00280 / 0.16 ( 36) link_ALPHA1-6 : angle 1.68717 / 1.15 ( 108) link_BETA1-4 : bond 0.01557 / 1.00 ( 81) link_BETA1-4 : angle 4.51231 / 3.00 ( 243) link_NAG-ASN : bond 0.03142 / 1.99 ( 45) link_NAG-ASN : angle 6.09617 / 4.34 ( 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 : 0.516 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: 0.0992 time to fit residues: 64.3848 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 : 0.494 ------------------------------------------------------------------------------- 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... 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 = 0.3499 r_free = 0.3499 target = 0.119530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097587 restraints weight = 22208.180| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.27 r_work: 0.3038 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16333 Z= 0.185 Angle : 0.946 9.955 22905 Z= 0.389 Chirality : 0.053 0.284 3240 Planarity : 0.005 0.046 2394 Dihedral : 6.062 58.074 1942 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.49 % Allowed : 9.97 % Favored : 86.54 % 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: 0.24 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.28 (0.18), residues: 711 loop : 0.19 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.002 TYR H 27 PHE 0.018 0.002 PHE F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (16074) covalent geometry : angle 0.84520 / 0.36 (22149) hydrogen bonds : bond 0.03101 / 2.13 ( 450) hydrogen bonds : angle 7.24022 / 4.99 ( 1275) glycosidic custom : bond 0.00644 / 0.41 ( 45) glycosidic custom : angle 2.66049 / 1.85 ( 135) Misc. bond : bond 0.00215 / 0.11 ( 7) link_ALPHA1-4 : bond 0.00798 / 0.49 ( 45) link_ALPHA1-4 : angle 1.75737 / 1.24 ( 135) link_ALPHA1-6 : bond 0.00655 / 0.41 ( 36) link_ALPHA1-6 : angle 1.28756 / 0.90 ( 108) link_BETA1-4 : bond 0.00513 / 0.34 ( 81) link_BETA1-4 : angle 2.21325 / 1.51 ( 243) link_NAG-ASN : bond 0.00405 / 0.25 ( 45) link_NAG-ASN : angle 3.79398 / 2.70 ( 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 387 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 152 THR cc_start: 0.8356 (m) cc_final: 0.7890 (p) REVERT: A 181 ASP cc_start: 0.7978 (t0) cc_final: 0.7755 (t70) REVERT: B 67 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7434 (mm110) REVERT: B 93 MET cc_start: 0.8238 (mmm) cc_final: 0.7880 (mmm) REVERT: B 102 TYR cc_start: 0.8190 (m-80) cc_final: 0.7671 (m-80) REVERT: B 112 TYR cc_start: 0.8233 (p90) cc_final: 0.7422 (p90) REVERT: B 125 TYR cc_start: 0.8458 (m-80) cc_final: 0.7923 (m-80) REVERT: B 194 MET cc_start: 0.8353 (mtm) cc_final: 0.8024 (mtp) REVERT: C 93 MET cc_start: 0.8411 (mmp) cc_final: 0.7987 (mmm) REVERT: C 102 TYR cc_start: 0.8372 (m-80) cc_final: 0.7528 (m-80) REVERT: C 104 TYR cc_start: 0.8603 (p90) cc_final: 0.8390 (p90) REVERT: C 177 THR cc_start: 0.8383 (m) cc_final: 0.7962 (p) REVERT: C 181 ASP cc_start: 0.7745 (t0) cc_final: 0.7535 (t0) REVERT: C 194 MET cc_start: 0.8163 (mtm) cc_final: 0.7865 (mtm) REVERT: D 29 TYR cc_start: 0.8159 (m-80) cc_final: 0.7952 (m-80) REVERT: D 79 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8262 (m) REVERT: E 42 MET cc_start: 0.8427 (ptm) cc_final: 0.8185 (ptm) REVERT: E 69 SER cc_start: 0.8080 (t) cc_final: 0.7787 (m) REVERT: E 125 TYR cc_start: 0.8467 (m-80) cc_final: 0.7294 (m-80) REVERT: F 29 TYR cc_start: 0.8166 (m-80) cc_final: 0.7935 (m-80) REVERT: F 38 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7583 (m) REVERT: F 102 TYR cc_start: 0.8391 (m-80) cc_final: 0.8155 (m-10) REVERT: F 125 TYR cc_start: 0.8838 (m-80) cc_final: 0.8201 (m-80) REVERT: F 177 THR cc_start: 0.8065 (m) cc_final: 0.7497 (p) REVERT: F 178 PRO cc_start: 0.8633 (Cg_exo) cc_final: 0.8395 (Cg_endo) REVERT: F 180 ASN cc_start: 0.7960 (p0) cc_final: 0.7648 (p0) REVERT: G 58 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8018 (p) REVERT: G 91 ASN cc_start: 0.8475 (t0) cc_final: 0.8233 (t0) REVERT: G 93 MET cc_start: 0.8324 (tpp) cc_final: 0.8121 (mmt) REVERT: G 102 TYR cc_start: 0.8355 (m-80) cc_final: 0.7763 (m-80) REVERT: G 194 MET cc_start: 0.8317 (mtm) cc_final: 0.8070 (mtp) REVERT: H 38 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7902 (m) REVERT: H 47 GLN cc_start: 0.8416 (mt0) cc_final: 0.7941 (mt0) REVERT: H 58 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7619 (m) REVERT: H 65 ASN cc_start: 0.8130 (t0) cc_final: 0.7906 (t0) REVERT: H 78 GLN cc_start: 0.7314 (tt0) cc_final: 0.7004 (tm-30) REVERT: H 129 GLN cc_start: 0.8082 (tt0) cc_final: 0.7830 (tt0) REVERT: H 130 GLN cc_start: 0.8248 (mp10) cc_final: 0.7825 (mp10) REVERT: H 148 THR cc_start: 0.8302 (p) cc_final: 0.7941 (p) REVERT: H 157 ASN cc_start: 0.7192 (m-40) cc_final: 0.6949 (m-40) REVERT: H 161 TYR cc_start: 0.8203 (m-80) cc_final: 0.7649 (m-80) REVERT: I 58 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7647 (m) REVERT: I 59 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7128 (m-40) REVERT: I 89 TYR cc_start: 0.7617 (m-80) cc_final: 0.7354 (m-80) REVERT: I 93 MET cc_start: 0.7914 (mmm) cc_final: 0.7657 (mmm) REVERT: I 125 TYR cc_start: 0.7882 (m-80) cc_final: 0.7676 (m-10) REVERT: I 186 THR cc_start: 0.8291 (m) cc_final: 0.7856 (p) outliers start: 49 outliers final: 24 residues processed: 372 average time/residue: 0.0930 time to fit residues: 56.8002 Evaluate side-chains 352 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 321 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 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: 0.9980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN B 78 GLN B 120 GLN B 129 GLN C 47 GLN E 59 ASN E 120 GLN F 120 GLN F 132 GLN G 87 ASN G 171 GLN G 188 ASN H 132 GLN H 188 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094654 restraints weight = 22556.583| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.32 r_work: 0.2907 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 16333 Z= 0.305 Angle : 0.933 9.378 22905 Z= 0.392 Chirality : 0.052 0.245 3240 Planarity : 0.005 0.048 2394 Dihedral : 5.987 54.066 1939 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.70 % Allowed : 12.75 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.07 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.13 (0.18), residues: 711 loop : 0.10 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR H 88 PHE 0.028 0.003 PHE E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.31 (16074) covalent geometry : angle 0.84198 / 0.37 (22149) hydrogen bonds : bond 0.03511 / 2.46 ( 450) hydrogen bonds : angle 7.06459 / 4.87 ( 1275) glycosidic custom : bond 0.00406 / 0.25 ( 45) glycosidic custom : angle 2.33514 / 1.65 ( 135) Misc. bond : bond 0.00278 / 0.14 ( 7) link_ALPHA1-4 : bond 0.00644 / 0.41 ( 45) link_ALPHA1-4 : angle 1.84542 / 1.31 ( 135) link_ALPHA1-6 : bond 0.00518 / 0.31 ( 36) link_ALPHA1-6 : angle 1.46888 / 1.04 ( 108) link_BETA1-4 : bond 0.00283 / 0.19 ( 81) link_BETA1-4 : angle 2.34319 / 1.61 ( 243) link_NAG-ASN : bond 0.00429 / 0.27 ( 45) link_NAG-ASN : angle 3.29664 / 2.25 ( 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 396 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 344 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8090 (m-80) cc_final: 0.7812 (m-80) REVERT: A 152 THR cc_start: 0.8361 (m) cc_final: 0.7909 (p) REVERT: B 67 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7541 (mm110) REVERT: B 93 MET cc_start: 0.8234 (mmm) cc_final: 0.7795 (mmm) REVERT: B 102 TYR cc_start: 0.8268 (m-80) cc_final: 0.7781 (m-80) REVERT: B 112 TYR cc_start: 0.8208 (p90) cc_final: 0.7880 (p90) REVERT: B 125 TYR cc_start: 0.8467 (m-80) cc_final: 0.7906 (m-80) REVERT: B 141 VAL cc_start: 0.8416 (t) cc_final: 0.7973 (m) REVERT: B 165 LEU cc_start: 0.8437 (tp) cc_final: 0.8163 (tt) REVERT: B 194 MET cc_start: 0.8462 (mtm) cc_final: 0.8130 (mtp) REVERT: C 93 MET cc_start: 0.8394 (mmp) cc_final: 0.7885 (mmm) REVERT: C 102 TYR cc_start: 0.8419 (m-80) cc_final: 0.7506 (m-80) REVERT: C 112 TYR cc_start: 0.8466 (p90) cc_final: 0.8057 (p90) REVERT: C 194 MET cc_start: 0.8268 (mtm) cc_final: 0.7970 (mtm) REVERT: D 79 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8396 (m) REVERT: D 97 VAL cc_start: 0.8314 (t) cc_final: 0.8039 (m) REVERT: D 201 ILE cc_start: 0.8494 (mt) cc_final: 0.8287 (mp) REVERT: E 59 ASN cc_start: 0.8272 (t0) cc_final: 0.8037 (t0) REVERT: E 69 SER cc_start: 0.7973 (t) cc_final: 0.7699 (m) REVERT: F 38 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7445 (m) REVERT: F 51 ASN cc_start: 0.8416 (t0) cc_final: 0.8133 (m-40) REVERT: F 59 ASN cc_start: 0.8327 (t0) cc_final: 0.7581 (t0) REVERT: F 102 TYR cc_start: 0.8399 (m-80) cc_final: 0.8159 (m-10) REVERT: F 177 THR cc_start: 0.8060 (m) cc_final: 0.7466 (p) REVERT: F 178 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8282 (t) cc_final: 0.7854 (m) REVERT: G 102 TYR cc_start: 0.8363 (m-80) cc_final: 0.7644 (m-80) REVERT: G 194 MET cc_start: 0.8403 (mtm) cc_final: 0.7939 (mtp) REVERT: G 195 THR cc_start: 0.8475 (p) cc_final: 0.7559 (t) REVERT: H 38 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7890 (m) REVERT: H 58 SER cc_start: 0.7942 (m) cc_final: 0.7709 (m) REVERT: H 128 ASN cc_start: 0.8064 (t0) cc_final: 0.7843 (m-40) REVERT: H 130 GLN cc_start: 0.8211 (mp10) cc_final: 0.7917 (mp10) REVERT: H 148 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7893 (p) REVERT: I 59 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7162 (m-40) REVERT: I 70 SER cc_start: 0.7875 (t) cc_final: 0.7567 (p) REVERT: I 89 TYR cc_start: 0.7637 (m-80) cc_final: 0.7360 (m-80) REVERT: I 102 TYR cc_start: 0.8054 (m-80) cc_final: 0.7726 (m-10) REVERT: I 105 LEU cc_start: 0.7824 (tp) cc_final: 0.7501 (tp) outliers start: 52 outliers final: 36 residues processed: 371 average time/residue: 0.0882 time to fit residues: 54.4385 Evaluate side-chains 358 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 98 SER 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 85 THR Chi-restraints excluded: chain H residue 86 TYR 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 166 LEU 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: 0.0770 chunk 124 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 129 GLN E 129 GLN G 87 ASN H 65 ASN H 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097293 restraints weight = 22274.262| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.31 r_work: 0.2947 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16333 Z= 0.149 Angle : 0.804 12.710 22905 Z= 0.336 Chirality : 0.047 0.341 3240 Planarity : 0.005 0.048 2394 Dihedral : 5.540 53.798 1939 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.35 % Allowed : 15.03 % Favored : 81.62 % 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 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.01 (0.19), residues: 729 loop : 0.26 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.030 0.002 TYR H 27 PHE 0.020 0.002 PHE A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (16074) covalent geometry : angle 0.72684 / 0.32 (22149) hydrogen bonds : bond 0.02642 / 1.83 ( 450) hydrogen bonds : angle 6.68568 / 4.61 ( 1275) glycosidic custom : bond 0.00362 / 0.23 ( 45) glycosidic custom : angle 1.87223 / 1.30 ( 135) Misc. bond : bond 0.00082 / 0.04 ( 7) link_ALPHA1-4 : bond 0.00660 / 0.41 ( 45) link_ALPHA1-4 : angle 1.64721 / 1.18 ( 135) link_ALPHA1-6 : bond 0.00576 / 0.36 ( 36) link_ALPHA1-6 : angle 1.41278 / 0.98 ( 108) link_BETA1-4 : bond 0.00299 / 0.20 ( 81) link_BETA1-4 : angle 1.81781 / 1.25 ( 243) link_NAG-ASN : bond 0.00450 / 0.23 ( 45) link_NAG-ASN : angle 3.02786 / 2.07 ( 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 390 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8098 (m-80) cc_final: 0.7841 (m-80) REVERT: A 152 THR cc_start: 0.8337 (m) cc_final: 0.7894 (p) REVERT: B 67 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7447 (mm110) REVERT: B 93 MET cc_start: 0.8093 (mmm) cc_final: 0.7583 (mmm) REVERT: B 102 TYR cc_start: 0.8232 (m-80) cc_final: 0.7731 (m-80) REVERT: B 125 TYR cc_start: 0.8453 (m-80) cc_final: 0.7627 (m-80) REVERT: B 141 VAL cc_start: 0.8385 (t) cc_final: 0.7985 (m) REVERT: B 165 LEU cc_start: 0.8436 (tp) cc_final: 0.8130 (tt) REVERT: B 194 MET cc_start: 0.8419 (mtm) cc_final: 0.8110 (mtp) REVERT: C 93 MET cc_start: 0.8383 (mmp) cc_final: 0.7965 (mmm) REVERT: C 102 TYR cc_start: 0.8411 (m-80) cc_final: 0.7454 (m-80) REVERT: C 112 TYR cc_start: 0.8435 (p90) cc_final: 0.8101 (p90) REVERT: C 194 MET cc_start: 0.8227 (mtm) cc_final: 0.7892 (mtm) REVERT: E 42 MET cc_start: 0.8411 (ptm) cc_final: 0.8176 (ptm) REVERT: E 69 SER cc_start: 0.7952 (t) cc_final: 0.7708 (m) REVERT: F 38 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7399 (m) REVERT: F 102 TYR cc_start: 0.8434 (m-80) cc_final: 0.8153 (m-10) REVERT: F 177 THR cc_start: 0.8029 (m) cc_final: 0.7429 (p) REVERT: F 178 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8272 (t) cc_final: 0.7905 (m) REVERT: G 102 TYR cc_start: 0.8368 (m-80) cc_final: 0.7656 (m-80) REVERT: G 152 THR cc_start: 0.8437 (m) cc_final: 0.8040 (p) REVERT: G 194 MET cc_start: 0.8426 (mtm) cc_final: 0.8084 (mtm) REVERT: G 195 THR cc_start: 0.8432 (p) cc_final: 0.7471 (t) REVERT: H 38 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7718 (m) REVERT: H 58 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7632 (p) REVERT: H 128 ASN cc_start: 0.7994 (t0) cc_final: 0.7785 (m-40) REVERT: H 130 GLN cc_start: 0.8210 (mp10) cc_final: 0.7959 (mp10) REVERT: H 155 GLN cc_start: 0.8436 (tt0) cc_final: 0.8170 (tt0) REVERT: I 58 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7677 (m) REVERT: I 59 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.7141 (m-40) REVERT: I 67 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6849 (mm-40) REVERT: I 78 GLN cc_start: 0.7317 (tt0) cc_final: 0.7067 (tt0) REVERT: I 89 TYR cc_start: 0.7494 (m-80) cc_final: 0.7269 (m-80) REVERT: I 102 TYR cc_start: 0.8101 (m-80) cc_final: 0.7464 (m-80) REVERT: I 105 LEU cc_start: 0.7704 (tp) cc_final: 0.7363 (tp) REVERT: I 110 TYR cc_start: 0.8094 (t80) cc_final: 0.7890 (t80) REVERT: I 125 TYR cc_start: 0.7909 (m-80) cc_final: 0.6470 (m-80) outliers start: 47 outliers final: 35 residues processed: 370 average time/residue: 0.0879 time to fit residues: 53.8622 Evaluate side-chains 377 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain 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 157 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 0.7980 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 129 GLN E 171 GLN F 120 GLN F 132 GLN H 59 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN H 188 ASN I 59 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095492 restraints weight = 22435.647| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.31 r_work: 0.3007 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2672 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= 0.242 Angle : 0.840 12.517 22905 Z= 0.354 Chirality : 0.049 0.332 3240 Planarity : 0.005 0.048 2394 Dihedral : 5.590 51.144 1938 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.77 % Allowed : 15.10 % Favored : 81.13 % 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: 0.02 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.05 (0.19), residues: 729 loop : 0.22 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR H 86 PHE 0.028 0.003 PHE A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (16074) covalent geometry : angle 0.76080 / 0.34 (22149) hydrogen bonds : bond 0.03078 / 2.15 ( 450) hydrogen bonds : angle 6.69979 / 4.63 ( 1275) glycosidic custom : bond 0.00299 / 0.18 ( 45) glycosidic custom : angle 1.99578 / 1.41 ( 135) Misc. bond : bond 0.00205 / 0.11 ( 7) link_ALPHA1-4 : bond 0.00612 / 0.39 ( 45) link_ALPHA1-4 : angle 1.74922 / 1.24 ( 135) link_ALPHA1-6 : bond 0.00492 / 0.30 ( 36) link_ALPHA1-6 : angle 1.49536 / 1.06 ( 108) link_BETA1-4 : bond 0.00286 / 0.19 ( 81) link_BETA1-4 : angle 1.97028 / 1.35 ( 243) link_NAG-ASN : bond 0.00327 / 0.18 ( 45) link_NAG-ASN : angle 2.99463 / 2.06 ( 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 378 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8096 (m-80) cc_final: 0.7828 (m-80) REVERT: A 134 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 152 THR cc_start: 0.8346 (m) cc_final: 0.7914 (p) REVERT: B 67 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7398 (mm110) REVERT: B 102 TYR cc_start: 0.8308 (m-80) cc_final: 0.7867 (m-80) REVERT: B 125 TYR cc_start: 0.8442 (m-80) cc_final: 0.7717 (m-80) REVERT: B 141 VAL cc_start: 0.8486 (t) cc_final: 0.8084 (m) REVERT: B 165 LEU cc_start: 0.8461 (tp) cc_final: 0.8206 (tt) REVERT: B 194 MET cc_start: 0.8417 (mtm) cc_final: 0.8138 (mtp) REVERT: C 93 MET cc_start: 0.8361 (mmp) cc_final: 0.7868 (mmm) REVERT: C 102 TYR cc_start: 0.8425 (m-80) cc_final: 0.7613 (m-80) REVERT: C 112 TYR cc_start: 0.8433 (p90) cc_final: 0.8137 (p90) REVERT: C 156 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8246 (tt) REVERT: C 187 VAL cc_start: 0.8553 (t) cc_final: 0.8040 (p) REVERT: D 201 ILE cc_start: 0.8516 (mp) cc_final: 0.8270 (mm) REVERT: F 38 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7319 (m) REVERT: F 102 TYR cc_start: 0.8427 (m-80) cc_final: 0.8203 (m-10) REVERT: F 177 THR cc_start: 0.8095 (m) cc_final: 0.7498 (p) REVERT: F 178 PRO cc_start: 0.8615 (Cg_exo) cc_final: 0.8374 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8314 (t) cc_final: 0.7928 (m) REVERT: G 102 TYR cc_start: 0.8340 (m-80) cc_final: 0.7761 (m-80) REVERT: G 194 MET cc_start: 0.8391 (mtm) cc_final: 0.7923 (mtp) REVERT: H 38 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7794 (m) REVERT: H 58 SER cc_start: 0.7914 (m) cc_final: 0.7663 (m) REVERT: H 128 ASN cc_start: 0.7991 (t0) cc_final: 0.7782 (m-40) REVERT: H 130 GLN cc_start: 0.8213 (mp10) cc_final: 0.7985 (mp10) REVERT: H 148 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7808 (p) REVERT: H 155 GLN cc_start: 0.8508 (tt0) cc_final: 0.8237 (tt0) REVERT: I 51 ASN cc_start: 0.7960 (t0) cc_final: 0.7685 (t0) REVERT: I 58 SER cc_start: 0.8210 (m) cc_final: 0.7800 (m) REVERT: I 89 TYR cc_start: 0.7622 (m-80) cc_final: 0.7369 (m-80) REVERT: I 102 TYR cc_start: 0.8142 (m-80) cc_final: 0.7941 (m-10) outliers start: 53 outliers final: 43 residues processed: 353 average time/residue: 0.0895 time to fit residues: 52.4682 Evaluate side-chains 361 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 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 33 ILE Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain 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 148 THR 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 59 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 94 optimal weight: 0.0570 chunk 143 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN B 120 GLN C 49 ASN D 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 = 0.3495 r_free = 0.3495 target = 0.118819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097038 restraints weight = 22288.280| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.30 r_work: 0.3030 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16333 Z= 0.162 Angle : 0.793 12.402 22905 Z= 0.332 Chirality : 0.047 0.314 3240 Planarity : 0.005 0.049 2394 Dihedral : 5.368 50.076 1938 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.77 % Allowed : 15.67 % Favored : 80.56 % 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: 0.08 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.04 (0.19), residues: 729 loop : 0.29 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR H 27 PHE 0.019 0.002 PHE H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16074) covalent geometry : angle 0.71756 / 0.31 (22149) hydrogen bonds : bond 0.02675 / 1.85 ( 450) hydrogen bonds : angle 6.51822 / 4.51 ( 1275) glycosidic custom : bond 0.00296 / 0.18 ( 45) glycosidic custom : angle 1.76675 / 1.23 ( 135) Misc. bond : bond 0.00116 / 0.06 ( 7) link_ALPHA1-4 : bond 0.00624 / 0.39 ( 45) link_ALPHA1-4 : angle 1.63979 / 1.17 ( 135) link_ALPHA1-6 : bond 0.00529 / 0.33 ( 36) link_ALPHA1-6 : angle 1.43474 / 1.00 ( 108) link_BETA1-4 : bond 0.00270 / 0.18 ( 81) link_BETA1-4 : angle 1.73381 / 1.18 ( 243) link_NAG-ASN : bond 0.00414 / 0.22 ( 45) link_NAG-ASN : angle 3.06283 / 2.09 ( 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 406 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8103 (m-80) cc_final: 0.7874 (m-80) REVERT: A 134 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 152 THR cc_start: 0.8344 (m) cc_final: 0.7906 (p) REVERT: A 184 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 67 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7366 (mm110) REVERT: B 102 TYR cc_start: 0.8275 (m-80) cc_final: 0.7821 (m-80) REVERT: B 112 TYR cc_start: 0.8185 (p90) cc_final: 0.7069 (p90) REVERT: B 125 TYR cc_start: 0.8429 (m-80) cc_final: 0.7655 (m-80) REVERT: B 141 VAL cc_start: 0.8469 (t) cc_final: 0.8085 (m) REVERT: B 165 LEU cc_start: 0.8460 (tp) cc_final: 0.8204 (tt) REVERT: B 194 MET cc_start: 0.8406 (mtm) cc_final: 0.8110 (mtp) REVERT: C 76 THR cc_start: 0.8512 (m) cc_final: 0.8031 (p) REVERT: C 93 MET cc_start: 0.8343 (mmp) cc_final: 0.7836 (mmm) REVERT: C 102 TYR cc_start: 0.8418 (m-80) cc_final: 0.7490 (m-80) REVERT: C 112 TYR cc_start: 0.8423 (p90) cc_final: 0.8174 (p90) REVERT: C 156 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 187 VAL cc_start: 0.8554 (t) cc_final: 0.8051 (p) REVERT: F 102 TYR cc_start: 0.8453 (m-80) cc_final: 0.8206 (m-10) REVERT: F 177 THR cc_start: 0.8086 (m) cc_final: 0.7485 (p) REVERT: F 178 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: G 58 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8164 (p) REVERT: G 97 VAL cc_start: 0.8284 (t) cc_final: 0.7911 (m) REVERT: G 102 TYR cc_start: 0.8340 (m-80) cc_final: 0.7703 (m-80) REVERT: G 152 THR cc_start: 0.8468 (m) cc_final: 0.8066 (p) REVERT: H 38 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7686 (m) REVERT: H 58 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7822 (p) REVERT: H 128 ASN cc_start: 0.7971 (t0) cc_final: 0.7762 (m-40) REVERT: H 130 GLN cc_start: 0.8213 (mp10) cc_final: 0.7990 (mp10) REVERT: H 155 GLN cc_start: 0.8516 (tt0) cc_final: 0.8254 (tt0) REVERT: I 51 ASN cc_start: 0.7945 (t0) cc_final: 0.7635 (t0) REVERT: I 58 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7769 (m) REVERT: I 67 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6890 (mm-40) REVERT: I 78 GLN cc_start: 0.7477 (tt0) cc_final: 0.7228 (tm-30) REVERT: I 89 TYR cc_start: 0.7539 (m-80) cc_final: 0.7297 (m-80) REVERT: I 102 TYR cc_start: 0.8133 (m-80) cc_final: 0.7499 (m-80) outliers start: 53 outliers final: 38 residues processed: 381 average time/residue: 0.0853 time to fit residues: 53.7912 Evaluate side-chains 391 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain 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 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 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 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: 1.9990 chunk 121 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN C 49 ASN D 129 GLN E 129 GLN F 120 GLN F 129 GLN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096134 restraints weight = 22342.139| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.30 r_work: 0.2942 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16333 Z= 0.202 Angle : 0.812 12.400 22905 Z= 0.340 Chirality : 0.048 0.325 3240 Planarity : 0.005 0.047 2394 Dihedral : 5.397 47.999 1938 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.92 % Allowed : 16.31 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.15 (0.19), residues: 774 loop : 0.47 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR H 86 PHE 0.022 0.003 PHE E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (16074) covalent geometry : angle 0.73192 / 0.32 (22149) hydrogen bonds : bond 0.02823 / 1.95 ( 450) hydrogen bonds : angle 6.52335 / 4.51 ( 1275) glycosidic custom : bond 0.00286 / 0.18 ( 45) glycosidic custom : angle 1.84356 / 1.29 ( 135) Misc. bond : bond 0.00162 / 0.09 ( 7) link_ALPHA1-4 : bond 0.00607 / 0.38 ( 45) link_ALPHA1-4 : angle 1.67677 / 1.19 ( 135) link_ALPHA1-6 : bond 0.00487 / 0.30 ( 36) link_ALPHA1-6 : angle 1.47906 / 1.04 ( 108) link_BETA1-4 : bond 0.00268 / 0.18 ( 81) link_BETA1-4 : angle 1.79671 / 1.23 ( 243) link_NAG-ASN : bond 0.00473 / 0.32 ( 45) link_NAG-ASN : angle 3.21160 / 2.13 ( 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 390 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8102 (m-80) cc_final: 0.7876 (m-80) REVERT: A 134 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8374 (p) REVERT: A 152 THR cc_start: 0.8305 (m) cc_final: 0.7884 (p) REVERT: A 184 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 67 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7391 (mm110) REVERT: B 102 TYR cc_start: 0.8273 (m-80) cc_final: 0.7798 (m-80) REVERT: B 112 TYR cc_start: 0.8176 (p90) cc_final: 0.7011 (p90) REVERT: B 125 TYR cc_start: 0.8433 (m-80) cc_final: 0.7634 (m-80) REVERT: B 141 VAL cc_start: 0.8472 (t) cc_final: 0.8094 (m) REVERT: B 165 LEU cc_start: 0.8440 (tp) cc_final: 0.8178 (tt) REVERT: B 194 MET cc_start: 0.8441 (mtm) cc_final: 0.8139 (mtp) REVERT: C 76 THR cc_start: 0.8492 (m) cc_final: 0.8001 (p) REVERT: C 93 MET cc_start: 0.8356 (mmp) cc_final: 0.7827 (mmm) REVERT: C 102 TYR cc_start: 0.8418 (m-80) cc_final: 0.7509 (m-80) REVERT: C 112 TYR cc_start: 0.8413 (p90) cc_final: 0.8179 (p90) REVERT: C 156 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8213 (tt) REVERT: C 166 LEU cc_start: 0.8179 (tp) cc_final: 0.7968 (tt) REVERT: C 187 VAL cc_start: 0.8506 (t) cc_final: 0.8016 (p) REVERT: C 194 MET cc_start: 0.8193 (mtm) cc_final: 0.7852 (mtp) REVERT: F 102 TYR cc_start: 0.8460 (m-80) cc_final: 0.8212 (m-10) REVERT: F 152 THR cc_start: 0.8532 (m) cc_final: 0.8244 (t) REVERT: F 177 THR cc_start: 0.8066 (m) cc_final: 0.7463 (p) REVERT: F 178 PRO cc_start: 0.8589 (Cg_exo) cc_final: 0.8352 (Cg_endo) REVERT: G 58 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8204 (p) REVERT: G 97 VAL cc_start: 0.8271 (t) cc_final: 0.7898 (m) REVERT: G 102 TYR cc_start: 0.8336 (m-80) cc_final: 0.7670 (m-80) REVERT: G 152 THR cc_start: 0.8457 (m) cc_final: 0.8045 (p) REVERT: H 38 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (m) REVERT: H 128 ASN cc_start: 0.8005 (t0) cc_final: 0.7803 (m-40) REVERT: H 130 GLN cc_start: 0.8225 (mp10) cc_final: 0.7997 (mp10) REVERT: H 148 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7930 (p) REVERT: H 155 GLN cc_start: 0.8480 (tt0) cc_final: 0.8225 (tt0) REVERT: I 51 ASN cc_start: 0.7966 (t0) cc_final: 0.7623 (t0) REVERT: I 58 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7773 (m) REVERT: I 67 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6838 (mm-40) REVERT: I 78 GLN cc_start: 0.7458 (tt0) cc_final: 0.7202 (tm-30) REVERT: I 89 TYR cc_start: 0.7555 (m-80) cc_final: 0.7243 (m-80) REVERT: I 102 TYR cc_start: 0.8146 (m-80) cc_final: 0.7931 (m-10) outliers start: 55 outliers final: 43 residues processed: 363 average time/residue: 0.0898 time to fit residues: 54.1834 Evaluate side-chains 370 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 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 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 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: 2.9990 chunk 67 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 0.0030 chunk 122 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN A 155 GLN C 49 ASN D 129 GLN E 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095136 restraints weight = 22548.324| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.34 r_work: 0.2922 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.053 16333 Z= 0.245 Angle : 0.840 12.564 22905 Z= 0.354 Chirality : 0.048 0.307 3240 Planarity : 0.005 0.046 2394 Dihedral : 5.560 43.875 1938 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.92 % Allowed : 17.09 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.24 (0.19), residues: 774 loop : 0.42 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR B 43 PHE 0.028 0.003 PHE E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (16074) covalent geometry : angle 0.75850 / 0.34 (22149) hydrogen bonds : bond 0.03101 / 2.15 ( 450) hydrogen bonds : angle 6.63176 / 4.58 ( 1275) glycosidic custom : bond 0.00291 / 0.18 ( 45) glycosidic custom : angle 1.96623 / 1.38 ( 135) Misc. bond : bond 0.00218 / 0.11 ( 7) link_ALPHA1-4 : bond 0.00603 / 0.38 ( 45) link_ALPHA1-4 : angle 1.71134 / 1.21 ( 135) link_ALPHA1-6 : bond 0.00446 / 0.27 ( 36) link_ALPHA1-6 : angle 1.53943 / 1.08 ( 108) link_BETA1-4 : bond 0.00281 / 0.19 ( 81) link_BETA1-4 : angle 1.86622 / 1.28 ( 243) link_NAG-ASN : bond 0.00443 / 0.30 ( 45) link_NAG-ASN : angle 3.20419 / 2.13 ( 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 382 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 152 THR cc_start: 0.8314 (m) cc_final: 0.7885 (p) REVERT: A 184 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8174 (p) REVERT: B 67 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7456 (mm110) REVERT: B 102 TYR cc_start: 0.8299 (m-80) cc_final: 0.7795 (m-80) REVERT: B 112 TYR cc_start: 0.8149 (p90) cc_final: 0.7017 (p90) REVERT: B 125 TYR cc_start: 0.8436 (m-80) cc_final: 0.7840 (m-80) REVERT: B 141 VAL cc_start: 0.8493 (t) cc_final: 0.8107 (m) REVERT: B 194 MET cc_start: 0.8464 (mtm) cc_final: 0.8149 (mtp) REVERT: C 76 THR cc_start: 0.8494 (m) cc_final: 0.8017 (p) REVERT: C 93 MET cc_start: 0.8361 (mmp) cc_final: 0.7797 (mmm) REVERT: C 102 TYR cc_start: 0.8424 (m-80) cc_final: 0.7492 (m-80) REVERT: C 112 TYR cc_start: 0.8402 (p90) cc_final: 0.8173 (p90) REVERT: C 152 THR cc_start: 0.8409 (m) cc_final: 0.8167 (p) REVERT: C 156 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8206 (tt) REVERT: C 166 LEU cc_start: 0.8206 (tp) cc_final: 0.7995 (tt) REVERT: C 187 VAL cc_start: 0.8498 (t) cc_final: 0.8067 (p) REVERT: D 201 ILE cc_start: 0.8565 (mp) cc_final: 0.8344 (mm) REVERT: F 102 TYR cc_start: 0.8463 (m-80) cc_final: 0.8233 (m-10) REVERT: F 152 THR cc_start: 0.8590 (m) cc_final: 0.8329 (t) REVERT: F 177 THR cc_start: 0.8078 (m) cc_final: 0.7477 (p) REVERT: F 178 PRO cc_start: 0.8588 (Cg_exo) cc_final: 0.8364 (Cg_endo) REVERT: G 58 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8194 (p) REVERT: G 97 VAL cc_start: 0.8298 (t) cc_final: 0.7916 (m) REVERT: G 102 TYR cc_start: 0.8308 (m-80) cc_final: 0.7659 (m-80) REVERT: G 152 THR cc_start: 0.8460 (m) cc_final: 0.8151 (t) REVERT: G 170 TYR cc_start: 0.8176 (m-10) cc_final: 0.7914 (m-80) REVERT: G 194 MET cc_start: 0.8354 (mtm) cc_final: 0.7831 (mtp) REVERT: H 38 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7772 (m) REVERT: H 128 ASN cc_start: 0.8028 (t0) cc_final: 0.7811 (m-40) REVERT: H 130 GLN cc_start: 0.8224 (mp10) cc_final: 0.7982 (mp10) REVERT: H 148 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.7955 (p) REVERT: I 51 ASN cc_start: 0.8037 (t0) cc_final: 0.7678 (t0) REVERT: I 67 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6848 (mm-40) REVERT: I 78 GLN cc_start: 0.7477 (tt0) cc_final: 0.6974 (tt0) REVERT: I 102 TYR cc_start: 0.8154 (m-80) cc_final: 0.7385 (m-80) outliers start: 55 outliers final: 44 residues processed: 356 average time/residue: 0.0909 time to fit residues: 53.6799 Evaluate side-chains 372 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 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 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain 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 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN C 49 ASN D 129 GLN E 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095294 restraints weight = 22619.614| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.33 r_work: 0.2927 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16333 Z= 0.233 Angle : 0.829 12.613 22905 Z= 0.349 Chirality : 0.048 0.307 3240 Planarity : 0.005 0.046 2394 Dihedral : 5.487 28.890 1936 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.63 % Allowed : 17.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.19), residues: 774 loop : 0.43 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR F 29 PHE 0.025 0.003 PHE E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (16074) covalent geometry : angle 0.74965 / 0.33 (22149) hydrogen bonds : bond 0.03017 / 2.08 ( 450) hydrogen bonds : angle 6.62659 / 4.59 ( 1275) glycosidic custom : bond 0.00293 / 0.18 ( 45) glycosidic custom : angle 1.93120 / 1.35 ( 135) Misc. bond : bond 0.00198 / 0.10 ( 7) link_ALPHA1-4 : bond 0.00598 / 0.37 ( 45) link_ALPHA1-4 : angle 1.68016 / 1.19 ( 135) link_ALPHA1-6 : bond 0.00454 / 0.27 ( 36) link_ALPHA1-6 : angle 1.53050 / 1.08 ( 108) link_BETA1-4 : bond 0.00268 / 0.18 ( 81) link_BETA1-4 : angle 1.81391 / 1.24 ( 243) link_NAG-ASN : bond 0.00423 / 0.29 ( 45) link_NAG-ASN : angle 3.15378 / 2.09 ( 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 377 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8379 (p) REVERT: A 152 THR cc_start: 0.8325 (m) cc_final: 0.7904 (p) REVERT: A 184 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 67 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7440 (mm110) REVERT: B 102 TYR cc_start: 0.8293 (m-80) cc_final: 0.7797 (m-80) REVERT: B 112 TYR cc_start: 0.8167 (p90) cc_final: 0.7007 (p90) REVERT: B 125 TYR cc_start: 0.8442 (m-80) cc_final: 0.7695 (m-80) REVERT: B 141 VAL cc_start: 0.8484 (t) cc_final: 0.8114 (m) REVERT: B 165 LEU cc_start: 0.8406 (tp) cc_final: 0.8141 (tt) REVERT: B 194 MET cc_start: 0.8473 (mtm) cc_final: 0.8161 (mtp) REVERT: C 76 THR cc_start: 0.8496 (m) cc_final: 0.8023 (p) REVERT: C 93 MET cc_start: 0.8363 (mmp) cc_final: 0.7788 (mmm) REVERT: C 102 TYR cc_start: 0.8428 (m-80) cc_final: 0.7563 (m-80) REVERT: C 112 TYR cc_start: 0.8393 (p90) cc_final: 0.8178 (p90) REVERT: C 152 THR cc_start: 0.8407 (m) cc_final: 0.8179 (p) REVERT: C 156 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8234 (tt) REVERT: C 160 SER cc_start: 0.7886 (p) cc_final: 0.7650 (p) REVERT: C 166 LEU cc_start: 0.8212 (tp) cc_final: 0.7997 (tt) REVERT: C 187 VAL cc_start: 0.8498 (t) cc_final: 0.8071 (p) REVERT: D 59 ASN cc_start: 0.8288 (t0) cc_final: 0.7824 (t0) REVERT: D 201 ILE cc_start: 0.8507 (mp) cc_final: 0.8295 (mm) REVERT: F 102 TYR cc_start: 0.8475 (m-80) cc_final: 0.8243 (m-10) REVERT: F 152 THR cc_start: 0.8598 (m) cc_final: 0.8339 (t) REVERT: F 177 THR cc_start: 0.8093 (m) cc_final: 0.7489 (p) REVERT: F 178 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8360 (Cg_endo) REVERT: G 58 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8213 (p) REVERT: G 97 VAL cc_start: 0.8309 (t) cc_final: 0.7951 (m) REVERT: G 102 TYR cc_start: 0.8305 (m-80) cc_final: 0.7636 (m-80) REVERT: G 152 THR cc_start: 0.8418 (m) cc_final: 0.8105 (t) REVERT: G 170 TYR cc_start: 0.8149 (m-10) cc_final: 0.7913 (m-80) REVERT: G 194 MET cc_start: 0.8320 (mtm) cc_final: 0.7687 (mtp) REVERT: H 38 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7766 (m) REVERT: H 128 ASN cc_start: 0.8037 (t0) cc_final: 0.7833 (m-40) REVERT: H 130 GLN cc_start: 0.8220 (mp10) cc_final: 0.7980 (mp10) REVERT: H 148 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7937 (p) REVERT: I 67 GLN cc_start: 0.7441 (mm-40) cc_final: 0.6874 (mm-40) REVERT: I 78 GLN cc_start: 0.7525 (tt0) cc_final: 0.6997 (tt0) REVERT: I 102 TYR cc_start: 0.8156 (m-80) cc_final: 0.7346 (m-80) outliers start: 51 outliers final: 41 residues processed: 353 average time/residue: 0.0891 time to fit residues: 52.0954 Evaluate side-chains 363 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 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 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 G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 112 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN C 49 ASN D 129 GLN E 129 GLN F 129 GLN H 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095997 restraints weight = 22386.147| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.34 r_work: 0.2949 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16333 Z= 0.169 Angle : 0.784 12.535 22905 Z= 0.330 Chirality : 0.046 0.306 3240 Planarity : 0.005 0.047 2394 Dihedral : 5.259 29.353 1936 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.42 % Allowed : 18.02 % Favored : 78.56 % 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: 0.05 (0.23), residues: 1629 helix: None (None), residues: 0 sheet: -0.26 (0.19), residues: 774 loop : 0.53 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR E 125 PHE 0.020 0.002 PHE H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16074) covalent geometry : angle 0.71182 / 0.31 (22149) hydrogen bonds : bond 0.02714 / 1.86 ( 450) hydrogen bonds : angle 6.46543 / 4.48 ( 1275) glycosidic custom : bond 0.00277 / 0.17 ( 45) glycosidic custom : angle 1.72581 / 1.20 ( 135) Misc. bond : bond 0.00121 / 0.06 ( 7) link_ALPHA1-4 : bond 0.00604 / 0.38 ( 45) link_ALPHA1-4 : angle 1.60269 / 1.14 ( 135) link_ALPHA1-6 : bond 0.00508 / 0.31 ( 36) link_ALPHA1-6 : angle 1.45744 / 1.02 ( 108) link_BETA1-4 : bond 0.00254 / 0.17 ( 81) link_BETA1-4 : angle 1.64302 / 1.12 ( 243) link_NAG-ASN : bond 0.00421 / 0.29 ( 45) link_NAG-ASN : angle 3.01071 / 1.99 ( 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 387 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 152 THR cc_start: 0.8312 (m) cc_final: 0.7876 (p) REVERT: A 170 TYR cc_start: 0.8342 (m-10) cc_final: 0.7867 (m-80) REVERT: A 184 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8169 (p) REVERT: B 67 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7380 (mm110) REVERT: B 102 TYR cc_start: 0.8280 (m-80) cc_final: 0.7776 (m-80) REVERT: B 112 TYR cc_start: 0.8139 (p90) cc_final: 0.6985 (p90) REVERT: B 125 TYR cc_start: 0.8436 (m-80) cc_final: 0.7669 (m-80) REVERT: B 141 VAL cc_start: 0.8481 (t) cc_final: 0.8101 (m) REVERT: B 165 LEU cc_start: 0.8401 (tp) cc_final: 0.8123 (tt) REVERT: B 194 MET cc_start: 0.8465 (mtm) cc_final: 0.8155 (mtp) REVERT: C 32 GLN cc_start: 0.8248 (tt0) cc_final: 0.8011 (tt0) REVERT: C 70 SER cc_start: 0.7989 (t) cc_final: 0.7685 (t) REVERT: C 76 THR cc_start: 0.8455 (m) cc_final: 0.7982 (p) REVERT: C 93 MET cc_start: 0.8325 (mmp) cc_final: 0.7793 (mmm) REVERT: C 102 TYR cc_start: 0.8420 (m-80) cc_final: 0.8096 (m-80) REVERT: C 112 TYR cc_start: 0.8394 (p90) cc_final: 0.8184 (p90) REVERT: C 152 THR cc_start: 0.8402 (m) cc_final: 0.8176 (p) REVERT: C 156 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8210 (tt) REVERT: C 166 LEU cc_start: 0.8217 (tp) cc_final: 0.7987 (tt) REVERT: C 187 VAL cc_start: 0.8465 (t) cc_final: 0.8059 (p) REVERT: F 38 VAL cc_start: 0.7742 (p) cc_final: 0.7118 (m) REVERT: F 59 ASN cc_start: 0.8208 (t0) cc_final: 0.7813 (t0) REVERT: F 102 TYR cc_start: 0.8473 (m-80) cc_final: 0.8216 (m-10) REVERT: F 152 THR cc_start: 0.8529 (m) cc_final: 0.8273 (t) REVERT: F 177 THR cc_start: 0.8081 (m) cc_final: 0.7480 (p) REVERT: F 178 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8349 (Cg_endo) REVERT: G 58 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8164 (p) REVERT: G 97 VAL cc_start: 0.8275 (t) cc_final: 0.7910 (m) REVERT: G 102 TYR cc_start: 0.8283 (m-80) cc_final: 0.7579 (m-80) REVERT: G 152 THR cc_start: 0.8409 (m) cc_final: 0.8105 (t) REVERT: G 170 TYR cc_start: 0.8114 (m-10) cc_final: 0.7906 (m-80) REVERT: G 194 MET cc_start: 0.8323 (mtm) cc_final: 0.7694 (mtp) REVERT: H 38 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7610 (m) REVERT: H 128 ASN cc_start: 0.8008 (t0) cc_final: 0.7801 (m-40) REVERT: H 130 GLN cc_start: 0.8214 (mp10) cc_final: 0.7982 (mp10) REVERT: H 148 THR cc_start: 0.8369 (p) cc_final: 0.7909 (p) REVERT: I 51 ASN cc_start: 0.7977 (t0) cc_final: 0.7662 (t0) REVERT: I 67 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6822 (mm-40) REVERT: I 78 GLN cc_start: 0.7513 (tt0) cc_final: 0.6984 (tt0) REVERT: I 89 TYR cc_start: 0.7482 (m-80) cc_final: 0.7198 (m-80) REVERT: I 102 TYR cc_start: 0.8156 (m-80) cc_final: 0.7418 (m-80) outliers start: 48 outliers final: 42 residues processed: 363 average time/residue: 0.0872 time to fit residues: 52.3305 Evaluate side-chains 381 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 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 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 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 G residue 195 THR Chi-restraints excluded: chain G residue 197 SER 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 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 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: 0.8980 chunk 2 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN C 116 ASN C 120 GLN D 188 ASN E 30 GLN E 129 GLN F 129 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091420 restraints weight = 23094.303| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.31 r_work: 0.3035 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 16333 Z= 0.196 Angle : 0.941 59.168 22905 Z= 0.471 Chirality : 0.050 0.918 3240 Planarity : 0.005 0.047 2394 Dihedral : 5.251 29.371 1936 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 18.38 % Favored : 78.21 % Cbeta Deviations : 0.07 % 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: -0.27 (0.19), residues: 774 loop : 0.53 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR H 86 PHE 0.026 0.002 PHE H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (16074) covalent geometry : angle 0.88293 / 0.46 (22149) hydrogen bonds : bond 0.02946 / 2.00 ( 450) hydrogen bonds : angle 6.48178 / 4.49 ( 1275) glycosidic custom : bond 0.00276 / 0.17 ( 45) glycosidic custom : angle 1.72041 / 1.19 ( 135) Misc. bond : bond 0.00109 / 0.06 ( 7) link_ALPHA1-4 : bond 0.00610 / 0.38 ( 45) link_ALPHA1-4 : angle 1.60214 / 1.14 ( 135) link_ALPHA1-6 : bond 0.00540 / 0.32 ( 36) link_ALPHA1-6 : angle 1.47748 / 1.04 ( 108) link_BETA1-4 : bond 0.00293 / 0.24 ( 81) link_BETA1-4 : angle 1.64079 / 1.12 ( 243) link_NAG-ASN : bond 0.00464 / 0.31 ( 45) link_NAG-ASN : angle 3.18537 / 2.08 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.72 seconds wall clock time: 63 minutes 21.48 seconds (3801.48 seconds total)