Starting phenix.real_space_refine on Mon Sep 14 12:45:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.cif Found real_map, /net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.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/5szs_8331/09_2026/5szs_8331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.cif" model { file = "/net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5szs_8331/09_2026/5szs_8331.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 129 5.16 5 C 19089 2.51 5 N 4743 2.21 5 O 6345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30306 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "C" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 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 chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" 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 chiralities: 3 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 chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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 chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "X" 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 chiralities: 3 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 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 chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "g" 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 chiralities: 3 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 chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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 chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "s" 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 chiralities: 3 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 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 chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "0" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "1" 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 chiralities: 3 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 chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "4" 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 chiralities: 3 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 chiralities: 2 Chain: "6" 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 chiralities: 2 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 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 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 chiralities: 2 Chain: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "BA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "DA" 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 chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.50, per 1000 atoms: 0.25 Number of scatterers: 30306 At special positions: 0 Unit cell: (150.96, 141.44, 178.16, 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 129 16.00 O 6345 8.00 N 4743 7.00 C 19089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 210 " distance=2.21 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 497 " - pdb=" SG CYS A 500 " distance=2.04 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 567 " distance=2.05 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 678 " distance=2.25 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 737 " distance=2.02 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 811 " distance=2.07 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS A 800 " distance=2.02 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 907 " distance=2.04 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1195 " distance=1.74 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 210 " distance=2.21 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 500 " distance=2.04 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 678 " distance=2.25 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 737 " distance=2.02 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 811 " distance=2.07 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 800 " distance=2.02 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 907 " distance=2.04 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1195 " distance=1.74 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 181 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 210 " distance=2.21 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 497 " - pdb=" SG CYS C 500 " distance=2.04 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 567 " distance=2.05 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 678 " distance=2.25 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 737 " distance=2.02 Simple disulfide: pdb=" SG CYS C 789 " - pdb=" SG CYS C 811 " distance=2.07 Simple disulfide: pdb=" SG CYS C 794 " - pdb=" SG CYS C 800 " distance=2.02 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 907 " distance=2.04 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1195 " distance=1.74 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 Atom "HETATM28675 O4 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM27812 O4 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29538 O4 NAG 1 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN D 4 " - " MAN D 5 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN Y 4 " - " MAN Y 5 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 8 " " BMA 3 3 " - " MAN 3 4 " " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " BMA 3 3 " - " MAN 3 5 " " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 7 " " BMA N 3 " - " MAN N 5 " " BMA V 3 " - " MAN V 5 " " BMA Y 3 " - " MAN Y 6 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 7 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " " BMA t 3 " - " MAN t 6 " " BMA x 3 " - " MAN x 4 " " BMABA 3 " - " MANBA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 2 " - " BMA g 3 " " 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 j 2 " - " BMA j 3 " " 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 426 " " NAG 1 1 " - " ASN C 486 " " NAG 2 1 " - " ASN C 506 " " NAG 3 1 " - " ASN C 666 " " NAG 4 1 " - " ASN C 699 " " NAG 5 1 " - " ASN C 723 " " NAG 6 1 " - " ASN C 749 " " NAG 7 1 " - " ASN C 762 " " NAG 8 1 " - " ASN C 768 " " NAG 9 1 " - " ASN C 844 " " NAG A1401 " - " ASN A 155 " " NAG A1402 " - " ASN A 187 " " NAG A1403 " - " ASN A 193 " " NAG A1439 " - " ASN A 512 " " NAG A1440 " - " ASN A 626 " " NAG A1441 " - " ASN A 645 " " NAG A1474 " - " ASN A1218 " " NAG B1401 " - " ASN B 155 " " NAG B1402 " - " ASN B 187 " " NAG B1403 " - " ASN B 193 " " NAG B1439 " - " ASN B 512 " " NAG B1440 " - " ASN B 626 " " NAG B1441 " - " ASN B 645 " " NAG B1474 " - " ASN B1218 " " NAG C1401 " - " ASN C 155 " " NAG C1402 " - " ASN C 187 " " NAG C1403 " - " ASN C 193 " " NAG C1439 " - " ASN C 512 " " NAG C1440 " - " ASN C 626 " " NAG C1441 " - " ASN C 645 " " NAG C1474 " - " ASN C1218 " " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 301 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 354 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 403 " " NAG K 1 " - " ASN A 426 " " NAG L 1 " - " ASN A 486 " " NAG M 1 " - " ASN A 506 " " NAG N 1 " - " ASN A 666 " " NAG O 1 " - " ASN A 699 " " NAG P 1 " - " ASN A 723 " " NAG Q 1 " - " ASN A 749 " " NAG R 1 " - " ASN A 762 " " NAG S 1 " - " ASN A 768 " " NAG T 1 " - " ASN A 844 " " NAG U 1 " - " ASN A 852 " " NAG V 1 " - " ASN A1111 " " NAG W 1 " - " ASN A1196 " " NAG X 1 " - " ASN A1201 " " NAG Y 1 " - " ASN B 240 " " NAG Z 1 " - " ASN B 276 " " NAG a 1 " - " ASN B 301 " " NAG b 1 " - " ASN B 330 " " NAG c 1 " - " ASN B 354 " " NAG d 1 " - " ASN B 358 " " NAG e 1 " - " ASN B 403 " " NAG f 1 " - " ASN B 426 " " NAG g 1 " - " ASN B 486 " " NAG h 1 " - " ASN B 506 " " NAG i 1 " - " ASN B 666 " " NAG j 1 " - " ASN B 699 " " NAG k 1 " - " ASN B 723 " " NAG l 1 " - " ASN B 749 " " NAG m 1 " - " ASN B 762 " " NAG n 1 " - " ASN B 768 " " NAG o 1 " - " ASN B 844 " " NAG p 1 " - " ASN B 852 " " NAG q 1 " - " ASN B1111 " " NAG r 1 " - " ASN B1196 " " NAG s 1 " - " ASN B1201 " " NAG t 1 " - " ASN C 240 " " NAG u 1 " - " ASN C 276 " " NAG v 1 " - " ASN C 301 " " NAG w 1 " - " ASN C 330 " " NAG x 1 " - " ASN C 354 " " NAG y 1 " - " ASN C 358 " " NAG z 1 " - " ASN C 403 " " NAGAA 1 " - " ASN C 852 " " NAGBA 1 " - " ASN C1111 " " NAGCA 1 " - " ASN C1196 " " NAGDA 1 " - " ASN C1201 " Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 25.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY A 849 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 850 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 922 through 936 Processing helix chain 'A' and resid 949 through 960 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1031 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1216 through 1224 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.572A pdb=" N ARG B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 799 through 804 Processing helix chain 'B' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY B 849 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 850 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 882 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR B 897 " --> pdb=" O LYS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 936 Processing helix chain 'B' and resid 949 through 960 Processing helix chain 'B' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1031 Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1205 through 1210 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 530 through 534 Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 799 through 804 Processing helix chain 'C' and resid 807 through 833 removed outlier: 4.802A pdb=" N THR C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 844 through 852 removed outlier: 4.137A pdb=" N GLY C 849 " --> pdb=" O THR C 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 850 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 882 Processing helix chain 'C' and resid 892 through 898 removed outlier: 4.117A pdb=" N THR C 897 " --> pdb=" O LYS C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 Processing helix chain 'C' and resid 922 through 936 Processing helix chain 'C' and resid 949 through 960 Processing helix chain 'C' and resid 969 through 992 removed outlier: 4.481A pdb=" N LYS C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1099 removed outlier: 5.114A pdb=" N GLN C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1185 through 1187 No H-bonds generated for 'chain 'C' and resid 1185 through 1187' Processing helix chain 'C' and resid 1205 through 1210 Processing helix chain 'C' and resid 1216 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR A 191 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 206 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 204 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 195 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA A 99 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 133 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 101 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 131 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 103 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 129 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 105 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 125 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.720A pdb=" N GLY A 62 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 299 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 415 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG A 297 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 417 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 295 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 384 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP A 422 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A 437 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 424 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 435 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 426 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 328 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 313 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE A 326 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A 694 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 685 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU A 662 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 654 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.457A pdb=" N SER A 601 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 603 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 562 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 585 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 595 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 579 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR A 597 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS A 577 " --> pdb=" O TYR A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE A 736 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR A 730 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1114 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS A1142 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1164 " --> pdb=" O TRP A1144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE A1202 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR B 191 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 206 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 204 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR B 195 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA B 99 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 133 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 101 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 131 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 103 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 129 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 105 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 125 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY B 62 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN B 299 " --> pdb=" O TRP B 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 415 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 297 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 417 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 295 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 384 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP B 422 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR B 437 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 424 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 435 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN B 426 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS B 328 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 313 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE B 326 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AC8, first strand: chain 'B' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN B 683 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 694 " --> pdb=" O GLN B 683 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 685 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU B 662 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR B 654 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER B 601 " --> pdb=" O LYS B 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY B 603 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS B 562 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 514 through 515 removed outlier: 4.183A pdb=" N SER B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP B 585 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 581 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA B 595 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 579 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 597 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS B 577 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE B 736 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR B 730 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS B1114 " --> pdb=" O LEU B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS B1142 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B1164 " --> pdb=" O TRP B1144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 787 Processing sheet with id=AD7, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE B1202 " --> pdb=" O CYS B1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR C 191 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 206 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR C 204 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 195 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA C 99 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 133 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 101 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 131 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 103 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C 129 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 105 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 125 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY C 62 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C 299 " --> pdb=" O TRP C 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 415 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG C 297 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE C 417 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 295 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE C 384 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP C 422 " --> pdb=" O TYR C 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C 437 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 424 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 435 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 426 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS C 328 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 313 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE C 326 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AE7, first strand: chain 'C' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN C 683 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 694 " --> pdb=" O GLN C 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 685 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU C 662 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR C 654 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER C 601 " --> pdb=" O LYS C 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 603 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS C 562 " --> pdb=" O GLY C 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER C 589 " --> pdb=" O TRP C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 585 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 581 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 595 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE C 579 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR C 597 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS C 577 " --> pdb=" O TYR C 597 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 727 through 731 removed outlier: 6.774A pdb=" N ILE C 736 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR C 730 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 734 " --> pdb=" O THR C 730 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1114 " --> pdb=" O LEU C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS C1142 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C1164 " --> pdb=" O TRP C1144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 785 through 787 Processing sheet with id=AF6, first strand: chain 'C' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE C1202 " --> pdb=" O CYS C1148 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3312 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: 8.28 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7568 1.33 - 1.47: 10479 1.47 - 1.61: 12694 1.61 - 1.75: 36 1.75 - 1.89: 141 Bond restraints: 30918 Sorted by residual: bond pdb=" C VAL B1190 " pdb=" N GLN B1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 9.05e+01 bond pdb=" C VAL C1190 " pdb=" N GLN C1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C VAL A1190 " pdb=" N GLN A1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C1 NAG u 2 " pdb=" O5 NAG u 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 30913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.83: 41393 8.83 - 17.66: 451 17.66 - 26.49: 238 26.49 - 35.33: 65 35.33 - 44.16: 12 Bond angle restraints: 42159 Sorted by residual: angle pdb=" C2 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 107.58 151.74 -44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 107.58 151.73 -44.15 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN K 4 " pdb=" C3 MAN K 4 " pdb=" O3 MAN K 4 " ideal model delta sigma weight residual 107.58 151.70 -44.12 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C4 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 111.95 70.52 41.43 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C4 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 111.95 70.53 41.42 3.00e+00 1.11e-01 1.91e+02 ... (remaining 42154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15735 17.99 - 35.97: 580 35.97 - 53.96: 143 53.96 - 71.94: 72 71.94 - 89.93: 18 Dihedral angle restraints: 16548 sinusoidal: 6225 harmonic: 10323 Sorted by residual: dihedral pdb=" C ALA B 810 " pdb=" N ALA B 810 " pdb=" CA ALA B 810 " pdb=" CB ALA B 810 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" C ALA C 810 " pdb=" N ALA C 810 " pdb=" CA ALA C 810 " pdb=" CB ALA C 810 " ideal model delta harmonic sigma weight residual -122.60 -146.40 23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" C ALA A 810 " pdb=" N ALA A 810 " pdb=" CA ALA A 810 " pdb=" CB ALA A 810 " ideal model delta harmonic sigma weight residual -122.60 -146.37 23.77 0 2.50e+00 1.60e-01 9.04e+01 ... (remaining 16545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4966 0.264 - 0.528: 385 0.528 - 0.792: 109 0.792 - 1.056: 51 1.056 - 1.320: 27 Chirality restraints: 5538 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG u 2 " pdb=" O4 NAG u 1 " pdb=" C2 NAG u 2 " pdb=" O5 NAG u 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.88e+02 ... (remaining 5535 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN B 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 486 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 486 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 486 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 486 " -0.157 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG 1 1 " -0.120 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 42 2.16 - 2.85: 10971 2.85 - 3.53: 39555 3.53 - 4.22: 74296 4.22 - 4.90: 118793 Nonbonded interactions: 243657 Sorted by model distance: nonbonded pdb=" O4 NAG g 1 " pdb=" C1 NAG g 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG L 1 " pdb=" C1 NAG L 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG 1 1 " pdb=" C1 NAG 1 2 " model vdw 1.476 3.470 nonbonded pdb=" O ASN C1111 " pdb=" OD1 ASN C1111 " model vdw 1.738 3.040 nonbonded pdb=" O ASN A1111 " pdb=" OD1 ASN A1111 " model vdw 1.738 3.040 ... (remaining 243652 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: 0.09 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'K' selection = chain 'f' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'DA' selection = chain 'L' selection = chain 'O' selection = chain 'X' selection = chain 'g' selection = chain 'j' selection = chain 's' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'w' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'BA' selection = chain 'N' selection = chain 'V' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'F' selection = chain 'H' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'p' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'Y' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 32.450 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.170 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.024 0.292 31185 Z= 1.257 Angle : 3.066 44.157 42912 Z= 1.346 Chirality : 0.199 1.320 5538 Planarity : 0.012 0.113 5064 Dihedral : 11.587 89.931 9792 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.70 % Favored : 93.70 % Rotamer: Outliers : 0.68 % Allowed : 1.45 % Favored : 97.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3507 helix: 0.72 (0.19), residues: 708 sheet: 0.72 (0.18), residues: 852 loop : -0.95 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 225 TYR 0.037 0.006 TYR C 654 PHE 0.023 0.005 PHE B 950 TRP 0.028 0.006 TRP A 600 HIS 0.007 0.002 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.02411 / 1.24 (30918) covalent geometry : angle 3.03603 / 1.34 (42159) SS BOND : bond 0.10224 / 6.47 ( 48) SS BOND : angle 4.59662 / 3.14 ( 96) hydrogen bonds : bond 0.15661 / 10.27 ( 1170) hydrogen bonds : angle 7.87241 / 5.50 ( 3312) link_ALPHA1-2 : bond 0.03696 / 2.56 ( 9) link_ALPHA1-2 : angle 2.23527 / 1.53 ( 27) link_ALPHA1-3 : bond 0.03654 / 2.38 ( 21) link_ALPHA1-3 : angle 5.41311 / 4.35 ( 63) link_ALPHA1-6 : bond 0.02856 / 1.89 ( 15) link_ALPHA1-6 : angle 2.62886 / 1.84 ( 45) link_BETA1-4 : bond 0.03008 / 2.03 ( 90) link_BETA1-4 : angle 5.30253 / 4.40 ( 270) link_NAG-ASN : bond 0.03511 / 2.45 ( 84) link_NAG-ASN : angle 3.39731 / 2.28 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 468 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 VAL cc_start: 0.8463 (t) cc_final: 0.8066 (p) REVERT: A 515 VAL cc_start: 0.8523 (t) cc_final: 0.8288 (p) REVERT: A 851 TYR cc_start: 0.7618 (m-80) cc_final: 0.7017 (m-80) REVERT: A 916 VAL cc_start: 0.8431 (t) cc_final: 0.7994 (t) REVERT: B 153 LEU cc_start: 0.8295 (mt) cc_final: 0.7976 (mt) REVERT: B 362 VAL cc_start: 0.8143 (t) cc_final: 0.7649 (p) REVERT: B 538 ASP cc_start: 0.6525 (m-30) cc_final: 0.6209 (m-30) REVERT: B 916 VAL cc_start: 0.8667 (t) cc_final: 0.8381 (t) REVERT: C 362 VAL cc_start: 0.8268 (t) cc_final: 0.7848 (p) REVERT: C 763 LEU cc_start: 0.9091 (mt) cc_final: 0.8865 (mp) outliers start: 21 outliers final: 13 residues processed: 489 average time/residue: 0.2079 time to fit residues: 160.2986 Evaluate side-chains 185 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 1111 ASN Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain C residue 1138 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN C 433 GLN C1021 GLN C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089426 restraints weight = 60912.648| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.32 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31185 Z= 0.197 Angle : 0.991 17.710 42912 Z= 0.443 Chirality : 0.052 0.417 5538 Planarity : 0.006 0.072 5064 Dihedral : 6.541 59.738 3857 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.96 % Favored : 95.52 % Rotamer: Outliers : 2.00 % Allowed : 5.59 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3507 helix: 1.37 (0.20), residues: 708 sheet: 0.74 (0.18), residues: 900 loop : -0.90 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 748 TYR 0.018 0.002 TYR A 176 PHE 0.027 0.002 PHE C 563 TRP 0.014 0.002 TRP B 261 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (30918) covalent geometry : angle 0.87792 / 0.42 (42159) SS BOND : bond 0.00630 / 0.40 ( 48) SS BOND : angle 1.95885 / 1.37 ( 96) hydrogen bonds : bond 0.07054 / 4.65 ( 1170) hydrogen bonds : angle 5.99559 / 4.19 ( 3312) link_ALPHA1-2 : bond 0.00965 / 0.69 ( 9) link_ALPHA1-2 : angle 1.69720 / 1.11 ( 27) link_ALPHA1-3 : bond 0.00804 / 0.51 ( 21) link_ALPHA1-3 : angle 2.76927 / 1.94 ( 63) link_ALPHA1-6 : bond 0.00969 / 0.58 ( 15) link_ALPHA1-6 : angle 1.85263 / 1.22 ( 45) link_BETA1-4 : bond 0.01353 / 0.87 ( 90) link_BETA1-4 : angle 4.33915 / 3.09 ( 270) link_NAG-ASN : bond 0.00539 / 0.40 ( 84) link_NAG-ASN : angle 3.73585 / 2.61 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (mm) REVERT: A 1016 ASP cc_start: 0.8188 (t0) cc_final: 0.7945 (t0) REVERT: A 1113 THR cc_start: 0.8840 (m) cc_final: 0.8558 (p) REVERT: A 1192 ILE cc_start: 0.8573 (pt) cc_final: 0.8366 (pt) REVERT: B 954 LEU cc_start: 0.9263 (mp) cc_final: 0.9061 (mm) REVERT: B 1060 ASP cc_start: 0.7784 (t70) cc_final: 0.7529 (m-30) REVERT: B 1113 THR cc_start: 0.9111 (m) cc_final: 0.8871 (p) REVERT: C 250 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8521 (mtm180) REVERT: C 275 PHE cc_start: 0.7942 (m-80) cc_final: 0.7707 (m-80) REVERT: C 763 LEU cc_start: 0.8997 (mt) cc_final: 0.8777 (mp) REVERT: C 828 ASP cc_start: 0.8156 (t0) cc_final: 0.7926 (t0) REVERT: C 1113 THR cc_start: 0.9140 (m) cc_final: 0.8776 (p) outliers start: 62 outliers final: 39 residues processed: 309 average time/residue: 0.1954 time to fit residues: 99.1739 Evaluate side-chains 196 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1161 ASN Chi-restraints excluded: chain C residue 1193 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 155 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 ASN A 679 ASN A 827 ASN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.114562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086665 restraints weight = 60093.310| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.33 r_work: 0.3066 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31185 Z= 0.189 Angle : 0.867 17.497 42912 Z= 0.389 Chirality : 0.049 0.475 5538 Planarity : 0.005 0.057 5064 Dihedral : 5.905 58.199 3849 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.82 % Favored : 94.70 % Rotamer: Outliers : 2.42 % Allowed : 7.89 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3507 helix: 1.85 (0.20), residues: 693 sheet: 0.89 (0.17), residues: 885 loop : -1.17 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1088 TYR 0.021 0.002 TYR B1153 PHE 0.026 0.002 PHE A 124 TRP 0.011 0.001 TRP B 769 HIS 0.006 0.001 HIS B1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (30918) covalent geometry : angle 0.76457 / 0.37 (42159) SS BOND : bond 0.00642 / 0.44 ( 48) SS BOND : angle 1.82480 / 1.34 ( 96) hydrogen bonds : bond 0.06149 / 4.06 ( 1170) hydrogen bonds : angle 5.41458 / 3.78 ( 3312) link_ALPHA1-2 : bond 0.00794 / 0.56 ( 9) link_ALPHA1-2 : angle 1.34857 / 0.90 ( 27) link_ALPHA1-3 : bond 0.00827 / 0.53 ( 21) link_ALPHA1-3 : angle 2.80332 / 1.99 ( 63) link_ALPHA1-6 : bond 0.00957 / 0.61 ( 15) link_ALPHA1-6 : angle 1.68514 / 1.12 ( 45) link_BETA1-4 : bond 0.01196 / 0.76 ( 90) link_BETA1-4 : angle 3.84195 / 2.81 ( 270) link_NAG-ASN : bond 0.00458 / 0.33 ( 84) link_NAG-ASN : angle 3.23303 / 2.30 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 851 TYR cc_start: 0.8100 (m-80) cc_final: 0.7793 (m-80) REVERT: B 340 ILE cc_start: 0.8693 (mm) cc_final: 0.8428 (mm) REVERT: B 954 LEU cc_start: 0.9439 (mp) cc_final: 0.9191 (mm) REVERT: B 1060 ASP cc_start: 0.7787 (t70) cc_final: 0.7566 (m-30) REVERT: B 1198 THR cc_start: 0.7967 (p) cc_final: 0.7725 (t) REVERT: B 1200 VAL cc_start: 0.8356 (t) cc_final: 0.8149 (p) REVERT: C 250 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8609 (mtm180) REVERT: C 296 MET cc_start: 0.8791 (mtm) cc_final: 0.8440 (mtm) REVERT: C 763 LEU cc_start: 0.9203 (mt) cc_final: 0.8975 (mp) REVERT: C 1060 ASP cc_start: 0.7947 (t70) cc_final: 0.7498 (m-30) REVERT: C 1113 THR cc_start: 0.9225 (m) cc_final: 0.8995 (p) REVERT: C 1124 ASP cc_start: 0.8595 (m-30) cc_final: 0.8297 (m-30) outliers start: 75 outliers final: 55 residues processed: 249 average time/residue: 0.1771 time to fit residues: 74.6748 Evaluate side-chains 219 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 131 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 280 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 HIS A1140 ASN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084408 restraints weight = 59784.664| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.32 r_work: 0.3021 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31185 Z= 0.198 Angle : 0.829 18.461 42912 Z= 0.374 Chirality : 0.049 0.461 5538 Planarity : 0.005 0.054 5064 Dihedral : 5.762 56.948 3849 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.62 % Favored : 94.95 % Rotamer: Outliers : 2.75 % Allowed : 8.08 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3507 helix: 1.68 (0.20), residues: 705 sheet: 0.73 (0.16), residues: 933 loop : -1.42 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1088 TYR 0.018 0.002 TYR A 851 PHE 0.029 0.002 PHE A 402 TRP 0.012 0.001 TRP B 769 HIS 0.007 0.002 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (30918) covalent geometry : angle 0.73466 / 0.35 (42159) SS BOND : bond 0.00594 / 0.38 ( 48) SS BOND : angle 1.81351 / 1.35 ( 96) hydrogen bonds : bond 0.06089 / 4.04 ( 1170) hydrogen bonds : angle 5.34140 / 3.74 ( 3312) link_ALPHA1-2 : bond 0.00760 / 0.54 ( 9) link_ALPHA1-2 : angle 1.42864 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00714 / 0.46 ( 21) link_ALPHA1-3 : angle 2.60450 / 1.82 ( 63) link_ALPHA1-6 : bond 0.00772 / 0.50 ( 15) link_ALPHA1-6 : angle 1.62933 / 1.07 ( 45) link_BETA1-4 : bond 0.01146 / 0.72 ( 90) link_BETA1-4 : angle 3.72412 / 2.73 ( 270) link_NAG-ASN : bond 0.00449 / 0.34 ( 84) link_NAG-ASN : angle 2.84778 / 2.05 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 172 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 926 MET cc_start: 0.9009 (mmm) cc_final: 0.8715 (mmm) REVERT: A 1108 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7032 (t80) REVERT: B 81 TYR cc_start: 0.7819 (p90) cc_final: 0.7598 (p90) REVERT: B 1060 ASP cc_start: 0.7794 (t70) cc_final: 0.7567 (m-30) REVERT: B 1198 THR cc_start: 0.8344 (p) cc_final: 0.7919 (t) REVERT: C 763 LEU cc_start: 0.9252 (mt) cc_final: 0.9024 (mp) REVERT: C 1060 ASP cc_start: 0.8008 (t70) cc_final: 0.7593 (m-30) REVERT: C 1113 THR cc_start: 0.9282 (m) cc_final: 0.9069 (p) REVERT: C 1124 ASP cc_start: 0.8676 (m-30) cc_final: 0.8350 (m-30) outliers start: 85 outliers final: 64 residues processed: 239 average time/residue: 0.1796 time to fit residues: 72.8925 Evaluate side-chains 211 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 145 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 277 optimal weight: 0.0050 chunk 253 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 341 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 235 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 ASN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS C1034 HIS C1140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086964 restraints weight = 59735.100| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.27 r_work: 0.3056 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31185 Z= 0.127 Angle : 0.745 17.577 42912 Z= 0.333 Chirality : 0.047 0.449 5538 Planarity : 0.004 0.048 5064 Dihedral : 5.422 58.553 3849 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.22 % Favored : 95.41 % Rotamer: Outliers : 2.10 % Allowed : 9.12 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3507 helix: 1.95 (0.20), residues: 696 sheet: 0.68 (0.17), residues: 951 loop : -1.39 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.011 0.001 TYR B 58 PHE 0.027 0.001 PHE B 568 TRP 0.007 0.001 TRP A 261 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (30918) covalent geometry : angle 0.65280 / 0.31 (42159) SS BOND : bond 0.00540 / 0.36 ( 48) SS BOND : angle 1.79261 / 1.30 ( 96) hydrogen bonds : bond 0.05198 / 3.43 ( 1170) hydrogen bonds : angle 5.07016 / 3.54 ( 3312) link_ALPHA1-2 : bond 0.00643 / 0.45 ( 9) link_ALPHA1-2 : angle 1.43006 / 0.93 ( 27) link_ALPHA1-3 : bond 0.00746 / 0.48 ( 21) link_ALPHA1-3 : angle 2.36283 / 1.65 ( 63) link_ALPHA1-6 : bond 0.00867 / 0.55 ( 15) link_ALPHA1-6 : angle 1.51358 / 0.99 ( 45) link_BETA1-4 : bond 0.01153 / 0.72 ( 90) link_BETA1-4 : angle 3.55500 / 2.62 ( 270) link_NAG-ASN : bond 0.00398 / 0.30 ( 84) link_NAG-ASN : angle 2.53323 / 1.83 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7630 (mtm) cc_final: 0.7301 (ttm) REVERT: A 30 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 1108 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.6815 (t80) REVERT: B 1198 THR cc_start: 0.8211 (p) cc_final: 0.7816 (t) REVERT: C 763 LEU cc_start: 0.9264 (mt) cc_final: 0.9058 (mp) REVERT: C 828 ASP cc_start: 0.8173 (t0) cc_final: 0.7963 (t0) REVERT: C 1124 ASP cc_start: 0.8524 (m-30) cc_final: 0.8252 (m-30) outliers start: 65 outliers final: 52 residues processed: 219 average time/residue: 0.1780 time to fit residues: 66.7231 Evaluate side-chains 199 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 91 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084321 restraints weight = 59662.255| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.26 r_work: 0.3016 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31185 Z= 0.194 Angle : 0.767 17.593 42912 Z= 0.348 Chirality : 0.049 0.456 5538 Planarity : 0.004 0.047 5064 Dihedral : 5.364 52.049 3849 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.65 % Favored : 94.90 % Rotamer: Outliers : 2.52 % Allowed : 9.63 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3507 helix: 1.77 (0.20), residues: 726 sheet: 0.68 (0.17), residues: 909 loop : -1.30 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 870 TYR 0.012 0.001 TYR C 731 PHE 0.022 0.002 PHE C 563 TRP 0.011 0.001 TRP B 769 HIS 0.014 0.002 HIS C1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (30918) covalent geometry : angle 0.68437 / 0.33 (42159) SS BOND : bond 0.00578 / 0.38 ( 48) SS BOND : angle 1.80196 / 1.27 ( 96) hydrogen bonds : bond 0.05769 / 3.82 ( 1170) hydrogen bonds : angle 5.10349 / 3.58 ( 3312) link_ALPHA1-2 : bond 0.00710 / 0.50 ( 9) link_ALPHA1-2 : angle 1.40310 / 0.92 ( 27) link_ALPHA1-3 : bond 0.00723 / 0.47 ( 21) link_ALPHA1-3 : angle 2.51345 / 1.75 ( 63) link_ALPHA1-6 : bond 0.00766 / 0.48 ( 15) link_ALPHA1-6 : angle 1.60640 / 1.05 ( 45) link_BETA1-4 : bond 0.01107 / 0.69 ( 90) link_BETA1-4 : angle 3.54877 / 2.62 ( 270) link_NAG-ASN : bond 0.00483 / 0.36 ( 84) link_NAG-ASN : angle 2.22377 / 1.58 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7739 (mtm) cc_final: 0.7413 (ttm) REVERT: A 1108 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7021 (t80) REVERT: C 611 TYR cc_start: 0.8514 (p90) cc_final: 0.8255 (p90) REVERT: C 1005 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7096 (p-80) REVERT: C 1060 ASP cc_start: 0.7807 (t70) cc_final: 0.7500 (m-30) REVERT: C 1124 ASP cc_start: 0.8595 (m-30) cc_final: 0.8311 (m-30) outliers start: 78 outliers final: 61 residues processed: 196 average time/residue: 0.1805 time to fit residues: 59.6016 Evaluate side-chains 197 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 212 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083582 restraints weight = 59981.743| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.26 r_work: 0.3001 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31185 Z= 0.200 Angle : 0.761 17.617 42912 Z= 0.346 Chirality : 0.048 0.461 5538 Planarity : 0.004 0.045 5064 Dihedral : 5.119 49.861 3843 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.82 % Favored : 94.72 % Rotamer: Outliers : 2.49 % Allowed : 10.02 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3507 helix: 1.72 (0.20), residues: 726 sheet: 0.66 (0.17), residues: 909 loop : -1.36 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 925 TYR 0.013 0.001 TYR C 851 PHE 0.020 0.002 PHE C 124 TRP 0.010 0.001 TRP B 769 HIS 0.011 0.001 HIS C1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (30918) covalent geometry : angle 0.68412 / 0.33 (42159) SS BOND : bond 0.00598 / 0.39 ( 48) SS BOND : angle 1.86323 / 1.29 ( 96) hydrogen bonds : bond 0.05886 / 3.90 ( 1170) hydrogen bonds : angle 5.14483 / 3.60 ( 3312) link_ALPHA1-2 : bond 0.00738 / 0.52 ( 9) link_ALPHA1-2 : angle 1.36898 / 0.90 ( 27) link_ALPHA1-3 : bond 0.00721 / 0.47 ( 21) link_ALPHA1-3 : angle 2.52474 / 1.77 ( 63) link_ALPHA1-6 : bond 0.00752 / 0.48 ( 15) link_ALPHA1-6 : angle 1.60709 / 1.05 ( 45) link_BETA1-4 : bond 0.01112 / 0.69 ( 90) link_BETA1-4 : angle 3.50611 / 2.59 ( 270) link_NAG-ASN : bond 0.00528 / 0.38 ( 84) link_NAG-ASN : angle 1.90399 / 1.37 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 144 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7849 (mtm) cc_final: 0.7536 (ttm) REVERT: A 647 SER cc_start: 0.8353 (m) cc_final: 0.7798 (p) REVERT: A 1108 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7161 (t80) REVERT: B 296 MET cc_start: 0.8557 (mtm) cc_final: 0.8337 (mtm) REVERT: B 499 VAL cc_start: 0.8561 (t) cc_final: 0.8335 (t) REVERT: B 1138 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: C 611 TYR cc_start: 0.8534 (p90) cc_final: 0.8236 (p90) REVERT: C 616 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8379 (tt) REVERT: C 1060 ASP cc_start: 0.7963 (t70) cc_final: 0.7594 (m-30) REVERT: C 1124 ASP cc_start: 0.8614 (m-30) cc_final: 0.8342 (m-30) outliers start: 77 outliers final: 63 residues processed: 204 average time/residue: 0.1794 time to fit residues: 62.0006 Evaluate side-chains 196 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 130 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1166 SER Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 130 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084396 restraints weight = 59839.205| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.32 r_work: 0.3016 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31185 Z= 0.146 Angle : 0.723 17.497 42912 Z= 0.327 Chirality : 0.047 0.450 5538 Planarity : 0.004 0.043 5064 Dihedral : 4.975 48.479 3843 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.36 % Favored : 95.18 % Rotamer: Outliers : 2.20 % Allowed : 10.51 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3507 helix: 1.81 (0.20), residues: 726 sheet: 0.63 (0.17), residues: 927 loop : -1.35 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 925 TYR 0.011 0.001 TYR C 731 PHE 0.021 0.001 PHE C 124 TRP 0.008 0.001 TRP B 769 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30918) covalent geometry : angle 0.64387 / 0.31 (42159) SS BOND : bond 0.00482 / 0.31 ( 48) SS BOND : angle 1.73720 / 1.24 ( 96) hydrogen bonds : bond 0.05471 / 3.62 ( 1170) hydrogen bonds : angle 5.04429 / 3.53 ( 3312) link_ALPHA1-2 : bond 0.00676 / 0.47 ( 9) link_ALPHA1-2 : angle 1.40496 / 0.91 ( 27) link_ALPHA1-3 : bond 0.00712 / 0.46 ( 21) link_ALPHA1-3 : angle 2.38584 / 1.67 ( 63) link_ALPHA1-6 : bond 0.00802 / 0.51 ( 15) link_ALPHA1-6 : angle 1.54814 / 1.02 ( 45) link_BETA1-4 : bond 0.01119 / 0.70 ( 90) link_BETA1-4 : angle 3.43485 / 2.54 ( 270) link_NAG-ASN : bond 0.00393 / 0.28 ( 84) link_NAG-ASN : angle 1.94509 / 1.38 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7794 (mtm) cc_final: 0.7465 (ttm) REVERT: A 499 VAL cc_start: 0.8427 (t) cc_final: 0.8204 (t) REVERT: A 1108 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 130 LEU cc_start: 0.8620 (mt) cc_final: 0.8296 (mt) REVERT: B 296 MET cc_start: 0.8528 (mtm) cc_final: 0.8320 (mtm) REVERT: B 499 VAL cc_start: 0.8540 (t) cc_final: 0.8301 (t) REVERT: B 1138 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: C 65 TYR cc_start: 0.8493 (p90) cc_final: 0.8109 (p90) REVERT: C 611 TYR cc_start: 0.8604 (p90) cc_final: 0.8285 (p90) REVERT: C 616 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (tt) REVERT: C 1060 ASP cc_start: 0.7944 (t70) cc_final: 0.7494 (m-30) REVERT: C 1124 ASP cc_start: 0.8631 (m-30) cc_final: 0.8337 (m-30) outliers start: 68 outliers final: 58 residues processed: 193 average time/residue: 0.1810 time to fit residues: 60.1955 Evaluate side-chains 192 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 131 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1166 SER Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083940 restraints weight = 59863.907| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.33 r_work: 0.3006 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31185 Z= 0.164 Angle : 0.727 17.392 42912 Z= 0.330 Chirality : 0.048 0.449 5538 Planarity : 0.004 0.043 5064 Dihedral : 4.937 46.573 3843 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.73 % Favored : 94.84 % Rotamer: Outliers : 2.26 % Allowed : 10.67 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3507 helix: 1.80 (0.20), residues: 726 sheet: 0.70 (0.17), residues: 909 loop : -1.31 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.012 0.001 TYR C 731 PHE 0.022 0.001 PHE C 124 TRP 0.008 0.001 TRP B 769 HIS 0.006 0.001 HIS C1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (30918) covalent geometry : angle 0.64930 / 0.31 (42159) SS BOND : bond 0.00542 / 0.36 ( 48) SS BOND : angle 1.80426 / 1.26 ( 96) hydrogen bonds : bond 0.05524 / 3.66 ( 1170) hydrogen bonds : angle 5.03872 / 3.52 ( 3312) link_ALPHA1-2 : bond 0.00675 / 0.47 ( 9) link_ALPHA1-2 : angle 1.40064 / 0.91 ( 27) link_ALPHA1-3 : bond 0.00717 / 0.46 ( 21) link_ALPHA1-3 : angle 2.39102 / 1.67 ( 63) link_ALPHA1-6 : bond 0.00788 / 0.50 ( 15) link_ALPHA1-6 : angle 1.56321 / 1.03 ( 45) link_BETA1-4 : bond 0.01091 / 0.68 ( 90) link_BETA1-4 : angle 3.41033 / 2.52 ( 270) link_NAG-ASN : bond 0.00372 / 0.27 ( 84) link_NAG-ASN : angle 1.93720 / 1.40 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7807 (mtm) cc_final: 0.7481 (ttm) REVERT: A 499 VAL cc_start: 0.8444 (t) cc_final: 0.8228 (t) REVERT: A 647 SER cc_start: 0.8310 (m) cc_final: 0.7840 (p) REVERT: A 648 LEU cc_start: 0.8074 (mm) cc_final: 0.7839 (mt) REVERT: A 1108 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 130 LEU cc_start: 0.8620 (mt) cc_final: 0.8295 (mt) REVERT: B 296 MET cc_start: 0.8542 (mtm) cc_final: 0.8336 (mtm) REVERT: B 499 VAL cc_start: 0.8555 (t) cc_final: 0.8329 (t) REVERT: C 65 TYR cc_start: 0.8487 (p90) cc_final: 0.8115 (p90) REVERT: C 611 TYR cc_start: 0.8623 (p90) cc_final: 0.8329 (p90) REVERT: C 616 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8385 (tt) REVERT: C 1060 ASP cc_start: 0.7915 (t70) cc_final: 0.7546 (m-30) REVERT: C 1124 ASP cc_start: 0.8632 (m-30) cc_final: 0.8340 (m-30) outliers start: 70 outliers final: 63 residues processed: 186 average time/residue: 0.1777 time to fit residues: 56.6774 Evaluate side-chains 192 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 127 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1166 SER Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 293 optimal weight: 0.0980 chunk 258 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 GLN C1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084422 restraints weight = 59751.958| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.32 r_work: 0.3014 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31185 Z= 0.145 Angle : 0.709 17.418 42912 Z= 0.320 Chirality : 0.047 0.445 5538 Planarity : 0.003 0.042 5064 Dihedral : 4.810 36.059 3841 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.36 % Favored : 95.24 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3507 helix: 1.85 (0.20), residues: 726 sheet: 0.65 (0.17), residues: 927 loop : -1.30 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.012 0.001 TYR C 851 PHE 0.021 0.001 PHE C 124 TRP 0.006 0.001 TRP B 769 HIS 0.007 0.001 HIS C1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30918) covalent geometry : angle 0.63161 / 0.30 (42159) SS BOND : bond 0.00493 / 0.32 ( 48) SS BOND : angle 1.72738 / 1.19 ( 96) hydrogen bonds : bond 0.05387 / 3.56 ( 1170) hydrogen bonds : angle 5.00521 / 3.50 ( 3312) link_ALPHA1-2 : bond 0.00652 / 0.45 ( 9) link_ALPHA1-2 : angle 1.41718 / 0.92 ( 27) link_ALPHA1-3 : bond 0.00713 / 0.46 ( 21) link_ALPHA1-3 : angle 2.33218 / 1.63 ( 63) link_ALPHA1-6 : bond 0.00806 / 0.51 ( 15) link_ALPHA1-6 : angle 1.54093 / 1.02 ( 45) link_BETA1-4 : bond 0.01121 / 0.70 ( 90) link_BETA1-4 : angle 3.37679 / 2.50 ( 270) link_NAG-ASN : bond 0.00344 / 0.25 ( 84) link_NAG-ASN : angle 1.89957 / 1.38 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 VAL cc_start: 0.8429 (t) cc_final: 0.8197 (t) REVERT: A 647 SER cc_start: 0.8300 (m) cc_final: 0.7857 (p) REVERT: A 648 LEU cc_start: 0.8072 (mm) cc_final: 0.7848 (mt) REVERT: A 1108 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6986 (t80) REVERT: B 130 LEU cc_start: 0.8432 (mt) cc_final: 0.8118 (mt) REVERT: B 296 MET cc_start: 0.8531 (mtm) cc_final: 0.8324 (mtm) REVERT: B 499 VAL cc_start: 0.8402 (t) cc_final: 0.8194 (t) REVERT: C 65 TYR cc_start: 0.8466 (p90) cc_final: 0.8067 (p90) REVERT: C 616 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 803 LEU cc_start: 0.9256 (mt) cc_final: 0.8976 (mp) REVERT: C 1060 ASP cc_start: 0.7907 (t70) cc_final: 0.7449 (m-30) REVERT: C 1124 ASP cc_start: 0.8602 (m-30) cc_final: 0.8315 (m-30) outliers start: 66 outliers final: 62 residues processed: 187 average time/residue: 0.1779 time to fit residues: 56.8534 Evaluate side-chains 192 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 329 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 chunk 212 optimal weight: 0.3980 chunk 323 optimal weight: 2.9990 chunk 276 optimal weight: 0.1980 chunk 239 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085199 restraints weight = 59910.344| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.26 r_work: 0.3022 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31185 Z= 0.132 Angle : 0.695 17.321 42912 Z= 0.313 Chirality : 0.047 0.441 5538 Planarity : 0.003 0.042 5064 Dihedral : 4.696 31.283 3839 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.42 % Favored : 95.21 % Rotamer: Outliers : 1.78 % Allowed : 11.41 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3507 helix: 1.89 (0.20), residues: 726 sheet: 0.67 (0.17), residues: 927 loop : -1.30 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.019 0.001 TYR A1214 PHE 0.021 0.001 PHE C 124 TRP 0.010 0.001 TRP B 769 HIS 0.007 0.001 HIS C1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (30918) covalent geometry : angle 0.61862 / 0.30 (42159) SS BOND : bond 0.00463 / 0.30 ( 48) SS BOND : angle 1.63522 / 1.13 ( 96) hydrogen bonds : bond 0.05210 / 3.44 ( 1170) hydrogen bonds : angle 4.94695 / 3.46 ( 3312) link_ALPHA1-2 : bond 0.00622 / 0.43 ( 9) link_ALPHA1-2 : angle 1.44960 / 0.93 ( 27) link_ALPHA1-3 : bond 0.00710 / 0.46 ( 21) link_ALPHA1-3 : angle 2.26877 / 1.58 ( 63) link_ALPHA1-6 : bond 0.00829 / 0.52 ( 15) link_ALPHA1-6 : angle 1.52329 / 1.01 ( 45) link_BETA1-4 : bond 0.01122 / 0.70 ( 90) link_BETA1-4 : angle 3.33384 / 2.46 ( 270) link_NAG-ASN : bond 0.00329 / 0.24 ( 84) link_NAG-ASN : angle 1.84233 / 1.34 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6118.02 seconds wall clock time: 106 minutes 27.90 seconds (6387.90 seconds total)