Starting phenix.real_space_refine on Sat Dec 28 08:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7j_31773/12_2024/7v7j_31773.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 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 222 5.16 5 C 32442 2.51 5 N 8274 2.21 5 O 10134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51072 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "E" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "F" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "IA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "KA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "LA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "MA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "NA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "OA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "PA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 23.36, per 1000 atoms: 0.46 Number of scatterers: 51072 At special positions: 0 Unit cell: (171.6, 155.1, 326.7, 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 222 16.00 O 10134 8.00 N 8274 7.00 C 32442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=74, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " NAG-ASN " NAG 0 1 " - " ASN D1098 " " NAG 1 1 " - " ASN D1134 " " NAG 2 1 " - " ASN E 122 " " NAG 3 1 " - " ASN E 165 " " NAG 4 1 " - " ASN E 234 " " NAG 5 1 " - " ASN E 282 " " NAG 6 1 " - " ASN E 343 " " NAG 7 1 " - " ASN E 616 " " NAG 8 1 " - " ASN E 709 " " NAG 9 1 " - " ASN E 717 " " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 331 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 331 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 331 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D2001 " - " ASN D 61 " " NAG D2002 " - " ASN D 331 " " NAG D2003 " - " ASN D 603 " " NAG D2004 " - " ASN D 657 " " NAG E2001 " - " ASN E 61 " " NAG E2002 " - " ASN E 331 " " NAG E2003 " - " ASN E 603 " " NAG E2004 " - " ASN E 657 " " NAG F2001 " - " ASN F 61 " " NAG F2002 " - " ASN F 331 " " NAG F2003 " - " ASN F 603 " " NAG F2004 " - " ASN F 657 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 343 " " NAG L 1 " - " ASN A 616 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 165 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B1098 " " NAG d 1 " - " ASN B1134 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 165 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 282 " " NAG i 1 " - " ASN C 343 " " NAG j 1 " - " ASN C 616 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN D 122 " " NAG r 1 " - " ASN D 165 " " NAG s 1 " - " ASN D 234 " " NAG t 1 " - " ASN D 282 " " NAG u 1 " - " ASN D 343 " " NAG v 1 " - " ASN D 616 " " NAG w 1 " - " ASN D 709 " " NAG x 1 " - " ASN D 717 " " NAG y 1 " - " ASN D 801 " " NAG z 1 " - " ASN D1074 " " NAGAA 1 " - " ASN E 801 " " NAGBA 1 " - " ASN E1074 " " NAGCA 1 " - " ASN E1098 " " NAGDA 1 " - " ASN E1134 " " NAGEA 1 " - " ASN F 122 " " NAGFA 1 " - " ASN F 165 " " NAGGA 1 " - " ASN F 234 " " NAGHA 1 " - " ASN F 282 " " NAGIA 1 " - " ASN F 343 " " NAGJA 1 " - " ASN F 616 " " NAGKA 1 " - " ASN F 709 " " NAGLA 1 " - " ASN F 717 " " NAGMA 1 " - " ASN F 801 " " NAGNA 1 " - " ASN F1074 " " NAGOA 1 " - " ASN F1098 " " NAGPA 1 " - " ASN F1134 " Time building additional restraints: 11.43 Conformation dependent library (CDL) restraints added in 4.8 seconds 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 90 sheets defined 25.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.969A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.112A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.538A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.277A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.526A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.553A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.566A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.629A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.105A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.465A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.785A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.109A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 6.715A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.653A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.851A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.640A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.142A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.759A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.675A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.822A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.779A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.849A pdb=" N SER D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.057A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.584A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.757A pdb=" N ALA D 766 " --> pdb=" O GLN D 762 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.617A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.513A pdb=" N GLN D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.359A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 4.027A pdb=" N LEU D 984 " --> pdb=" O ILE D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1034 removed outlier: 4.400A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D1034 " --> pdb=" O SER D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 removed outlier: 3.536A pdb=" N ASP D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.641A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.572A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.661A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.349A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 767 " --> pdb=" O LEU E 763 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 768 " --> pdb=" O ASN E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 884 removed outlier: 3.537A pdb=" N ILE E 870 " --> pdb=" O THR E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.524A pdb=" N GLN E 901 " --> pdb=" O PRO E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.390A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.644A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.816A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1146 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.164A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.532A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 3.627A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 755 removed outlier: 3.905A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 removed outlier: 3.550A pdb=" N LEU F 763 " --> pdb=" O PHE F 759 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 767 " --> pdb=" O LEU F 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.500A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 912 through 941 removed outlier: 4.343A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) Processing helix chain 'F' and resid 946 through 965 Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.985A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.881A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.913A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.149A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.378A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.161A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.588A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.094A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.278A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.807A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.592A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.355A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.090A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.818A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.253A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 575 through 576 removed outlier: 7.285A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.561A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.079A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.852A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 11.167A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 143 through 144 removed outlier: 4.979A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.529A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.269A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.810A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.482A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF1, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.727A pdb=" N PHE D 43 " --> pdb=" O ARG F 567 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY F 566 " --> pdb=" O ASP F 574 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.189A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.822A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N VAL D 126 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU D 169 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE D 128 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR D 167 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 130 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN D 165 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU D 132 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA D 163 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN D 134 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS D 136 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N VAL D 159 " --> pdb=" O CYS D 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 143 through 144 removed outlier: 5.516A pdb=" N VAL D 143 " --> pdb=" O ARG D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.486A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 325 through 328 removed outlier: 7.643A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AF9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'D' and resid 573 through 576 removed outlier: 3.693A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 654 through 660 removed outlier: 5.844A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AG5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 735 through 736 Processing sheet with id=AG7, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AG8, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 5.448A pdb=" N VAL D1122 " --> pdb=" O PHE D1089 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE D1089 " --> pdb=" O VAL D1122 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY D1124 " --> pdb=" O ALA D1087 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1094 through 1096 Processing sheet with id=AH1, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.852A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.117A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.801A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN E 165 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN E 134 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA E 163 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 325 through 326 removed outlier: 5.797A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.937A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH9, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AI1, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.213A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 701 through 703 Processing sheet with id=AI3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.498A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E1047 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AI5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 5.470A pdb=" N VAL E1122 " --> pdb=" O PHE E1089 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE E1089 " --> pdb=" O VAL E1122 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY E1124 " --> pdb=" O ALA E1087 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 1094 through 1096 Processing sheet with id=AI7, first strand: chain 'F' and resid 27 through 30 removed outlier: 8.051A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 47 through 55 removed outlier: 4.165A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.812A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE F 105 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN F 165 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN F 134 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 163 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.218A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AJ3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AJ4, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AJ5, first strand: chain 'F' and resid 654 through 659 removed outlier: 5.949A pdb=" N THR F 696 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASN F 658 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.883A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.883A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 5.293A pdb=" N VAL F1122 " --> pdb=" O PHE F1089 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE F1089 " --> pdb=" O VAL F1122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY F1124 " --> pdb=" O ALA F1087 " (cutoff:3.500A) 1981 hydrogen bonds defined for protein. 5364 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: 21.47 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16052 1.34 - 1.46: 12810 1.46 - 1.58: 23050 1.58 - 1.70: 0 1.70 - 1.82: 276 Bond restraints: 52188 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" C1 NAG 2 2 " pdb=" O5 NAG 2 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAGEA 1 " pdb=" O5 NAGEA 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 52183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 69955 2.21 - 4.42: 969 4.42 - 6.63: 81 6.63 - 8.84: 19 8.84 - 11.05: 4 Bond angle restraints: 71028 Sorted by residual: angle pdb=" C LEU F 518 " pdb=" CA LEU F 518 " pdb=" CB LEU F 518 " ideal model delta sigma weight residual 115.79 108.47 7.32 1.19e+00 7.06e-01 3.78e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 113.20 109.61 3.59 9.60e-01 1.09e+00 1.40e+01 angle pdb=" N GLN F1002 " pdb=" CA GLN F1002 " pdb=" CB GLN F1002 " ideal model delta sigma weight residual 110.12 115.26 -5.14 1.47e+00 4.63e-01 1.22e+01 angle pdb=" C VAL B 781 " pdb=" N PHE B 782 " pdb=" CA PHE B 782 " ideal model delta sigma weight residual 122.60 116.42 6.18 1.88e+00 2.83e-01 1.08e+01 ... (remaining 71023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 31197 23.12 - 46.23: 1728 46.23 - 69.35: 228 69.35 - 92.46: 100 92.46 - 115.58: 53 Dihedral angle restraints: 33306 sinusoidal: 15180 harmonic: 18126 Sorted by residual: dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -175.87 89.87 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS F 662 " pdb=" SG CYS F 662 " pdb=" SG CYS F 671 " pdb=" CB CYS F 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.70 88.70 1 1.00e+01 1.00e-02 9.38e+01 ... (remaining 33303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 8532 0.163 - 0.326: 35 0.326 - 0.488: 3 0.488 - 0.651: 3 0.651 - 0.814: 1 Chirality restraints: 8574 Sorted by residual: chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG D2001 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D2001 " pdb=" O5 NAG D2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" C1 NAG 3 1 " pdb=" ND2 ASN E 165 " pdb=" C2 NAG 3 1 " pdb=" O5 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.02e+00 ... (remaining 8571 not shown) Planarity restraints: 9054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B1041 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ASP B1041 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP B1041 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE B1042 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 986 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 61 " 0.019 2.00e-02 2.50e+03 1.78e-02 3.95e+00 pdb=" CG ASN E 61 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN E 61 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN E 61 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG E2001 " 0.018 2.00e-02 2.50e+03 ... (remaining 9051 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1582 2.70 - 3.25: 51295 3.25 - 3.80: 79089 3.80 - 4.35: 95455 4.35 - 4.90: 162445 Nonbonded interactions: 389866 Sorted by model distance: nonbonded pdb=" O GLU E 661 " pdb=" OH TYR E 695 " model vdw 2.144 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.151 3.040 nonbonded pdb=" OG SER E 116 " pdb=" O CYS E 131 " model vdw 2.158 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O ARG A 452 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP D 568 " pdb=" OG1 THR D 572 " model vdw 2.161 3.040 ... (remaining 389861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'J' selection = chain 'JA' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = 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 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' 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 'z' } ncs_group { reference = chain '6' selection = chain 'IA' selection = chain 'K' selection = chain 'W' selection = chain 'i' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.530 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 93.780 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.005 0.059 52188 Z= 0.297 Angle : 0.643 11.047 71028 Z= 0.319 Chirality : 0.049 0.814 8574 Planarity : 0.004 0.053 8958 Dihedral : 14.697 115.577 21420 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 6132 helix: 1.78 (0.15), residues: 1316 sheet: 0.54 (0.14), residues: 1382 loop : -1.50 (0.10), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 104 HIS 0.005 0.001 HIS B1083 PHE 0.027 0.001 PHE B 559 TYR 0.027 0.001 TYR A 873 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 PHE cc_start: 0.7996 (m-80) cc_final: 0.7605 (m-80) REVERT: B 369 TYR cc_start: 0.8847 (t80) cc_final: 0.8634 (t80) REVERT: B 941 THR cc_start: 0.7152 (m) cc_final: 0.6765 (p) REVERT: B 1002 GLN cc_start: 0.8924 (tp40) cc_final: 0.8539 (tp40) REVERT: C 780 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 1029 MET cc_start: 0.8860 (tmm) cc_final: 0.8242 (tmm) REVERT: D 220 PHE cc_start: 0.7629 (t80) cc_final: 0.7282 (t80) REVERT: D 979 ASP cc_start: 0.8730 (m-30) cc_final: 0.8340 (p0) REVERT: E 170 TYR cc_start: 0.9144 (t80) cc_final: 0.8925 (t80) REVERT: E 739 THR cc_start: 0.8464 (p) cc_final: 0.8250 (t) REVERT: E 869 MET cc_start: 0.9017 (mpp) cc_final: 0.8468 (mpp) REVERT: F 933 LYS cc_start: 0.9750 (ttmm) cc_final: 0.9342 (mtmm) REVERT: F 1002 GLN cc_start: 0.8642 (mp10) cc_final: 0.8386 (mp10) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.4620 time to fit residues: 147.9733 Evaluate side-chains 128 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 8.9990 chunk 468 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 294 optimal weight: 8.9990 chunk 360 optimal weight: 0.8980 chunk 561 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 81 ASN B 474 GLN B 506 GLN C 474 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN E 774 GLN E 949 GLN E 953 ASN F 188 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 949 GLN F 953 ASN F1048 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52188 Z= 0.196 Angle : 0.562 9.583 71028 Z= 0.283 Chirality : 0.045 0.540 8574 Planarity : 0.004 0.056 8958 Dihedral : 9.242 102.486 10320 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 0.17 % Allowed : 5.40 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6132 helix: 1.72 (0.15), residues: 1346 sheet: 0.56 (0.14), residues: 1452 loop : -1.46 (0.11), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS B1083 PHE 0.018 0.001 PHE B 559 TYR 0.025 0.001 TYR B1138 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.8759 (m-80) cc_final: 0.8503 (m-80) REVERT: B 369 TYR cc_start: 0.8689 (t80) cc_final: 0.8489 (t80) REVERT: B 941 THR cc_start: 0.6967 (m) cc_final: 0.6613 (p) REVERT: B 1002 GLN cc_start: 0.8902 (tp40) cc_final: 0.8528 (tp40) REVERT: C 780 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 1029 MET cc_start: 0.8726 (tmm) cc_final: 0.8512 (ttm) REVERT: D 220 PHE cc_start: 0.7585 (t80) cc_final: 0.7257 (t80) REVERT: D 571 ASP cc_start: 0.8790 (t70) cc_final: 0.8576 (p0) REVERT: E 170 TYR cc_start: 0.9159 (t80) cc_final: 0.8931 (t80) REVERT: E 739 THR cc_start: 0.8376 (p) cc_final: 0.8122 (t) REVERT: E 869 MET cc_start: 0.9038 (mpp) cc_final: 0.8293 (mpp) REVERT: F 779 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8777 (tm-30) REVERT: F 933 LYS cc_start: 0.9746 (ttmm) cc_final: 0.9356 (mtmm) outliers start: 9 outliers final: 4 residues processed: 152 average time/residue: 0.4675 time to fit residues: 127.2756 Evaluate side-chains 132 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain D residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 467 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 562 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 10.0000 chunk 557 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 451 optimal weight: 8.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1106 GLN B 506 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1106 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 52188 Z= 0.388 Angle : 0.634 9.286 71028 Z= 0.319 Chirality : 0.047 0.530 8574 Planarity : 0.004 0.055 8958 Dihedral : 8.018 95.212 10320 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 0.55 % Allowed : 9.61 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 6132 helix: 1.38 (0.15), residues: 1344 sheet: 0.34 (0.13), residues: 1460 loop : -1.55 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.005 0.001 HIS A 49 PHE 0.019 0.002 PHE B 559 TYR 0.024 0.001 TYR F1067 ARG 0.014 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 941 THR cc_start: 0.7091 (m) cc_final: 0.6736 (p) REVERT: B 1002 GLN cc_start: 0.9059 (tp40) cc_final: 0.8642 (tp40) REVERT: C 780 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 1116 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8239 (p) REVERT: D 220 PHE cc_start: 0.7717 (t80) cc_final: 0.7409 (t80) REVERT: D 1029 MET cc_start: 0.9064 (tpp) cc_final: 0.8767 (tpp) REVERT: E 170 TYR cc_start: 0.9167 (t80) cc_final: 0.8928 (t80) REVERT: E 739 THR cc_start: 0.8413 (p) cc_final: 0.8191 (t) REVERT: E 869 MET cc_start: 0.9190 (mpp) cc_final: 0.8414 (mpp) REVERT: F 869 MET cc_start: 0.9116 (mtt) cc_final: 0.8651 (mtm) REVERT: F 933 LYS cc_start: 0.9759 (ttmm) cc_final: 0.9396 (mtmm) outliers start: 30 outliers final: 16 residues processed: 152 average time/residue: 0.4445 time to fit residues: 122.6735 Evaluate side-chains 136 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain F residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 268 optimal weight: 4.9990 chunk 377 optimal weight: 0.9990 chunk 564 optimal weight: 1.9990 chunk 597 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 534 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 606 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 52188 Z= 0.159 Angle : 0.528 8.779 71028 Z= 0.267 Chirality : 0.045 0.542 8574 Planarity : 0.004 0.059 8958 Dihedral : 7.108 93.529 10320 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.83 % Allowed : 11.04 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 6132 helix: 1.54 (0.15), residues: 1372 sheet: 0.58 (0.14), residues: 1432 loop : -1.48 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.000 HIS B1083 PHE 0.015 0.001 PHE A 220 TYR 0.021 0.001 TYR B1138 ARG 0.004 0.000 ARG D1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6139 (pmm) cc_final: 0.5847 (pmm) REVERT: B 106 PHE cc_start: 0.8660 (m-80) cc_final: 0.8324 (m-80) REVERT: B 1002 GLN cc_start: 0.8872 (tp40) cc_final: 0.8511 (tp40) REVERT: C 581 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9006 (p) REVERT: C 1116 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8213 (p) REVERT: D 220 PHE cc_start: 0.7644 (t80) cc_final: 0.7318 (t80) REVERT: D 1029 MET cc_start: 0.8976 (tpp) cc_final: 0.8658 (tpp) REVERT: E 170 TYR cc_start: 0.9123 (t80) cc_final: 0.8886 (t80) REVERT: E 869 MET cc_start: 0.9236 (mpp) cc_final: 0.8461 (mpp) REVERT: F 858 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8950 (pp) REVERT: F 933 LYS cc_start: 0.9751 (ttmm) cc_final: 0.9421 (mtmm) outliers start: 45 outliers final: 16 residues processed: 180 average time/residue: 0.4823 time to fit residues: 155.9487 Evaluate side-chains 145 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 444 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 509 optimal weight: 4.9990 chunk 412 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 305 optimal weight: 1.9990 chunk 536 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 52188 Z= 0.295 Angle : 0.571 9.594 71028 Z= 0.287 Chirality : 0.045 0.537 8574 Planarity : 0.004 0.057 8958 Dihedral : 6.949 91.800 10320 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 0.92 % Allowed : 12.86 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 6132 helix: 1.51 (0.15), residues: 1352 sheet: 0.46 (0.14), residues: 1442 loop : -1.49 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE B 559 TYR 0.021 0.001 TYR F1067 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.8696 (m-80) cc_final: 0.8403 (m-80) REVERT: B 1002 GLN cc_start: 0.9006 (tp40) cc_final: 0.8643 (tp40) REVERT: C 144 TYR cc_start: 0.8526 (m-10) cc_final: 0.8287 (m-10) REVERT: C 581 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9022 (p) REVERT: C 1116 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8321 (p) REVERT: D 220 PHE cc_start: 0.7680 (t80) cc_final: 0.7330 (t80) REVERT: D 1029 MET cc_start: 0.9055 (tpp) cc_final: 0.8741 (tpp) REVERT: E 170 TYR cc_start: 0.9121 (t80) cc_final: 0.8877 (t80) REVERT: E 869 MET cc_start: 0.9289 (mpp) cc_final: 0.8447 (mpp) REVERT: F 858 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8973 (pp) outliers start: 50 outliers final: 26 residues processed: 169 average time/residue: 0.4282 time to fit residues: 132.2683 Evaluate side-chains 144 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 9.9990 chunk 537 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 597 optimal weight: 3.9990 chunk 496 optimal weight: 4.9990 chunk 276 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52188 Z= 0.206 Angle : 0.535 8.272 71028 Z= 0.269 Chirality : 0.044 0.538 8574 Planarity : 0.004 0.058 8958 Dihedral : 6.743 90.385 10320 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 1.21 % Allowed : 13.45 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6132 helix: 1.61 (0.15), residues: 1348 sheet: 0.52 (0.14), residues: 1426 loop : -1.46 (0.11), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS B1083 PHE 0.013 0.001 PHE B 559 TYR 0.018 0.001 TYR F1067 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 133 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.8652 (m-80) cc_final: 0.8332 (m-80) REVERT: B 1002 GLN cc_start: 0.8923 (tp40) cc_final: 0.8560 (tp40) REVERT: C 144 TYR cc_start: 0.8495 (m-10) cc_final: 0.8229 (m-10) REVERT: C 581 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 1116 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8295 (p) REVERT: D 220 PHE cc_start: 0.7665 (t80) cc_final: 0.7306 (t80) REVERT: D 1029 MET cc_start: 0.9017 (tpp) cc_final: 0.8692 (tpp) REVERT: E 170 TYR cc_start: 0.9109 (t80) cc_final: 0.8860 (t80) REVERT: E 869 MET cc_start: 0.9291 (mpp) cc_final: 0.8429 (mpp) REVERT: F 858 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8958 (pp) outliers start: 66 outliers final: 35 residues processed: 189 average time/residue: 0.4293 time to fit residues: 147.7033 Evaluate side-chains 163 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1002 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 436 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 503 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 595 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 363 optimal weight: 0.1980 chunk 275 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 52188 Z= 0.297 Angle : 0.573 8.320 71028 Z= 0.288 Chirality : 0.045 0.534 8574 Planarity : 0.004 0.057 8958 Dihedral : 6.741 88.694 10320 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 1.43 % Allowed : 13.86 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 6132 helix: 1.62 (0.15), residues: 1315 sheet: 0.30 (0.14), residues: 1450 loop : -1.50 (0.11), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B1071 PHE 0.024 0.001 PHE D 392 TYR 0.021 0.001 TYR F1067 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 125 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.8725 (m-80) cc_final: 0.8398 (m-80) REVERT: B 900 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: B 1002 GLN cc_start: 0.8993 (tp40) cc_final: 0.8625 (tp40) REVERT: C 144 TYR cc_start: 0.8525 (m-10) cc_final: 0.8192 (m-10) REVERT: C 581 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9020 (p) REVERT: C 1116 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8382 (p) REVERT: D 220 PHE cc_start: 0.7700 (t80) cc_final: 0.7374 (t80) REVERT: D 697 MET cc_start: 0.7507 (mpp) cc_final: 0.7247 (mpp) REVERT: D 1029 MET cc_start: 0.9062 (tpp) cc_final: 0.8734 (tpp) REVERT: E 170 TYR cc_start: 0.9131 (t80) cc_final: 0.8884 (t80) REVERT: E 869 MET cc_start: 0.9290 (mpp) cc_final: 0.8364 (mpp) REVERT: F 441 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9447 (mm) REVERT: F 858 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8974 (pp) REVERT: F 900 MET cc_start: 0.8215 (ppp) cc_final: 0.8009 (ppp) outliers start: 78 outliers final: 49 residues processed: 195 average time/residue: 0.4338 time to fit residues: 156.4229 Evaluate side-chains 174 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 826 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 355 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 378 optimal weight: 0.8980 chunk 405 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 468 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 52188 Z= 0.157 Angle : 0.524 10.969 71028 Z= 0.265 Chirality : 0.044 0.536 8574 Planarity : 0.004 0.059 8958 Dihedral : 6.473 86.890 10320 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 14.39 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6132 helix: 1.61 (0.15), residues: 1357 sheet: 0.49 (0.14), residues: 1438 loop : -1.46 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS B1083 PHE 0.012 0.001 PHE B 898 TYR 0.016 0.001 TYR F1067 ARG 0.006 0.000 ARG F1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 106 PHE cc_start: 0.8634 (m-80) cc_final: 0.8307 (m-80) REVERT: B 740 MET cc_start: 0.8676 (mmm) cc_final: 0.8414 (mmm) REVERT: B 1002 GLN cc_start: 0.8864 (tp40) cc_final: 0.8496 (tp40) REVERT: C 144 TYR cc_start: 0.8582 (m-10) cc_final: 0.8314 (m-10) REVERT: C 560 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9093 (mp) REVERT: C 581 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8972 (p) REVERT: C 1116 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (p) REVERT: D 220 PHE cc_start: 0.7621 (t80) cc_final: 0.7275 (t80) REVERT: D 697 MET cc_start: 0.7464 (mpp) cc_final: 0.7107 (mpp) REVERT: D 1029 MET cc_start: 0.9019 (tpp) cc_final: 0.8685 (tpp) REVERT: E 170 TYR cc_start: 0.9096 (t80) cc_final: 0.8851 (t80) REVERT: E 762 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9056 (mp10) REVERT: E 869 MET cc_start: 0.9277 (mpp) cc_final: 0.8413 (mpp) REVERT: F 858 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8938 (pp) outliers start: 63 outliers final: 47 residues processed: 192 average time/residue: 0.4314 time to fit residues: 150.8806 Evaluate side-chains 183 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain E residue 762 GLN Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 826 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 5.9990 chunk 570 optimal weight: 4.9990 chunk 520 optimal weight: 1.9990 chunk 555 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 241 optimal weight: 0.0570 chunk 435 optimal weight: 10.0000 chunk 170 optimal weight: 0.0020 chunk 501 optimal weight: 2.9990 chunk 524 optimal weight: 20.0000 chunk 553 optimal weight: 8.9990 overall best weight: 2.0112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 52188 Z= 0.202 Angle : 0.540 10.279 71028 Z= 0.271 Chirality : 0.044 0.537 8574 Planarity : 0.004 0.058 8958 Dihedral : 6.398 85.103 10320 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 1.21 % Allowed : 14.57 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 6132 helix: 1.64 (0.15), residues: 1341 sheet: 0.45 (0.14), residues: 1451 loop : -1.46 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS B1071 PHE 0.012 0.001 PHE B 559 TYR 0.018 0.001 TYR F1067 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8671 (mm) REVERT: B 106 PHE cc_start: 0.8643 (m-80) cc_final: 0.8349 (m-80) REVERT: B 740 MET cc_start: 0.8694 (mmm) cc_final: 0.8431 (mmm) REVERT: B 981 LEU cc_start: 0.9033 (mt) cc_final: 0.8532 (pp) REVERT: B 1002 GLN cc_start: 0.8907 (tp40) cc_final: 0.8530 (tp40) REVERT: C 144 TYR cc_start: 0.8577 (m-10) cc_final: 0.8290 (m-10) REVERT: C 560 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 581 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 1116 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (p) REVERT: D 220 PHE cc_start: 0.7646 (t80) cc_final: 0.7298 (t80) REVERT: D 697 MET cc_start: 0.7524 (mpp) cc_final: 0.7193 (mpp) REVERT: E 170 TYR cc_start: 0.9122 (t80) cc_final: 0.8891 (t80) REVERT: E 762 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.9136 (mp10) REVERT: E 869 MET cc_start: 0.9266 (mpp) cc_final: 0.8378 (mpp) REVERT: F 858 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8946 (pp) outliers start: 66 outliers final: 54 residues processed: 188 average time/residue: 0.4345 time to fit residues: 150.1904 Evaluate side-chains 186 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain E residue 762 GLN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 826 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 278 optimal weight: 0.0040 chunk 408 optimal weight: 0.7980 chunk 615 optimal weight: 5.9990 chunk 566 optimal weight: 6.9990 chunk 490 optimal weight: 0.0010 chunk 50 optimal weight: 0.9980 chunk 378 optimal weight: 0.7980 chunk 300 optimal weight: 0.0970 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C1083 HIS ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 52188 Z= 0.128 Angle : 0.521 10.928 71028 Z= 0.261 Chirality : 0.044 0.526 8574 Planarity : 0.004 0.061 8958 Dihedral : 6.077 81.396 10320 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 0.85 % Allowed : 14.98 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 6132 helix: 1.66 (0.15), residues: 1355 sheet: 0.64 (0.14), residues: 1422 loop : -1.35 (0.11), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 436 HIS 0.002 0.000 HIS A1048 PHE 0.016 0.001 PHE B 898 TYR 0.030 0.001 TYR E 200 ARG 0.004 0.000 ARG C 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 106 PHE cc_start: 0.8663 (m-80) cc_final: 0.8391 (m-80) REVERT: B 740 MET cc_start: 0.8645 (mmm) cc_final: 0.8421 (mmm) REVERT: B 981 LEU cc_start: 0.8999 (mt) cc_final: 0.8526 (pp) REVERT: C 144 TYR cc_start: 0.8550 (m-10) cc_final: 0.8247 (m-10) REVERT: C 560 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9042 (mp) REVERT: C 581 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 1116 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8329 (p) REVERT: D 153 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5460 (tmm) REVERT: D 220 PHE cc_start: 0.7555 (t80) cc_final: 0.7245 (t80) REVERT: D 571 ASP cc_start: 0.8694 (p0) cc_final: 0.8493 (t0) REVERT: D 697 MET cc_start: 0.7550 (mpp) cc_final: 0.7195 (mpp) REVERT: E 170 TYR cc_start: 0.9099 (t80) cc_final: 0.8880 (t80) REVERT: E 762 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9096 (mp10) REVERT: E 869 MET cc_start: 0.9234 (mpp) cc_final: 0.8418 (mpp) REVERT: F 869 MET cc_start: 0.8587 (mtm) cc_final: 0.8343 (pmm) REVERT: F 933 LYS cc_start: 0.9726 (ttmm) cc_final: 0.9450 (mtmm) outliers start: 46 outliers final: 36 residues processed: 198 average time/residue: 0.4446 time to fit residues: 160.4890 Evaluate side-chains 182 residues out of total 5442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain E residue 762 GLN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 10.0000 chunk 522 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 452 optimal weight: 7.9990 chunk 72 optimal weight: 0.0060 chunk 136 optimal weight: 4.9990 chunk 491 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 504 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.065668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046208 restraints weight = 219300.517| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.60 r_work: 0.2794 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 52188 Z= 0.262 Angle : 0.559 9.705 71028 Z= 0.281 Chirality : 0.044 0.534 8574 Planarity : 0.004 0.058 8958 Dihedral : 6.170 79.321 10320 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.07 % Allowed : 14.99 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6132 helix: 1.68 (0.15), residues: 1332 sheet: 0.44 (0.14), residues: 1435 loop : -1.40 (0.11), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1102 HIS 0.004 0.001 HIS E1064 PHE 0.014 0.001 PHE B 559 TYR 0.019 0.001 TYR E 369 ARG 0.003 0.000 ARG C 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.09 seconds wall clock time: 112 minutes 31.16 seconds (6751.16 seconds total)