Starting phenix.real_space_refine on Thu Aug 6 03:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nr_67848/08_2026/21nr_67848.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 8 5.16 5 C 7180 2.51 5 N 540 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2412 Classifications: {'peptide': 344} Link IDs: {'TRANS': 343} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BGC': 2, 'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 359 Unusual residues: {'BGC': 14, 'GAL': 3, 'GLA': 1, 'MAN': 1, 'NAG': 3, 'XYP': 12} Classifications: {'undetermined': 34} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 34 Chain: "D" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 274 Unusual residues: {'AHR': 4, 'BGC': 10, 'BMA': 1, 'FUB': 3, 'MAN': 4, 'NAG': 2, 'XYP': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 26 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FUB': 1, 'GZL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 237 Unusual residues: {'A2G': 2, 'BGC': 7, 'MAN': 5, 'NAG': 1, 'XYP': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 22 Chain: "H" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 213 Unusual residues: {'A2G': 1, 'BGC': 4, 'GAL': 2, 'MAN': 3, 'NAG': 2, 'XYP': 8} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 20 Chain: "I" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 109 Unusual residues: {'BGC': 5, 'MAN': 2, 'NAG': 1, 'XYP': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "J" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 216 Unusual residues: {'A2G': 2, 'BGC': 4, 'GAL': 3, 'MAN': 3, 'NAG': 3, 'XYP': 4} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "K" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 512 Unusual residues: {'AHR': 1, 'BGC': 15, 'BMA': 6, 'FUB': 1, 'GLA': 1, 'MAN': 5, 'NAG': 7, 'XYP': 11} Classifications: {'undetermined': 47} Link IDs: {None: 46} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 47 Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 107 Unusual residues: {'BGC': 4, 'GAL': 1, 'MAN': 1, 'NAG': 1, 'XYP': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "M" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 185 Unusual residues: {'AHR': 1, 'BGC': 9, 'MAN': 2, 'NAG': 2, 'XYP': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "N" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 219 Unusual residues: {'A2G': 1, 'AHR': 5, 'BGC': 3, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'XYP': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Chain: "O" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BGC': 2, 'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "P" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 359 Unusual residues: {'BGC': 14, 'GAL': 3, 'GLA': 1, 'MAN': 1, 'NAG': 3, 'XYP': 12} Classifications: {'undetermined': 34} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 34 Chain: "Q" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 274 Unusual residues: {'AHR': 4, 'BGC': 10, 'BMA': 1, 'FUB': 3, 'MAN': 4, 'NAG': 2, 'XYP': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 26 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FUB': 1, 'GZL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 237 Unusual residues: {'A2G': 2, 'BGC': 7, 'MAN': 5, 'NAG': 1, 'XYP': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 22 Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 213 Unusual residues: {'A2G': 1, 'BGC': 4, 'GAL': 2, 'MAN': 3, 'NAG': 2, 'XYP': 8} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 20 Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 109 Unusual residues: {'BGC': 5, 'MAN': 2, 'NAG': 1, 'XYP': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "W" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 216 Unusual residues: {'A2G': 2, 'BGC': 4, 'GAL': 3, 'MAN': 3, 'NAG': 3, 'XYP': 4} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "X" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 512 Unusual residues: {'AHR': 1, 'BGC': 15, 'BMA': 6, 'FUB': 1, 'GLA': 1, 'MAN': 5, 'NAG': 7, 'XYP': 11} Classifications: {'undetermined': 47} Link IDs: {None: 46} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 47 Chain: "Y" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 107 Unusual residues: {'BGC': 4, 'GAL': 1, 'MAN': 1, 'NAG': 1, 'XYP': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Z" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 185 Unusual residues: {'AHR': 1, 'BGC': 9, 'MAN': 2, 'NAG': 2, 'XYP': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "a" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 219 Unusual residues: {'A2G': 1, 'AHR': 5, 'BGC': 3, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'XYP': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Chain: "b" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BGC': 2, 'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "c" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 359 Unusual residues: {'BGC': 14, 'GAL': 3, 'GLA': 1, 'MAN': 1, 'NAG': 3, 'XYP': 12} Classifications: {'undetermined': 34} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 34 Chain: "d" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 274 Unusual residues: {'AHR': 4, 'BGC': 10, 'BMA': 1, 'FUB': 3, 'MAN': 4, 'NAG': 2, 'XYP': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 26 Chain: "e" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FUB': 1, 'GZL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 237 Unusual residues: {'A2G': 2, 'BGC': 7, 'MAN': 5, 'NAG': 1, 'XYP': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 22 Chain: "h" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 213 Unusual residues: {'A2G': 1, 'BGC': 4, 'GAL': 2, 'MAN': 3, 'NAG': 2, 'XYP': 8} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 20 Chain: "i" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 109 Unusual residues: {'BGC': 5, 'MAN': 2, 'NAG': 1, 'XYP': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 216 Unusual residues: {'A2G': 2, 'BGC': 4, 'GAL': 3, 'MAN': 3, 'NAG': 3, 'XYP': 4} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "k" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 512 Unusual residues: {'AHR': 1, 'BGC': 15, 'BMA': 6, 'FUB': 1, 'GLA': 1, 'MAN': 5, 'NAG': 7, 'XYP': 11} Classifications: {'undetermined': 47} Link IDs: {None: 46} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 47 Chain: "l" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 107 Unusual residues: {'BGC': 4, 'GAL': 1, 'MAN': 1, 'NAG': 1, 'XYP': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "m" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 185 Unusual residues: {'AHR': 1, 'BGC': 9, 'MAN': 2, 'NAG': 2, 'XYP': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "n" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 219 Unusual residues: {'A2G': 1, 'AHR': 5, 'BGC': 3, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'XYP': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Chain: "o" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BGC': 2, 'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "p" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 359 Unusual residues: {'BGC': 14, 'GAL': 3, 'GLA': 1, 'MAN': 1, 'NAG': 3, 'XYP': 12} Classifications: {'undetermined': 34} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 34 Chain: "q" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 274 Unusual residues: {'AHR': 4, 'BGC': 10, 'BMA': 1, 'FUB': 3, 'MAN': 4, 'NAG': 2, 'XYP': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 26 Chain: "r" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FUB': 1, 'GZL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 237 Unusual residues: {'A2G': 2, 'BGC': 7, 'MAN': 5, 'NAG': 1, 'XYP': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 22 Chain: "u" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 213 Unusual residues: {'A2G': 1, 'BGC': 4, 'GAL': 2, 'MAN': 3, 'NAG': 2, 'XYP': 8} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 20 Chain: "v" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 109 Unusual residues: {'BGC': 5, 'MAN': 2, 'NAG': 1, 'XYP': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "w" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 216 Unusual residues: {'A2G': 2, 'BGC': 4, 'GAL': 3, 'MAN': 3, 'NAG': 3, 'XYP': 4} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "x" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 512 Unusual residues: {'AHR': 1, 'BGC': 15, 'BMA': 6, 'FUB': 1, 'GLA': 1, 'MAN': 5, 'NAG': 7, 'XYP': 11} Classifications: {'undetermined': 47} Link IDs: {None: 46} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 47 Chain: "y" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 107 Unusual residues: {'BGC': 4, 'GAL': 1, 'MAN': 1, 'NAG': 1, 'XYP': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "z" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 185 Unusual residues: {'AHR': 1, 'BGC': 9, 'MAN': 2, 'NAG': 2, 'XYP': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "0" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 219 Unusual residues: {'A2G': 1, 'AHR': 5, 'BGC': 3, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'XYP': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Time building chain proxies: 2.87, per 1000 atoms: 0.22 Number of scatterers: 12836 At special positions: 0 Unit cell: (76.853, 76.853, 181.154, 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 8 16.00 O 5108 8.00 N 540 7.00 C 7180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 228 " distance=2.04 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 314 " distance=2.04 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 400 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=32, symmetry=0 Links applied ?1-2 " MAN F 1 " - " GZL F 2 " " MAN S 1 " - " GZL S 2 " " MAN f 1 " - " GZL f 2 " " MAN s 1 " - " GZL s 2 " ALPHA1-2 " GAL B 3 " - " MAN B 4 " " FUB D 16 " - " FUB D 22 " ~> Even though FUB is a beta isomer, an alpha linkage is required... " MAN G 9 " - " MAN G 10 " " BGC H 15 " - " MAN H 16 " " BGC K 8 " - " MAN K 29 " " GAL O 3 " - " MAN O 4 " " FUB Q 16 " - " FUB Q 22 " " MAN T 9 " - " MAN T 10 " " BGC U 15 " - " MAN U 16 " " BGC X 8 " - " MAN X 29 " " GAL b 3 " - " MAN b 4 " " FUB d 16 " - " FUB d 22 " " MAN g 9 " - " MAN g 10 " " BGC h 15 " - " MAN h 16 " " BGC k 8 " - " MAN k 29 " " GAL o 3 " - " MAN o 4 " " FUB q 16 " - " FUB q 22 " " MAN t 9 " - " MAN t 10 " " BGC u 15 " - " MAN u 16 " " BGC x 8 " - " MAN x 29 " ALPHA1-3 " XYP 0 2 " - " A2G 0 3 " " BGC D 3 " - " MAN D 4 " " GZL F 2 " - " FUB F 3 " " BGC G 2 " - " MAN G 15 " " A2G G 7 " - " MAN G 8 " " MAN G 9 " - " MAN G 11 " " XYP H 9 " - " MAN H 11 " " MAN H 16 " - " A2G H 17 " " BGC I 1 " - " MAN I 2 " " GAL J 5 " - " A2G J 6 " " GAL J 7 " - " A2G J 8 " " BGC J 9 " - " MAN J 10 " " BMA K 9 " - " GLA K 10 " " XYP K 36 " - " MAN K 37 " " BGC M 2 " - " MAN M 3 " " BGC M 6 " - " MAN M 11 " " XYP N 2 " - " A2G N 3 " " BGC Q 3 " - " MAN Q 4 " " GZL S 2 " - " FUB S 3 " " BGC T 2 " - " MAN T 15 " " A2G T 7 " - " MAN T 8 " " MAN T 9 " - " MAN T 11 " " XYP U 9 " - " MAN U 11 " " MAN U 16 " - " A2G U 17 " " BGC V 1 " - " MAN V 2 " " GAL W 5 " - " A2G W 6 " " GAL W 7 " - " A2G W 8 " " BGC W 9 " - " MAN W 10 " " BMA X 9 " - " GLA X 10 " " XYP X 36 " - " MAN X 37 " " BGC Z 2 " - " MAN Z 3 " " BGC Z 6 " - " MAN Z 11 " " XYP a 2 " - " A2G a 3 " " BGC d 3 " - " MAN d 4 " " GZL f 2 " - " FUB f 3 " " BGC g 2 " - " MAN g 15 " " A2G g 7 " - " MAN g 8 " " MAN g 9 " - " MAN g 11 " " XYP h 9 " - " MAN h 11 " " MAN h 16 " - " A2G h 17 " " BGC i 1 " - " MAN i 2 " " GAL j 5 " - " A2G j 6 " " GAL j 7 " - " A2G j 8 " " BGC j 9 " - " MAN j 10 " " BMA k 9 " - " GLA k 10 " " XYP k 36 " - " MAN k 37 " " BGC m 2 " - " MAN m 3 " " BGC m 6 " - " MAN m 11 " " XYP n 2 " - " A2G n 3 " " BGC q 3 " - " MAN q 4 " " GZL s 2 " - " FUB s 3 " " BGC t 2 " - " MAN t 15 " " A2G t 7 " - " MAN t 8 " " MAN t 9 " - " MAN t 11 " " XYP u 9 " - " MAN u 11 " " MAN u 16 " - " A2G u 17 " " BGC v 1 " - " MAN v 2 " " GAL w 5 " - " A2G w 6 " " GAL w 7 " - " A2G w 8 " " BGC w 9 " - " MAN w 10 " " BMA x 9 " - " GLA x 10 " " XYP x 36 " - " MAN x 37 " " BGC z 2 " - " MAN z 3 " " BGC z 6 " - " MAN z 11 " ALPHA1-4 " NAG B 2 " - " MAN B 9 " " XYP C 6 " - " MAN C 12 " " BGC G 2 " - " A2G G 3 " " XYP G 6 " - " A2G G 7 " " XYP H 19 " - " MAN H 20 " " BGC I 3 " - " MAN I 6 " " NAG J 2 " - " MAN J 19 " " GAL J 7 " - " MAN J 13 " " BGC K 2 " - " MAN K 42 " " NAG K 5 " - " FUB K 6 " " NAG K 20 " - " MAN K 22 " " BGC L 5 " - " MAN L 6 " " NAG O 2 " - " MAN O 9 " " XYP P 6 " - " MAN P 12 " " BGC T 2 " - " A2G T 3 " " XYP T 6 " - " A2G T 7 " " XYP U 19 " - " MAN U 20 " " BGC V 3 " - " MAN V 6 " " NAG W 2 " - " MAN W 19 " " GAL W 7 " - " MAN W 13 " " BGC X 2 " - " MAN X 42 " " NAG X 5 " - " FUB X 6 " " NAG X 20 " - " MAN X 22 " " BGC Y 5 " - " MAN Y 6 " " NAG b 2 " - " MAN b 9 " " XYP c 6 " - " MAN c 12 " " BGC g 2 " - " A2G g 3 " " XYP g 6 " - " A2G g 7 " " XYP h 19 " - " MAN h 20 " " BGC i 3 " - " MAN i 6 " " NAG j 2 " - " MAN j 19 " " GAL j 7 " - " MAN j 13 " " BGC k 2 " - " MAN k 42 " " NAG k 5 " - " FUB k 6 " " NAG k 20 " - " MAN k 22 " " BGC l 5 " - " MAN l 6 " " NAG o 2 " - " MAN o 9 " " XYP p 6 " - " MAN p 12 " " BGC t 2 " - " A2G t 3 " " XYP t 6 " - " A2G t 7 " " XYP u 19 " - " MAN u 20 " " BGC v 3 " - " MAN v 6 " " NAG w 2 " - " MAN w 19 " " GAL w 7 " - " MAN w 13 " " BGC x 2 " - " MAN x 42 " " NAG x 5 " - " FUB x 6 " " NAG x 20 " - " MAN x 22 " " BGC y 5 " - " MAN y 6 " ALPHA1-5 " AHR D 12 " - " FUB D 13 " " AHR D 17 " - " MAN D 18 " " AHR Q 12 " - " FUB Q 13 " " AHR Q 17 " - " MAN Q 18 " " AHR d 12 " - " FUB d 13 " " AHR d 17 " - " MAN d 18 " " AHR q 12 " - " FUB q 13 " " AHR q 17 " - " MAN q 18 " ALPHA1-6 " MAN D 1 " - " FUB D 16 " " MAN D 4 " - " MAN D 11 " " BGC G 5 " - " MAN G 9 " " MAN Q 1 " - " FUB Q 16 " " MAN Q 4 " - " MAN Q 11 " " BGC T 5 " - " MAN T 9 " " MAN d 1 " - " FUB d 16 " " MAN d 4 " - " MAN d 11 " " BGC g 5 " - " MAN g 9 " " MAN q 1 " - " FUB q 16 " " MAN q 4 " - " MAN q 11 " " BGC t 5 " - " MAN t 9 " BETA1-2 " XYP 0 2 " - " NAG 0 18 " " GAL 0 4 " - " AHR 0 5 " ~> Even though AHR is an alpha isomer, a beta linkage is required... " XYP 0 6 " - " NAG 0 7 " " BGC 0 10 " - " XYP 0 11 " " XYP 0 11 " - " BGC 0 16 " " XYP 0 20 " - " AHR 0 21 " " MAN B 4 " - " BGC B 5 " " BMA B 7 " - " GAL B 8 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 18 " " GAL C 4 " - " NAG C 13 " " XYP C 6 " - " BGC C 7 " " XYP C 8 " - " BGC C 9 " " XYP C 14 " - " BGC C 15 " " BGC C 18 " - " BGC C 19 " " XYP C 22 " - " XYP C 23 " " GAL C 24 " - " XYP C 33 " " GAL C 26 " - " BGC C 31 " " BGC C 27 " - " BGC C 30 " " MAN D 1 " - " AHR D 2 " " MAN D 4 " - " BGC D 5 " " BGC D 5 " - " BMA D 6 " " BMA D 6 " - " NAG D 7 " " FUB D 22 " - " AHR D 26 " " MAN E 1 " - " NAG E 2 " " XYP G 1 " - " BGC G 2 " " BGC G 4 " - " BGC G 5 " " BGC G 17 " - " BGC G 18 " " XYP G 21 " - " XYP G 22 " " GAL H 1 " - " NAG H 2 " " BGC H 3 " - " XYP H 4 " " XYP H 4 " - " XYP H 5 " " XYP H 5 " - " XYP H 6 " " XYP H 7 " - " GAL H 8 " " XYP H 9 " - " BGC H 10 " " BGC H 12 " - " XYP H 13 " " MAN I 2 " - " BGC I 3 " " BGC I 3 " - " NAG I 4 " " XYP I 9 " - " BGC I 10 " " XYP J 3 " - " XYP J 4 " " GAL J 5 " - " XYP J 15 " " GAL J 7 " - " XYP J 12 " " XYP K 3 " - " BMA K 4 " " BMA K 4 " - " NAG K 5 " " FUB K 6 " - " BGC K 7 " " GLA K 10 " - " BGC K 11 " " BMA K 14 " - " BGC K 15 " " BGC K 15 " - " NAG K 16 " " XYP K 18 " - " BGC K 19 " " BGC K 25 " - " XYP K 26 " " XYP K 30 " - " BGC K 31 " " BGC K 35 " - " NAG K 38 " " BGC L 3 " - " XYP L 4 " " MAN L 6 " - " BGC L 7 " " BGC L 7 " - " BGC L 8 " " XYP M 1 " - " BGC M 2 " " MAN M 3 " - " NAG M 4 " " BGC M 5 " - " AHR M 12 " " BGC M 6 " - " BGC M 10 " " XYP M 13 " - " BGC M 14 " " BGC M 16 " - " BGC M 17 " " XYP N 2 " - " NAG N 18 " " GAL N 4 " - " AHR N 5 " " XYP N 6 " - " NAG N 7 " " BGC N 10 " - " XYP N 11 " " XYP N 11 " - " BGC N 16 " " XYP N 20 " - " AHR N 21 " " MAN O 4 " - " BGC O 5 " " BMA O 7 " - " GAL O 8 " " BGC P 2 " - " BGC P 3 " " BGC P 3 " - " BGC P 18 " " GAL P 4 " - " NAG P 13 " " XYP P 6 " - " BGC P 7 " " XYP P 8 " - " BGC P 9 " " XYP P 14 " - " BGC P 15 " " BGC P 18 " - " BGC P 19 " " XYP P 22 " - " XYP P 23 " " GAL P 24 " - " XYP P 33 " " GAL P 26 " - " BGC P 31 " " BGC P 27 " - " BGC P 30 " " MAN Q 1 " - " AHR Q 2 " " MAN Q 4 " - " BGC Q 5 " " BGC Q 5 " - " BMA Q 6 " " BMA Q 6 " - " NAG Q 7 " " FUB Q 22 " - " AHR Q 26 " " MAN R 1 " - " NAG R 2 " " XYP T 1 " - " BGC T 2 " " BGC T 4 " - " BGC T 5 " " BGC T 17 " - " BGC T 18 " " XYP T 21 " - " XYP T 22 " " GAL U 1 " - " NAG U 2 " " BGC U 3 " - " XYP U 4 " " XYP U 4 " - " XYP U 5 " " XYP U 5 " - " XYP U 6 " " XYP U 7 " - " GAL U 8 " " XYP U 9 " - " BGC U 10 " " BGC U 12 " - " XYP U 13 " " MAN V 2 " - " BGC V 3 " " BGC V 3 " - " NAG V 4 " " XYP V 9 " - " BGC V 10 " " XYP W 3 " - " XYP W 4 " " GAL W 5 " - " XYP W 15 " " GAL W 7 " - " XYP W 12 " " XYP X 3 " - " BMA X 4 " " BMA X 4 " - " NAG X 5 " " FUB X 6 " - " BGC X 7 " " GLA X 10 " - " BGC X 11 " " BMA X 14 " - " BGC X 15 " " BGC X 15 " - " NAG X 16 " " XYP X 18 " - " BGC X 19 " " BGC X 25 " - " XYP X 26 " " XYP X 30 " - " BGC X 31 " " BGC X 35 " - " NAG X 38 " " BGC Y 3 " - " XYP Y 4 " " MAN Y 6 " - " BGC Y 7 " " BGC Y 7 " - " BGC Y 8 " " XYP Z 1 " - " BGC Z 2 " " MAN Z 3 " - " NAG Z 4 " " BGC Z 5 " - " AHR Z 12 " " BGC Z 6 " - " BGC Z 10 " " XYP Z 13 " - " BGC Z 14 " " BGC Z 16 " - " BGC Z 17 " " XYP a 2 " - " NAG a 18 " " GAL a 4 " - " AHR a 5 " " XYP a 6 " - " NAG a 7 " " BGC a 10 " - " XYP a 11 " " XYP a 11 " - " BGC a 16 " " XYP a 20 " - " AHR a 21 " " MAN b 4 " - " BGC b 5 " " BMA b 7 " - " GAL b 8 " " BGC c 2 " - " BGC c 3 " " BGC c 3 " - " BGC c 18 " " GAL c 4 " - " NAG c 13 " " XYP c 6 " - " BGC c 7 " " XYP c 8 " - " BGC c 9 " " XYP c 14 " - " BGC c 15 " " BGC c 18 " - " BGC c 19 " " XYP c 22 " - " XYP c 23 " " GAL c 24 " - " XYP c 33 " " GAL c 26 " - " BGC c 31 " " BGC c 27 " - " BGC c 30 " " MAN d 1 " - " AHR d 2 " " MAN d 4 " - " BGC d 5 " " BGC d 5 " - " BMA d 6 " " BMA d 6 " - " NAG d 7 " " FUB d 22 " - " AHR d 26 " " MAN e 1 " - " NAG e 2 " " XYP g 1 " - " BGC g 2 " " BGC g 4 " - " BGC g 5 " " BGC g 17 " - " BGC g 18 " " XYP g 21 " - " XYP g 22 " " GAL h 1 " - " NAG h 2 " " BGC h 3 " - " XYP h 4 " " XYP h 4 " - " XYP h 5 " " XYP h 5 " - " XYP h 6 " " XYP h 7 " - " GAL h 8 " " XYP h 9 " - " BGC h 10 " " BGC h 12 " - " XYP h 13 " " MAN i 2 " - " BGC i 3 " " BGC i 3 " - " NAG i 4 " " XYP i 9 " - " BGC i 10 " " XYP j 3 " - " XYP j 4 " " GAL j 5 " - " XYP j 15 " " GAL j 7 " - " XYP j 12 " " XYP k 3 " - " BMA k 4 " " BMA k 4 " - " NAG k 5 " " FUB k 6 " - " BGC k 7 " " GLA k 10 " - " BGC k 11 " " BMA k 14 " - " BGC k 15 " " BGC k 15 " - " NAG k 16 " " XYP k 18 " - " BGC k 19 " " BGC k 25 " - " XYP k 26 " " XYP k 30 " - " BGC k 31 " " BGC k 35 " - " NAG k 38 " " BGC l 3 " - " XYP l 4 " " MAN l 6 " - " BGC l 7 " " BGC l 7 " - " BGC l 8 " " XYP m 1 " - " BGC m 2 " " MAN m 3 " - " NAG m 4 " " BGC m 5 " - " AHR m 12 " " BGC m 6 " - " BGC m 10 " " XYP m 13 " - " BGC m 14 " " BGC m 16 " - " BGC m 17 " " XYP n 2 " - " NAG n 18 " " GAL n 4 " - " AHR n 5 " " XYP n 6 " - " NAG n 7 " " BGC n 10 " - " XYP n 11 " " XYP n 11 " - " BGC n 16 " " XYP n 20 " - " AHR n 21 " " MAN o 4 " - " BGC o 5 " " BMA o 7 " - " GAL o 8 " " BGC p 2 " - " BGC p 3 " " BGC p 3 " - " BGC p 18 " " GAL p 4 " - " NAG p 13 " " XYP p 6 " - " BGC p 7 " " XYP p 8 " - " BGC p 9 " " XYP p 14 " - " BGC p 15 " " BGC p 18 " - " BGC p 19 " " XYP p 22 " - " XYP p 23 " " GAL p 24 " - " XYP p 33 " " GAL p 26 " - " BGC p 31 " " BGC p 27 " - " BGC p 30 " " MAN q 1 " - " AHR q 2 " " MAN q 4 " - " BGC q 5 " " BGC q 5 " - " BMA q 6 " " BMA q 6 " - " NAG q 7 " " FUB q 22 " - " AHR q 26 " " MAN r 1 " - " NAG r 2 " " XYP t 1 " - " BGC t 2 " " BGC t 4 " - " BGC t 5 " " BGC t 17 " - " BGC t 18 " " XYP t 21 " - " XYP t 22 " " GAL u 1 " - " NAG u 2 " " BGC u 3 " - " XYP u 4 " " XYP u 4 " - " XYP u 5 " " XYP u 5 " - " XYP u 6 " " XYP u 7 " - " GAL u 8 " " XYP u 9 " - " BGC u 10 " " BGC u 12 " - " XYP u 13 " " MAN v 2 " - " BGC v 3 " " BGC v 3 " - " NAG v 4 " " XYP v 9 " - " BGC v 10 " " XYP w 3 " - " XYP w 4 " " GAL w 5 " - " XYP w 15 " " GAL w 7 " - " XYP w 12 " " XYP x 3 " - " BMA x 4 " " BMA x 4 " - " NAG x 5 " " FUB x 6 " - " BGC x 7 " " GLA x 10 " - " BGC x 11 " " BMA x 14 " - " BGC x 15 " " BGC x 15 " - " NAG x 16 " " XYP x 18 " - " BGC x 19 " " BGC x 25 " - " XYP x 26 " " XYP x 30 " - " BGC x 31 " " BGC x 35 " - " NAG x 38 " " BGC y 3 " - " XYP y 4 " " MAN y 6 " - " BGC y 7 " " BGC y 7 " - " BGC y 8 " " XYP z 1 " - " BGC z 2 " " MAN z 3 " - " NAG z 4 " " BGC z 5 " - " AHR z 12 " " BGC z 6 " - " BGC z 10 " " XYP z 13 " - " BGC z 14 " " BGC z 16 " - " BGC z 17 " BETA1-3 " A2G 0 3 " - " GAL 0 4 " " GAL 0 4 " - " BGC 0 10 " " AHR 0 5 " - " XYP 0 6 " " AHR 0 8 " - " AHR 0 9 " " BGC 0 12 " - " XYP 0 13 " " XYP 0 13 " - " XYP 0 14 " " NAG 0 18 " - " NAG 0 19 " " NAG B 2 " - " GAL B 3 " " GAL B 3 " - " BMA B 7 " " GLA C 1 " - " XYP C 22 " " XYP C 5 " - " XYP C 6 " " XYP C 6 " - " NAG C 11 " " NAG C 13 " - " XYP C 14 " " GAL C 24 " - " BGC C 25 " " GAL C 26 " - " BGC C 32 " " BGC C 27 " - " XYP C 28 " " AHR D 12 " - " XYP D 15 " " FUB D 13 " - " NAG D 14 " " MAN D 18 " - " BGC D 19 " " BGC D 23 " - " BGC D 24 " " XYP G 1 " - " NAG G 16 " " A2G G 3 " - " BGC G 4 " " BGC G 4 " - " BGC G 12 " " NAG G 16 " - " BGC G 17 " " XYP H 4 " - " NAG H 14 " " XYP H 6 " - " XYP H 7 " " GAL H 8 " - " XYP H 9 " " NAG H 14 " - " BGC H 15 " " BGC H 15 " - " XYP H 18 " " MAN I 2 " - " BGC I 7 " " BGC I 3 " - " BGC I 5 " " GAL J 1 " - " NAG J 2 " " NAG J 2 " - " XYP J 3 " " XYP J 4 " - " GAL J 5 " " A2G J 6 " - " GAL J 7 " " A2G J 8 " - " NAG J 11 " " BGC K 2 " - " XYP K 3 " " BMA K 4 " - " BGC K 35 " " NAG K 5 " - " NAG K 34 " " BGC K 8 " - " XYP K 33 " " GLA K 10 " - " AHR K 17 " " BMA K 12 " - " NAG K 13 " " NAG K 13 " - " BMA K 14 " " AHR K 17 " - " XYP K 18 " " NAG K 20 " - " BMA K 21 " " XYP K 23 " - " BMA K 24 " " BMA K 24 " - " BGC K 25 " " MAN K 29 " - " XYP K 30 " " MAN K 42 " - " BGC K 43 " " BGC K 43 " - " XYP K 44 " " GAL L 1 " - " XYP L 2 " " XYP L 2 " - " BGC L 3 " " BGC L 3 " - " NAG L 9 " " XYP L 4 " - " BGC L 5 " " NAG M 4 " - " XYP M 13 " " XYP M 7 " - " BGC M 8 " " A2G N 3 " - " GAL N 4 " " GAL N 4 " - " BGC N 10 " " AHR N 5 " - " XYP N 6 " " AHR N 8 " - " AHR N 9 " " BGC N 12 " - " XYP N 13 " " XYP N 13 " - " XYP N 14 " " NAG N 18 " - " NAG N 19 " " NAG O 2 " - " GAL O 3 " " GAL O 3 " - " BMA O 7 " " GLA P 1 " - " XYP P 22 " " XYP P 5 " - " XYP P 6 " " XYP P 6 " - " NAG P 11 " " NAG P 13 " - " XYP P 14 " " GAL P 24 " - " BGC P 25 " " GAL P 26 " - " BGC P 32 " " BGC P 27 " - " XYP P 28 " " AHR Q 12 " - " XYP Q 15 " " FUB Q 13 " - " NAG Q 14 " " MAN Q 18 " - " BGC Q 19 " " BGC Q 23 " - " BGC Q 24 " " XYP T 1 " - " NAG T 16 " " A2G T 3 " - " BGC T 4 " " BGC T 4 " - " BGC T 12 " " NAG T 16 " - " BGC T 17 " " XYP U 4 " - " NAG U 14 " " XYP U 6 " - " XYP U 7 " " GAL U 8 " - " XYP U 9 " " NAG U 14 " - " BGC U 15 " " BGC U 15 " - " XYP U 18 " " MAN V 2 " - " BGC V 7 " " BGC V 3 " - " BGC V 5 " " GAL W 1 " - " NAG W 2 " " NAG W 2 " - " XYP W 3 " " XYP W 4 " - " GAL W 5 " " A2G W 6 " - " GAL W 7 " " A2G W 8 " - " NAG W 11 " " BGC X 2 " - " XYP X 3 " " BMA X 4 " - " BGC X 35 " " NAG X 5 " - " NAG X 34 " " BGC X 8 " - " XYP X 33 " " GLA X 10 " - " AHR X 17 " " BMA X 12 " - " NAG X 13 " " NAG X 13 " - " BMA X 14 " " AHR X 17 " - " XYP X 18 " " NAG X 20 " - " BMA X 21 " " XYP X 23 " - " BMA X 24 " " BMA X 24 " - " BGC X 25 " " MAN X 29 " - " XYP X 30 " " MAN X 42 " - " BGC X 43 " " BGC X 43 " - " XYP X 44 " " GAL Y 1 " - " XYP Y 2 " " XYP Y 2 " - " BGC Y 3 " " BGC Y 3 " - " NAG Y 9 " " XYP Y 4 " - " BGC Y 5 " " NAG Z 4 " - " XYP Z 13 " " XYP Z 7 " - " BGC Z 8 " " A2G a 3 " - " GAL a 4 " " GAL a 4 " - " BGC a 10 " " AHR a 5 " - " XYP a 6 " " AHR a 8 " - " AHR a 9 " " BGC a 12 " - " XYP a 13 " " XYP a 13 " - " XYP a 14 " " NAG a 18 " - " NAG a 19 " " NAG b 2 " - " GAL b 3 " " GAL b 3 " - " BMA b 7 " " GLA c 1 " - " XYP c 22 " " XYP c 5 " - " XYP c 6 " " XYP c 6 " - " NAG c 11 " " NAG c 13 " - " XYP c 14 " " GAL c 24 " - " BGC c 25 " " GAL c 26 " - " BGC c 32 " " BGC c 27 " - " XYP c 28 " " AHR d 12 " - " XYP d 15 " " FUB d 13 " - " NAG d 14 " " MAN d 18 " - " BGC d 19 " " BGC d 23 " - " BGC d 24 " " XYP g 1 " - " NAG g 16 " " A2G g 3 " - " BGC g 4 " " BGC g 4 " - " BGC g 12 " " NAG g 16 " - " BGC g 17 " " XYP h 4 " - " NAG h 14 " " XYP h 6 " - " XYP h 7 " " GAL h 8 " - " XYP h 9 " " NAG h 14 " - " BGC h 15 " " BGC h 15 " - " XYP h 18 " " MAN i 2 " - " BGC i 7 " " BGC i 3 " - " BGC i 5 " " GAL j 1 " - " NAG j 2 " " NAG j 2 " - " XYP j 3 " " XYP j 4 " - " GAL j 5 " " A2G j 6 " - " GAL j 7 " " A2G j 8 " - " NAG j 11 " " BGC k 2 " - " XYP k 3 " " BMA k 4 " - " BGC k 35 " " NAG k 5 " - " NAG k 34 " " BGC k 8 " - " XYP k 33 " " GLA k 10 " - " AHR k 17 " " BMA k 12 " - " NAG k 13 " " NAG k 13 " - " BMA k 14 " " AHR k 17 " - " XYP k 18 " " NAG k 20 " - " BMA k 21 " " XYP k 23 " - " BMA k 24 " " BMA k 24 " - " BGC k 25 " " MAN k 29 " - " XYP k 30 " " MAN k 42 " - " BGC k 43 " " BGC k 43 " - " XYP k 44 " " GAL l 1 " - " XYP l 2 " " XYP l 2 " - " BGC l 3 " " BGC l 3 " - " NAG l 9 " " XYP l 4 " - " BGC l 5 " " NAG m 4 " - " XYP m 13 " " XYP m 7 " - " BGC m 8 " " A2G n 3 " - " GAL n 4 " " GAL n 4 " - " BGC n 10 " " AHR n 5 " - " XYP n 6 " " AHR n 8 " - " AHR n 9 " " BGC n 12 " - " XYP n 13 " " XYP n 13 " - " XYP n 14 " " NAG n 18 " - " NAG n 19 " " NAG o 2 " - " GAL o 3 " " GAL o 3 " - " BMA o 7 " " GLA p 1 " - " XYP p 22 " " XYP p 5 " - " XYP p 6 " " XYP p 6 " - " NAG p 11 " " NAG p 13 " - " XYP p 14 " " GAL p 24 " - " BGC p 25 " " GAL p 26 " - " BGC p 32 " " BGC p 27 " - " XYP p 28 " " AHR q 12 " - " XYP q 15 " " FUB q 13 " - " NAG q 14 " " MAN q 18 " - " BGC q 19 " " BGC q 23 " - " BGC q 24 " " XYP t 1 " - " NAG t 16 " " A2G t 3 " - " BGC t 4 " " BGC t 4 " - " BGC t 12 " " NAG t 16 " - " BGC t 17 " " XYP u 4 " - " NAG u 14 " " XYP u 6 " - " XYP u 7 " " GAL u 8 " - " XYP u 9 " " NAG u 14 " - " BGC u 15 " " BGC u 15 " - " XYP u 18 " " MAN v 2 " - " BGC v 7 " " BGC v 3 " - " BGC v 5 " " GAL w 1 " - " NAG w 2 " " NAG w 2 " - " XYP w 3 " " XYP w 4 " - " GAL w 5 " " A2G w 6 " - " GAL w 7 " " A2G w 8 " - " NAG w 11 " " BGC x 2 " - " XYP x 3 " " BMA x 4 " - " BGC x 35 " " NAG x 5 " - " NAG x 34 " " BGC x 8 " - " XYP x 33 " " GLA x 10 " - " AHR x 17 " " BMA x 12 " - " NAG x 13 " " NAG x 13 " - " BMA x 14 " " AHR x 17 " - " XYP x 18 " " NAG x 20 " - " BMA x 21 " " XYP x 23 " - " BMA x 24 " " BMA x 24 " - " BGC x 25 " " MAN x 29 " - " XYP x 30 " " MAN x 42 " - " BGC x 43 " " BGC x 43 " - " XYP x 44 " " GAL y 1 " - " XYP y 2 " " XYP y 2 " - " BGC y 3 " " BGC y 3 " - " NAG y 9 " " XYP y 4 " - " BGC y 5 " " NAG z 4 " - " XYP z 13 " " XYP z 7 " - " BGC z 8 " BETA1-4 " MAN 0 1 " - " XYP 0 2 " " XYP 0 2 " - " XYP 0 20 " " XYP 0 11 " - " BGC 0 12 " " XYP 0 13 " - " AHR 0 15 " " BGC B 1 " - " NAG B 2 " " MAN B 4 " - " NAG B 6 " " BGC C 3 " - " GAL C 4 " " GAL C 4 " - " XYP C 5 " " BGC C 9 " - " XYP C 10 " " NAG C 13 " - " BGC C 16 " " BGC C 16 " - " XYP C 17 " " XYP C 20 " - " NAG C 21 " " XYP C 23 " - " GAL C 24 " " GAL C 24 " - " XYP C 34 " " BGC C 25 " - " GAL C 26 " " GAL C 26 " - " BGC C 27 " " XYP C 28 " - " BGC C 29 " " MAN D 4 " - " XYP D 10 " " BMA D 6 " - " BGC D 9 " " NAG D 7 " - " BGC D 8 " " BGC D 19 " - " BGC D 20 " " XYP G 1 " - " XYP G 21 " " BGC G 4 " - " BGC G 13 " " BGC G 5 " - " XYP G 6 " " XYP G 19 " - " XYP G 20 " " NAG H 2 " - " BGC H 3 " " GAL H 8 " - " BGC H 12 " " NAG H 14 " - " XYP H 19 " " BGC I 1 " - " XYP I 9 " " MAN I 2 " - " XYP I 8 " " XYP J 3 " - " BGC J 17 " " GAL J 5 " - " BGC J 16 " " A2G J 6 " - " BGC J 14 " " A2G J 8 " - " BGC J 9 " " MAN K 1 " - " BGC K 47 " " XYP K 3 " - " XYP K 40 " " BMA K 4 " - " XYP K 39 " " BGC K 8 " - " BMA K 9 " " BMA K 9 " - " NAG K 20 " " BMA K 24 " - " NAG K 28 " " BGC K 25 " - " XYP K 27 " " XYP K 30 " - " BGC K 32 " " BGC K 35 " - " XYP K 36 " " XYP K 40 " - " BGC K 41 " " BGC K 43 " - " BGC K 45 " " XYP L 2 " - " XYP L 10 " " NAG M 4 " - " BGC M 5 " " BGC M 5 " - " BGC M 6 " " BGC M 6 " - " XYP M 7 " " XYP M 7 " - " NAG M 9 " " BGC M 14 " - " BGC M 15 " " MAN N 1 " - " XYP N 2 " " XYP N 2 " - " XYP N 20 " " XYP N 11 " - " BGC N 12 " " XYP N 13 " - " AHR N 15 " " BGC O 1 " - " NAG O 2 " " MAN O 4 " - " NAG O 6 " " BGC P 3 " - " GAL P 4 " " GAL P 4 " - " XYP P 5 " " BGC P 9 " - " XYP P 10 " " NAG P 13 " - " BGC P 16 " " BGC P 16 " - " XYP P 17 " " XYP P 20 " - " NAG P 21 " " XYP P 23 " - " GAL P 24 " " GAL P 24 " - " XYP P 34 " " BGC P 25 " - " GAL P 26 " " GAL P 26 " - " BGC P 27 " " XYP P 28 " - " BGC P 29 " " MAN Q 4 " - " XYP Q 10 " " BMA Q 6 " - " BGC Q 9 " " NAG Q 7 " - " BGC Q 8 " " BGC Q 19 " - " BGC Q 20 " " XYP T 1 " - " XYP T 21 " " BGC T 4 " - " BGC T 13 " " BGC T 5 " - " XYP T 6 " " XYP T 19 " - " XYP T 20 " " NAG U 2 " - " BGC U 3 " " GAL U 8 " - " BGC U 12 " " NAG U 14 " - " XYP U 19 " " BGC V 1 " - " XYP V 9 " " MAN V 2 " - " XYP V 8 " " XYP W 3 " - " BGC W 17 " " GAL W 5 " - " BGC W 16 " " A2G W 6 " - " BGC W 14 " " A2G W 8 " - " BGC W 9 " " MAN X 1 " - " BGC X 47 " " XYP X 3 " - " XYP X 40 " " BMA X 4 " - " XYP X 39 " " BGC X 8 " - " BMA X 9 " " BMA X 9 " - " NAG X 20 " " BMA X 24 " - " NAG X 28 " " BGC X 25 " - " XYP X 27 " " XYP X 30 " - " BGC X 32 " " BGC X 35 " - " XYP X 36 " " XYP X 40 " - " BGC X 41 " " BGC X 43 " - " BGC X 45 " " XYP Y 2 " - " XYP Y 10 " " NAG Z 4 " - " BGC Z 5 " " BGC Z 5 " - " BGC Z 6 " " BGC Z 6 " - " XYP Z 7 " " XYP Z 7 " - " NAG Z 9 " " BGC Z 14 " - " BGC Z 15 " " MAN a 1 " - " XYP a 2 " " XYP a 2 " - " XYP a 20 " " XYP a 11 " - " BGC a 12 " " XYP a 13 " - " AHR a 15 " " BGC b 1 " - " NAG b 2 " " MAN b 4 " - " NAG b 6 " " BGC c 3 " - " GAL c 4 " " GAL c 4 " - " XYP c 5 " " BGC c 9 " - " XYP c 10 " " NAG c 13 " - " BGC c 16 " " BGC c 16 " - " XYP c 17 " " XYP c 20 " - " NAG c 21 " " XYP c 23 " - " GAL c 24 " " GAL c 24 " - " XYP c 34 " " BGC c 25 " - " GAL c 26 " " GAL c 26 " - " BGC c 27 " " XYP c 28 " - " BGC c 29 " " MAN d 4 " - " XYP d 10 " " BMA d 6 " - " BGC d 9 " " NAG d 7 " - " BGC d 8 " " BGC d 19 " - " BGC d 20 " " XYP g 1 " - " XYP g 21 " " BGC g 4 " - " BGC g 13 " " BGC g 5 " - " XYP g 6 " " XYP g 19 " - " XYP g 20 " " NAG h 2 " - " BGC h 3 " " GAL h 8 " - " BGC h 12 " " NAG h 14 " - " XYP h 19 " " BGC i 1 " - " XYP i 9 " " MAN i 2 " - " XYP i 8 " " XYP j 3 " - " BGC j 17 " " GAL j 5 " - " BGC j 16 " " A2G j 6 " - " BGC j 14 " " A2G j 8 " - " BGC j 9 " " MAN k 1 " - " BGC k 47 " " XYP k 3 " - " XYP k 40 " " BMA k 4 " - " XYP k 39 " " BGC k 8 " - " BMA k 9 " " BMA k 9 " - " NAG k 20 " " BMA k 24 " - " NAG k 28 " " BGC k 25 " - " XYP k 27 " " XYP k 30 " - " BGC k 32 " " BGC k 35 " - " XYP k 36 " " XYP k 40 " - " BGC k 41 " " BGC k 43 " - " BGC k 45 " " XYP l 2 " - " XYP l 10 " " NAG m 4 " - " BGC m 5 " " BGC m 5 " - " BGC m 6 " " BGC m 6 " - " XYP m 7 " " XYP m 7 " - " NAG m 9 " " BGC m 14 " - " BGC m 15 " " MAN n 1 " - " XYP n 2 " " XYP n 2 " - " XYP n 20 " " XYP n 11 " - " BGC n 12 " " XYP n 13 " - " AHR n 15 " " BGC o 1 " - " NAG o 2 " " MAN o 4 " - " NAG o 6 " " BGC p 3 " - " GAL p 4 " " GAL p 4 " - " XYP p 5 " " BGC p 9 " - " XYP p 10 " " NAG p 13 " - " BGC p 16 " " BGC p 16 " - " XYP p 17 " " XYP p 20 " - " NAG p 21 " " XYP p 23 " - " GAL p 24 " " GAL p 24 " - " XYP p 34 " " BGC p 25 " - " GAL p 26 " " GAL p 26 " - " BGC p 27 " " XYP p 28 " - " BGC p 29 " " MAN q 4 " - " XYP q 10 " " BMA q 6 " - " BGC q 9 " " NAG q 7 " - " BGC q 8 " " BGC q 19 " - " BGC q 20 " " XYP t 1 " - " XYP t 21 " " BGC t 4 " - " BGC t 13 " " BGC t 5 " - " XYP t 6 " " XYP t 19 " - " XYP t 20 " " NAG u 2 " - " BGC u 3 " " GAL u 8 " - " BGC u 12 " " NAG u 14 " - " XYP u 19 " " BGC v 1 " - " XYP v 9 " " MAN v 2 " - " XYP v 8 " " XYP w 3 " - " BGC w 17 " " GAL w 5 " - " BGC w 16 " " A2G w 6 " - " BGC w 14 " " A2G w 8 " - " BGC w 9 " " MAN x 1 " - " BGC x 47 " " XYP x 3 " - " XYP x 40 " " BMA x 4 " - " XYP x 39 " " BGC x 8 " - " BMA x 9 " " BMA x 9 " - " NAG x 20 " " BMA x 24 " - " NAG x 28 " " BGC x 25 " - " XYP x 27 " " XYP x 30 " - " BGC x 32 " " BGC x 35 " - " XYP x 36 " " XYP x 40 " - " BGC x 41 " " BGC x 43 " - " BGC x 45 " " XYP y 2 " - " XYP y 10 " " NAG z 4 " - " BGC z 5 " " BGC z 5 " - " BGC z 6 " " BGC z 6 " - " XYP z 7 " " XYP z 7 " - " NAG z 9 " " BGC z 14 " - " BGC z 15 " BETA1-5 " AHR D 2 " - " BGC D 3 " " FUB D 16 " - " AHR D 17 " " FUB D 22 " - " BGC D 23 " " FUB F 3 " - " NAG F 4 " " AHR Q 2 " - " BGC Q 3 " " FUB Q 16 " - " AHR Q 17 " " FUB Q 22 " - " BGC Q 23 " " FUB S 3 " - " NAG S 4 " " AHR d 2 " - " BGC d 3 " " FUB d 16 " - " AHR d 17 " " FUB d 22 " - " BGC d 23 " " FUB f 3 " - " NAG f 4 " " AHR q 2 " - " BGC q 3 " " FUB q 16 " - " AHR q 17 " " FUB q 22 " - " BGC q 23 " " FUB s 3 " - " NAG s 4 " BETA1-6 " GAL 0 4 " - " XYP 0 17 " " NAG 0 7 " - " AHR 0 8 " " GLA C 1 " - " BGC C 2 " " BGC C 3 " - " XYP C 20 " " BGC C 7 " - " XYP C 8 " " BGC D 3 " - " AHR D 12 " " MAN D 18 " - " BGC D 21 " " BGC D 23 " - " BGC D 25 " " BGC G 4 " - " XYP G 14 " " BGC G 18 " - " XYP G 19 " " BGC J 17 " - " NAG J 18 " " MAN K 1 " - " BGC K 2 " " BGC K 7 " - " BGC K 8 " " BGC K 8 " - " XYP K 23 " " BGC K 11 " - " BMA K 12 " " BGC K 43 " - " BGC K 46 " " MAN M 3 " - " BGC M 16 " " GAL N 4 " - " XYP N 17 " " NAG N 7 " - " AHR N 8 " " GLA P 1 " - " BGC P 2 " " BGC P 3 " - " XYP P 20 " " BGC P 7 " - " XYP P 8 " " BGC Q 3 " - " AHR Q 12 " " MAN Q 18 " - " BGC Q 21 " " BGC Q 23 " - " BGC Q 25 " " BGC T 4 " - " XYP T 14 " " BGC T 18 " - " XYP T 19 " " BGC W 17 " - " NAG W 18 " " MAN X 1 " - " BGC X 2 " " BGC X 7 " - " BGC X 8 " " BGC X 8 " - " XYP X 23 " " BGC X 11 " - " BMA X 12 " " BGC X 43 " - " BGC X 46 " " MAN Z 3 " - " BGC Z 16 " " GAL a 4 " - " XYP a 17 " " NAG a 7 " - " AHR a 8 " " GLA c 1 " - " BGC c 2 " " BGC c 3 " - " XYP c 20 " " BGC c 7 " - " XYP c 8 " " BGC d 3 " - " AHR d 12 " " MAN d 18 " - " BGC d 21 " " BGC d 23 " - " BGC d 25 " " BGC g 4 " - " XYP g 14 " " BGC g 18 " - " XYP g 19 " " BGC j 17 " - " NAG j 18 " " MAN k 1 " - " BGC k 2 " " BGC k 7 " - " BGC k 8 " " BGC k 8 " - " XYP k 23 " " BGC k 11 " - " BMA k 12 " " BGC k 43 " - " BGC k 46 " " MAN m 3 " - " BGC m 16 " " GAL n 4 " - " XYP n 17 " " NAG n 7 " - " AHR n 8 " " GLA p 1 " - " BGC p 2 " " BGC p 3 " - " XYP p 20 " " BGC p 7 " - " XYP p 8 " " BGC q 3 " - " AHR q 12 " " MAN q 18 " - " BGC q 21 " " BGC q 23 " - " BGC q 25 " " BGC t 4 " - " XYP t 14 " " BGC t 18 " - " XYP t 19 " " BGC w 17 " - " NAG w 18 " " MAN x 1 " - " BGC x 2 " " BGC x 7 " - " BGC x 8 " " BGC x 8 " - " XYP x 23 " " BGC x 11 " - " BMA x 12 " " BGC x 43 " - " BGC x 46 " " MAN z 3 " - " BGC z 16 " MAN-SER " MAN 0 1 " - " SER A 428 " " MAN D 1 " - " SER A 101 " " MAN E 1 " - " SER A 105 " " MAN F 1 " - " SER A 107 " " MAN K 1 " - " SER A 157 " " MAN N 1 " - " SER A 170 " " MAN Q 1 " - " SER A 187 " " MAN R 1 " - " SER A 191 " " MAN S 1 " - " SER A 193 " " MAN X 1 " - " SER A 243 " " MAN a 1 " - " SER A 256 " " MAN d 1 " - " SER A 273 " " MAN e 1 " - " SER A 277 " " MAN f 1 " - " SER A 279 " " MAN k 1 " - " SER A 329 " " MAN n 1 " - " SER A 342 " " MAN q 1 " - " SER A 359 " " MAN r 1 " - " SER A 363 " " MAN s 1 " - " SER A 365 " " MAN x 1 " - " SER A 415 " Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 342.0 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 632 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 removed outlier: 3.939A pdb=" N ALA A 111 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 109 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A 93 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 107 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 131 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.655A pdb=" N THR A 98 " --> pdb=" O SER A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 removed outlier: 3.529A pdb=" N LYS A 121 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 180 removed outlier: 6.881A pdb=" N PHE A 195 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 179 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 193 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 217 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.529A pdb=" N LYS A 207 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.760A pdb=" N THR A 264 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 279 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 303 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.649A pdb=" N THR A 270 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.529A pdb=" N LYS A 293 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.760A pdb=" N THR A 350 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 365 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER A 389 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.647A pdb=" N THR A 356 " --> pdb=" O SER A 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 385 through 386 removed outlier: 3.529A pdb=" N LYS A 379 " --> pdb=" O SER A 415 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 228 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: 1.92 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.75: 12839 1.75 - 2.31: 8 2.31 - 2.87: 0 2.87 - 3.44: 0 3.44 - 4.00: 4 Bond restraints: 12851 Sorted by residual: bond pdb=" C6 GZL s 2 " pdb=" O3 GZL s 2 " ideal model delta sigma weight residual 1.403 3.998 -2.595 2.00e-02 2.50e+03 1.68e+04 bond pdb=" C6 GZL F 2 " pdb=" O3 GZL F 2 " ideal model delta sigma weight residual 1.403 3.998 -2.595 2.00e-02 2.50e+03 1.68e+04 bond pdb=" C6 GZL f 2 " pdb=" O3 GZL f 2 " ideal model delta sigma weight residual 1.403 3.998 -2.595 2.00e-02 2.50e+03 1.68e+04 bond pdb=" C6 GZL S 2 " pdb=" O3 GZL S 2 " ideal model delta sigma weight residual 1.403 3.998 -2.595 2.00e-02 2.50e+03 1.68e+04 bond pdb=" C2 GZL S 2 " pdb=" C3 GZL S 2 " ideal model delta sigma weight residual 1.523 1.235 0.288 2.00e-02 2.50e+03 2.08e+02 ... (remaining 12846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.47: 17372 10.47 - 20.94: 21 20.94 - 31.41: 0 31.41 - 41.88: 4 41.88 - 52.35: 4 Bond angle restraints: 17401 Sorted by residual: angle pdb=" C5 GZL F 2 " pdb=" C6 GZL F 2 " pdb=" O3 GZL F 2 " ideal model delta sigma weight residual 103.85 51.50 52.35 3.00e+00 1.11e-01 3.05e+02 angle pdb=" C5 GZL f 2 " pdb=" C6 GZL f 2 " pdb=" O3 GZL f 2 " ideal model delta sigma weight residual 103.85 51.50 52.35 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C5 GZL S 2 " pdb=" C6 GZL S 2 " pdb=" O3 GZL S 2 " ideal model delta sigma weight residual 103.85 51.51 52.34 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C5 GZL s 2 " pdb=" C6 GZL s 2 " pdb=" O3 GZL s 2 " ideal model delta sigma weight residual 103.85 51.53 52.32 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C3 GZL s 2 " pdb=" O3 GZL s 2 " pdb=" C6 GZL s 2 " ideal model delta sigma weight residual 109.39 70.58 38.81 3.00e+00 1.11e-01 1.67e+02 ... (remaining 17396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.86: 17589 32.86 - 65.73: 585 65.73 - 98.59: 320 98.59 - 131.45: 157 131.45 - 164.31: 8 Dihedral angle restraints: 18659 sinusoidal: 17680 harmonic: 979 Sorted by residual: dihedral pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 11.79 81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 400 " pdb=" CB CYS A 400 " ideal model delta sinusoidal sigma weight residual 93.00 11.80 81.20 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 215 " pdb=" SG CYS A 215 " pdb=" SG CYS A 228 " pdb=" CB CYS A 228 " ideal model delta sinusoidal sigma weight residual 93.00 11.80 81.20 1 1.00e+01 1.00e-02 8.13e+01 ... (remaining 18656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.054: 4833 1.054 - 2.107: 23 2.107 - 3.161: 0 3.161 - 4.214: 4 4.214 - 5.268: 16 Chirality restraints: 4876 Sorted by residual: chirality pdb=" C1 BGC W 14 " pdb=" O4 A2G W 6 " pdb=" C2 BGC W 14 " pdb=" O5 BGC W 14 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.74e+03 chirality pdb=" C1 BGC j 14 " pdb=" O4 A2G j 6 " pdb=" C2 BGC j 14 " pdb=" O5 BGC j 14 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.71e+03 chirality pdb=" C1 BGC J 14 " pdb=" O4 A2G J 6 " pdb=" C2 BGC J 14 " pdb=" O5 BGC J 14 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.69e+03 ... (remaining 4873 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 18 " -0.359 2.00e-02 2.50e+03 3.07e-01 1.17e+03 pdb=" C7 NAG W 18 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG W 18 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG W 18 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG W 18 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 34 " 0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG K 34 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 34 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG K 34 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG K 34 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 34 " 0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG X 34 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG X 34 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG X 34 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG X 34 " 0.165 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 4 2.20 - 2.87: 5373 2.87 - 3.55: 14517 3.55 - 4.22: 32300 4.22 - 4.90: 42742 Nonbonded interactions: 94936 Sorted by model distance: nonbonded pdb=" C1 GZL f 2 " pdb=" O4 GZL f 2 " model vdw 1.521 3.440 nonbonded pdb=" C1 GZL s 2 " pdb=" O4 GZL s 2 " model vdw 1.522 3.440 nonbonded pdb=" C1 GZL F 2 " pdb=" O4 GZL F 2 " model vdw 1.522 3.440 nonbonded pdb=" C1 GZL S 2 " pdb=" O4 GZL S 2 " model vdw 1.522 3.440 nonbonded pdb=" C1 GZL f 2 " pdb=" C4 GZL f 2 " model vdw 2.219 2.928 ... (remaining 94931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 16) selection = (chain 'G' and resid 17) selection = (chain 'H' and resid 15) selection = (chain 'J' and resid 14) selection = (chain 'N' and resid 16) selection = (chain 'T' and resid 17) selection = (chain 'U' and resid 15) selection = (chain 'W' and resid 14) selection = (chain 'a' and resid 16) selection = (chain 'g' and resid 17) selection = (chain 'h' and resid 15) selection = (chain 'j' and resid 14) selection = (chain 'n' and resid 16) selection = (chain 't' and resid 17) selection = (chain 'u' and resid 15) selection = (chain 'w' and resid 14) } ncs_group { reference = chain 'B' selection = chain 'O' selection = chain 'b' selection = chain 'o' } ncs_group { reference = chain 'C' selection = chain 'P' selection = chain 'c' selection = chain 'p' } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'd' selection = chain 'q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'e' selection = chain 'r' } ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'f' selection = chain 's' } ncs_group { reference = (chain 'I' and (resid 3 or resid 5 through 7)) selection = (chain 'L' and (resid 3 or resid 5 through 7)) selection = (chain 'V' and (resid 3 or resid 5 through 7)) selection = (chain 'Y' and (resid 3 or resid 5 through 7)) selection = (chain 'i' and (resid 3 or resid 5 through 7)) selection = (chain 'l' and (resid 3 or resid 5 through 7)) selection = (chain 'v' and (resid 3 or resid 5 through 7)) selection = (chain 'y' and (resid 3 or resid 5 through 7)) } ncs_group { reference = chain 'K' selection = chain 'X' selection = chain 'k' selection = chain 'x' } ncs_group { reference = chain 'M' selection = chain 'Z' selection = chain 'm' selection = chain 'z' } 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: 3.510 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.048 2.595 13819 Z= 2.425 Angle : 6.073 64.577 20185 Z= 2.053 Chirality : 0.341 5.268 4876 Planarity : 0.098 0.307 555 Dihedral : 18.982 164.312 18015 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 2.05 % Allowed : 8.48 % Favored : 89.47 % Rotamer: Outliers : 5.90 % Allowed : 30.90 % Favored : 63.19 % Cbeta Deviations : 1.27 % 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: -2.96 (0.35), residues: 342 helix: None (None), residues: 0 sheet: -1.47 (0.42), residues: 108 loop : -2.36 (0.31), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 247 TYR 0.003 0.001 TYR A 295 PHE 0.001 0.000 PHE A 281 TRP 0.020 0.004 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.04910 / 2.48 (12851) covalent geometry : angle 2.34620 / 0.86 (17401) SS BOND : bond 0.00913 / 0.46 ( 4) SS BOND : angle 1.45250 / 0.69 ( 8) hydrogen bonds : bond 0.17065 / 12.17 ( 86) hydrogen bonds : angle 12.68234 / 8.93 ( 228) glycosidic custom : bond 0.01760 / 1.23 ( 28) glycosidic custom : angle 19.99327 / 13.61 ( 84) Misc. bond : bond 0.06875 / 4.74 ( 32) link_ALPHA1-2 : bond 0.02135 / 1.38 ( 20) link_ALPHA1-2 : angle 13.42144 / 9.02 ( 60) link_ALPHA1-3 : bond 0.01723 / 1.15 ( 64) link_ALPHA1-3 : angle 16.93652 / 11.51 ( 192) link_ALPHA1-4 : bond 0.02227 / 1.61 ( 48) link_ALPHA1-4 : angle 13.56950 / 7.92 ( 144) link_ALPHA1-6 : bond 0.02988 / 1.71 ( 12) link_ALPHA1-6 : angle 7.62418 / 4.90 ( 36) link_BETA1-2 : bond 0.02533 / 1.69 ( 244) link_BETA1-2 : angle 11.95034 / 7.88 ( 732) link_BETA1-3 : bond 0.01663 / 1.18 ( 224) link_BETA1-3 : angle 16.25857 / 10.66 ( 672) link_BETA1-4 : bond 0.02012 / 1.38 ( 204) link_BETA1-4 : angle 17.18794 / 11.67 ( 612) link_BETA1-6 : bond 0.01413 / 0.93 ( 68) link_BETA1-6 : angle 15.84006 / 10.60 ( 204) link_MAN-SER : bond 0.02010 / 1.38 ( 20) link_MAN-SER : angle 12.55648 / 7.40 ( 40) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.178 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 168 ASP cc_start: 0.8041 (t0) cc_final: 0.7536 (t0) REVERT: A 295 TYR cc_start: 0.8184 (m-80) cc_final: 0.7919 (m-80) REVERT: A 340 ASP cc_start: 0.8280 (t0) cc_final: 0.7974 (t0) outliers start: 17 outliers final: 10 residues processed: 47 average time/residue: 0.0653 time to fit residues: 5.5521 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 424 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107782 restraints weight = 26462.559| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.45 r_work: 0.3470 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13819 Z= 0.329 Angle : 2.526 17.934 20185 Z= 0.851 Chirality : 0.078 0.605 4876 Planarity : 0.003 0.013 555 Dihedral : 16.676 117.432 17531 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.82 % Allowed : 29.51 % Favored : 66.67 % 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: -2.42 (0.38), residues: 342 helix: None (None), residues: 0 sheet: -0.78 (0.49), residues: 108 loop : -2.16 (0.32), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.011 0.002 TYR A 209 PHE 0.003 0.001 PHE A 195 TRP 0.016 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.30 (12851) covalent geometry : angle 2.01900 / 0.69 (17401) SS BOND : bond 0.01180 / 0.59 ( 4) SS BOND : angle 2.96157 / 1.42 ( 8) hydrogen bonds : bond 0.03930 / 2.85 ( 86) hydrogen bonds : angle 9.75634 / 6.77 ( 228) glycosidic custom : bond 0.01823 / 1.29 ( 28) glycosidic custom : angle 3.83827 / 2.49 ( 84) Misc. bond : bond 0.00299 / 0.21 ( 32) link_ALPHA1-2 : bond 0.00973 / 0.68 ( 20) link_ALPHA1-2 : angle 3.34431 / 2.17 ( 60) link_ALPHA1-3 : bond 0.01597 / 1.10 ( 64) link_ALPHA1-3 : angle 4.48111 / 2.89 ( 192) link_ALPHA1-4 : bond 0.01646 / 1.28 ( 48) link_ALPHA1-4 : angle 3.26852 / 2.10 ( 144) link_ALPHA1-6 : bond 0.00738 / 0.44 ( 12) link_ALPHA1-6 : angle 2.17263 / 1.27 ( 36) link_BETA1-2 : bond 0.01305 / 0.88 ( 244) link_BETA1-2 : angle 4.80297 / 3.20 ( 732) link_BETA1-3 : bond 0.01107 / 0.81 ( 224) link_BETA1-3 : angle 4.85684 / 3.23 ( 672) link_BETA1-4 : bond 0.01086 / 0.77 ( 204) link_BETA1-4 : angle 4.95964 / 3.37 ( 612) link_BETA1-6 : bond 0.01175 / 0.84 ( 68) link_BETA1-6 : angle 3.41106 / 2.38 ( 204) link_MAN-SER : bond 0.00483 / 0.32 ( 20) link_MAN-SER : angle 1.74519 / 1.07 ( 40) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8172 (m-80) cc_final: 0.7972 (m-10) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.0625 time to fit residues: 2.9933 Evaluate side-chains 18 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092173 restraints weight = 27361.641| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.43 r_work: 0.3221 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13819 Z= 0.326 Angle : 2.482 16.758 20185 Z= 0.838 Chirality : 0.076 0.670 4876 Planarity : 0.003 0.015 555 Dihedral : 15.502 114.316 17519 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.29 % Allowed : 26.74 % Favored : 65.97 % 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: -2.65 (0.39), residues: 342 helix: None (None), residues: 0 sheet: -1.05 (0.51), residues: 108 loop : -2.25 (0.32), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.020 0.005 TYR A 295 PHE 0.009 0.002 PHE A 109 TRP 0.015 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.30 (12851) covalent geometry : angle 2.05377 / 0.70 (17401) SS BOND : bond 0.01278 / 0.64 ( 4) SS BOND : angle 3.32195 / 1.62 ( 8) hydrogen bonds : bond 0.04028 / 2.77 ( 86) hydrogen bonds : angle 6.96958 / 4.90 ( 228) glycosidic custom : bond 0.00885 / 0.62 ( 28) glycosidic custom : angle 3.10354 / 2.05 ( 84) Misc. bond : bond 0.00133 / 0.10 ( 32) link_ALPHA1-2 : bond 0.01010 / 0.70 ( 20) link_ALPHA1-2 : angle 3.09370 / 1.91 ( 60) link_ALPHA1-3 : bond 0.01588 / 1.09 ( 64) link_ALPHA1-3 : angle 3.97653 / 2.57 ( 192) link_ALPHA1-4 : bond 0.01442 / 1.12 ( 48) link_ALPHA1-4 : angle 3.27561 / 2.12 ( 144) link_ALPHA1-6 : bond 0.00531 / 0.31 ( 12) link_ALPHA1-6 : angle 1.95440 / 1.19 ( 36) link_BETA1-2 : bond 0.01180 / 0.78 ( 244) link_BETA1-2 : angle 4.88304 / 3.27 ( 732) link_BETA1-3 : bond 0.00995 / 0.72 ( 224) link_BETA1-3 : angle 4.66084 / 3.13 ( 672) link_BETA1-4 : bond 0.01023 / 0.72 ( 204) link_BETA1-4 : angle 4.27060 / 2.88 ( 612) link_BETA1-6 : bond 0.01064 / 0.78 ( 68) link_BETA1-6 : angle 2.69203 / 1.84 ( 204) link_MAN-SER : bond 0.00611 / 0.40 ( 20) link_MAN-SER : angle 1.50322 / 0.98 ( 40) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 14 time to evaluate : 0.257 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 35 average time/residue: 0.0892 time to fit residues: 5.1748 Evaluate side-chains 22 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 7 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094452 restraints weight = 26970.154| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.42 r_work: 0.3264 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13819 Z= 0.281 Angle : 2.232 16.320 20185 Z= 0.753 Chirality : 0.069 0.658 4876 Planarity : 0.002 0.015 555 Dihedral : 14.655 114.379 17519 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.51 % Allowed : 30.90 % Favored : 64.58 % 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: -3.11 (0.35), residues: 342 helix: None (None), residues: 0 sheet: -2.00 (0.58), residues: 68 loop : -2.28 (0.27), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 313 TYR 0.010 0.002 TYR A 123 PHE 0.001 0.000 PHE A 367 TRP 0.015 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 (12851) covalent geometry : angle 1.82296 / 0.62 (17401) SS BOND : bond 0.00907 / 0.45 ( 4) SS BOND : angle 2.84446 / 1.37 ( 8) hydrogen bonds : bond 0.03374 / 2.35 ( 86) hydrogen bonds : angle 6.93873 / 4.90 ( 228) glycosidic custom : bond 0.00785 / 0.56 ( 28) glycosidic custom : angle 2.31731 / 1.55 ( 84) Misc. bond : bond 0.00106 / 0.08 ( 32) link_ALPHA1-2 : bond 0.00790 / 0.56 ( 20) link_ALPHA1-2 : angle 2.68703 / 1.65 ( 60) link_ALPHA1-3 : bond 0.01482 / 1.02 ( 64) link_ALPHA1-3 : angle 3.70788 / 2.37 ( 192) link_ALPHA1-4 : bond 0.01424 / 1.11 ( 48) link_ALPHA1-4 : angle 2.74335 / 1.77 ( 144) link_ALPHA1-6 : bond 0.00411 / 0.23 ( 12) link_ALPHA1-6 : angle 1.97815 / 1.18 ( 36) link_BETA1-2 : bond 0.01149 / 0.77 ( 244) link_BETA1-2 : angle 4.49147 / 3.00 ( 732) link_BETA1-3 : bond 0.00983 / 0.72 ( 224) link_BETA1-3 : angle 4.30151 / 2.88 ( 672) link_BETA1-4 : bond 0.00879 / 0.62 ( 204) link_BETA1-4 : angle 3.92798 / 2.66 ( 612) link_BETA1-6 : bond 0.01007 / 0.72 ( 68) link_BETA1-6 : angle 2.45323 / 1.67 ( 204) link_MAN-SER : bond 0.00392 / 0.26 ( 20) link_MAN-SER : angle 1.26528 / 0.80 ( 40) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 11 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 23 average time/residue: 0.0640 time to fit residues: 2.8773 Evaluate side-chains 21 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091053 restraints weight = 27431.500| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.44 r_work: 0.3204 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13819 Z= 0.293 Angle : 2.279 16.482 20185 Z= 0.769 Chirality : 0.070 0.674 4876 Planarity : 0.002 0.015 555 Dihedral : 14.542 114.855 17519 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.21 % Allowed : 32.29 % Favored : 62.50 % 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: -3.17 (0.34), residues: 342 helix: None (None), residues: 0 sheet: -2.05 (0.58), residues: 68 loop : -2.32 (0.27), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 419 TYR 0.016 0.004 TYR A 295 PHE 0.006 0.001 PHE A 109 TRP 0.014 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.27 (12851) covalent geometry : angle 1.86900 / 0.64 (17401) SS BOND : bond 0.01146 / 0.57 ( 4) SS BOND : angle 3.06192 / 1.47 ( 8) hydrogen bonds : bond 0.03323 / 2.27 ( 86) hydrogen bonds : angle 6.80600 / 4.81 ( 228) glycosidic custom : bond 0.00738 / 0.52 ( 28) glycosidic custom : angle 2.50576 / 1.64 ( 84) Misc. bond : bond 0.00112 / 0.08 ( 32) link_ALPHA1-2 : bond 0.00822 / 0.57 ( 20) link_ALPHA1-2 : angle 2.79226 / 1.73 ( 60) link_ALPHA1-3 : bond 0.01513 / 1.04 ( 64) link_ALPHA1-3 : angle 3.71101 / 2.39 ( 192) link_ALPHA1-4 : bond 0.01420 / 1.10 ( 48) link_ALPHA1-4 : angle 2.91023 / 1.89 ( 144) link_ALPHA1-6 : bond 0.00509 / 0.29 ( 12) link_ALPHA1-6 : angle 2.01075 / 1.21 ( 36) link_BETA1-2 : bond 0.01096 / 0.73 ( 244) link_BETA1-2 : angle 4.59306 / 3.07 ( 732) link_BETA1-3 : bond 0.00957 / 0.70 ( 224) link_BETA1-3 : angle 4.38554 / 2.95 ( 672) link_BETA1-4 : bond 0.00879 / 0.62 ( 204) link_BETA1-4 : angle 3.94806 / 2.67 ( 612) link_BETA1-6 : bond 0.00902 / 0.65 ( 68) link_BETA1-6 : angle 2.25820 / 1.54 ( 204) link_MAN-SER : bond 0.00470 / 0.31 ( 20) link_MAN-SER : angle 1.31606 / 0.87 ( 40) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 12 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7615 (p) outliers start: 15 outliers final: 11 residues processed: 27 average time/residue: 0.0683 time to fit residues: 3.5821 Evaluate side-chains 21 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 9 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 0.0070 chunk 17 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097944 restraints weight = 26729.777| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.39 r_work: 0.3310 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13819 Z= 0.271 Angle : 2.048 16.160 20185 Z= 0.690 Chirality : 0.063 0.611 4876 Planarity : 0.002 0.013 555 Dihedral : 13.639 113.006 17519 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.51 % Allowed : 32.64 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.34), residues: 342 helix: None (None), residues: 0 sheet: -2.10 (0.54), residues: 80 loop : -2.30 (0.27), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 333 TYR 0.006 0.001 TYR A 123 PHE 0.002 0.001 PHE A 281 TRP 0.014 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 (12851) covalent geometry : angle 1.66434 / 0.57 (17401) SS BOND : bond 0.00851 / 0.43 ( 4) SS BOND : angle 2.58286 / 1.25 ( 8) hydrogen bonds : bond 0.03103 / 2.16 ( 86) hydrogen bonds : angle 6.78164 / 4.76 ( 228) glycosidic custom : bond 0.00794 / 0.56 ( 28) glycosidic custom : angle 2.14546 / 1.43 ( 84) Misc. bond : bond 0.00089 / 0.06 ( 32) link_ALPHA1-2 : bond 0.00852 / 0.60 ( 20) link_ALPHA1-2 : angle 2.47898 / 1.56 ( 60) link_ALPHA1-3 : bond 0.01518 / 1.04 ( 64) link_ALPHA1-3 : angle 3.39653 / 2.16 ( 192) link_ALPHA1-4 : bond 0.01492 / 1.15 ( 48) link_ALPHA1-4 : angle 2.55816 / 1.65 ( 144) link_ALPHA1-6 : bond 0.00361 / 0.21 ( 12) link_ALPHA1-6 : angle 1.63021 / 0.96 ( 36) link_BETA1-2 : bond 0.01152 / 0.77 ( 244) link_BETA1-2 : angle 4.22573 / 2.82 ( 732) link_BETA1-3 : bond 0.00993 / 0.73 ( 224) link_BETA1-3 : angle 3.96169 / 2.66 ( 672) link_BETA1-4 : bond 0.00924 / 0.65 ( 204) link_BETA1-4 : angle 3.59528 / 2.44 ( 612) link_BETA1-6 : bond 0.00936 / 0.66 ( 68) link_BETA1-6 : angle 2.01733 / 1.38 ( 204) link_MAN-SER : bond 0.00251 / 0.17 ( 20) link_MAN-SER : angle 1.05431 / 0.69 ( 40) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 12 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 23 average time/residue: 0.0626 time to fit residues: 2.7138 Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 11 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.093666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087854 restraints weight = 27601.501| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.44 r_work: 0.3140 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13819 Z= 0.312 Angle : 2.357 16.559 20185 Z= 0.795 Chirality : 0.072 0.693 4876 Planarity : 0.002 0.013 555 Dihedral : 14.490 117.393 17519 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 5.90 % Allowed : 31.94 % Favored : 62.15 % 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: -3.01 (0.37), residues: 342 helix: None (None), residues: 0 sheet: -1.50 (0.53), residues: 98 loop : -2.37 (0.29), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 419 TYR 0.014 0.003 TYR A 123 PHE 0.002 0.001 PHE A 109 TRP 0.012 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.29 (12851) covalent geometry : angle 1.94745 / 0.66 (17401) SS BOND : bond 0.01044 / 0.52 ( 4) SS BOND : angle 2.89998 / 1.39 ( 8) hydrogen bonds : bond 0.03340 / 2.24 ( 86) hydrogen bonds : angle 6.63218 / 4.68 ( 228) glycosidic custom : bond 0.00767 / 0.54 ( 28) glycosidic custom : angle 2.59583 / 1.67 ( 84) Misc. bond : bond 0.00122 / 0.08 ( 32) link_ALPHA1-2 : bond 0.00795 / 0.56 ( 20) link_ALPHA1-2 : angle 2.90596 / 1.79 ( 60) link_ALPHA1-3 : bond 0.01433 / 0.98 ( 64) link_ALPHA1-3 : angle 3.85968 / 2.50 ( 192) link_ALPHA1-4 : bond 0.01327 / 1.04 ( 48) link_ALPHA1-4 : angle 2.95939 / 1.91 ( 144) link_ALPHA1-6 : bond 0.00676 / 0.40 ( 12) link_ALPHA1-6 : angle 2.30870 / 1.40 ( 36) link_BETA1-2 : bond 0.01079 / 0.71 ( 244) link_BETA1-2 : angle 4.71626 / 3.15 ( 732) link_BETA1-3 : bond 0.00976 / 0.72 ( 224) link_BETA1-3 : angle 4.47901 / 3.00 ( 672) link_BETA1-4 : bond 0.00861 / 0.61 ( 204) link_BETA1-4 : angle 4.01208 / 2.70 ( 612) link_BETA1-6 : bond 0.00860 / 0.62 ( 68) link_BETA1-6 : angle 2.25204 / 1.52 ( 204) link_MAN-SER : bond 0.00573 / 0.38 ( 20) link_MAN-SER : angle 1.40455 / 0.93 ( 40) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 10 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7660 (p) outliers start: 17 outliers final: 16 residues processed: 27 average time/residue: 0.0534 time to fit residues: 2.8319 Evaluate side-chains 26 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 9 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089609 restraints weight = 27336.055| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.42 r_work: 0.3166 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13819 Z= 0.283 Angle : 2.231 16.319 20185 Z= 0.752 Chirality : 0.068 0.667 4876 Planarity : 0.002 0.013 555 Dihedral : 14.390 115.322 17519 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 7.64 % Allowed : 29.17 % Favored : 63.19 % 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: -3.10 (0.36), residues: 342 helix: None (None), residues: 0 sheet: -1.63 (0.51), residues: 98 loop : -2.40 (0.28), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.009 0.002 TYR A 123 PHE 0.002 0.001 PHE A 367 TRP 0.014 0.003 TRP A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.26 (12851) covalent geometry : angle 1.82744 / 0.62 (17401) SS BOND : bond 0.00953 / 0.48 ( 4) SS BOND : angle 2.71801 / 1.31 ( 8) hydrogen bonds : bond 0.03219 / 2.18 ( 86) hydrogen bonds : angle 6.66956 / 4.72 ( 228) glycosidic custom : bond 0.00794 / 0.56 ( 28) glycosidic custom : angle 2.43819 / 1.57 ( 84) Misc. bond : bond 0.00097 / 0.07 ( 32) link_ALPHA1-2 : bond 0.00791 / 0.56 ( 20) link_ALPHA1-2 : angle 2.67408 / 1.65 ( 60) link_ALPHA1-3 : bond 0.01437 / 0.98 ( 64) link_ALPHA1-3 : angle 3.70096 / 2.38 ( 192) link_ALPHA1-4 : bond 0.01376 / 1.07 ( 48) link_ALPHA1-4 : angle 2.78696 / 1.81 ( 144) link_ALPHA1-6 : bond 0.00453 / 0.26 ( 12) link_ALPHA1-6 : angle 2.00958 / 1.20 ( 36) link_BETA1-2 : bond 0.01102 / 0.73 ( 244) link_BETA1-2 : angle 4.56546 / 3.04 ( 732) link_BETA1-3 : bond 0.00979 / 0.72 ( 224) link_BETA1-3 : angle 4.28180 / 2.87 ( 672) link_BETA1-4 : bond 0.00860 / 0.61 ( 204) link_BETA1-4 : angle 3.80948 / 2.57 ( 612) link_BETA1-6 : bond 0.00892 / 0.64 ( 68) link_BETA1-6 : angle 2.12581 / 1.44 ( 204) link_MAN-SER : bond 0.00441 / 0.30 ( 20) link_MAN-SER : angle 1.25624 / 0.83 ( 40) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 10 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7591 (p) outliers start: 22 outliers final: 17 residues processed: 31 average time/residue: 0.0584 time to fit residues: 3.4418 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 9 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN A 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093334 restraints weight = 27213.374| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.43 r_work: 0.3228 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13819 Z= 0.267 Angle : 2.094 16.240 20185 Z= 0.706 Chirality : 0.064 0.634 4876 Planarity : 0.002 0.021 555 Dihedral : 13.821 113.471 17519 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.25 % Allowed : 29.86 % Favored : 63.89 % 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: -3.13 (0.36), residues: 342 helix: None (None), residues: 0 sheet: -1.80 (0.51), residues: 101 loop : -2.35 (0.28), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.008 0.002 TYR A 295 PHE 0.007 0.001 PHE A 195 TRP 0.015 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (12851) covalent geometry : angle 1.70456 / 0.58 (17401) SS BOND : bond 0.00588 / 0.30 ( 4) SS BOND : angle 1.95711 / 0.95 ( 8) hydrogen bonds : bond 0.03135 / 2.14 ( 86) hydrogen bonds : angle 6.85215 / 4.85 ( 228) glycosidic custom : bond 0.00779 / 0.55 ( 28) glycosidic custom : angle 2.23777 / 1.46 ( 84) Misc. bond : bond 0.00089 / 0.06 ( 32) link_ALPHA1-2 : bond 0.00813 / 0.57 ( 20) link_ALPHA1-2 : angle 2.49038 / 1.56 ( 60) link_ALPHA1-3 : bond 0.01417 / 0.97 ( 64) link_ALPHA1-3 : angle 3.49738 / 2.24 ( 192) link_ALPHA1-4 : bond 0.01423 / 1.10 ( 48) link_ALPHA1-4 : angle 2.62258 / 1.69 ( 144) link_ALPHA1-6 : bond 0.00381 / 0.22 ( 12) link_ALPHA1-6 : angle 1.82284 / 1.08 ( 36) link_BETA1-2 : bond 0.01121 / 0.75 ( 244) link_BETA1-2 : angle 4.34277 / 2.89 ( 732) link_BETA1-3 : bond 0.00981 / 0.72 ( 224) link_BETA1-3 : angle 4.03462 / 2.71 ( 672) link_BETA1-4 : bond 0.00875 / 0.62 ( 204) link_BETA1-4 : angle 3.62381 / 2.45 ( 612) link_BETA1-6 : bond 0.00887 / 0.63 ( 68) link_BETA1-6 : angle 1.97218 / 1.34 ( 204) link_MAN-SER : bond 0.00292 / 0.20 ( 20) link_MAN-SER : angle 1.15659 / 0.73 ( 40) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 12 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 30 average time/residue: 0.0594 time to fit residues: 3.3896 Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 9 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094035 restraints weight = 27062.371| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.42 r_work: 0.3236 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13819 Z= 0.264 Angle : 2.077 16.220 20185 Z= 0.700 Chirality : 0.064 0.682 4876 Planarity : 0.002 0.016 555 Dihedral : 13.578 113.277 17519 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 5.56 % Allowed : 31.60 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.38), residues: 342 helix: None (None), residues: 0 sheet: -1.39 (0.49), residues: 119 loop : -2.27 (0.30), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 227 TYR 0.009 0.002 TYR A 381 PHE 0.002 0.001 PHE A 281 TRP 0.014 0.003 TRP A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 (12851) covalent geometry : angle 1.69145 / 0.58 (17401) SS BOND : bond 0.01108 / 0.55 ( 4) SS BOND : angle 2.31975 / 1.11 ( 8) hydrogen bonds : bond 0.03176 / 2.18 ( 86) hydrogen bonds : angle 6.73934 / 4.78 ( 228) glycosidic custom : bond 0.00790 / 0.56 ( 28) glycosidic custom : angle 2.20412 / 1.44 ( 84) Misc. bond : bond 0.00092 / 0.06 ( 32) link_ALPHA1-2 : bond 0.00805 / 0.57 ( 20) link_ALPHA1-2 : angle 2.53583 / 1.59 ( 60) link_ALPHA1-3 : bond 0.01365 / 0.93 ( 64) link_ALPHA1-3 : angle 3.49164 / 2.24 ( 192) link_ALPHA1-4 : bond 0.01409 / 1.08 ( 48) link_ALPHA1-4 : angle 2.60788 / 1.68 ( 144) link_ALPHA1-6 : bond 0.00369 / 0.21 ( 12) link_ALPHA1-6 : angle 1.87760 / 1.12 ( 36) link_BETA1-2 : bond 0.01102 / 0.74 ( 244) link_BETA1-2 : angle 4.29718 / 2.86 ( 732) link_BETA1-3 : bond 0.00973 / 0.72 ( 224) link_BETA1-3 : angle 4.01022 / 2.69 ( 672) link_BETA1-4 : bond 0.00856 / 0.61 ( 204) link_BETA1-4 : angle 3.58626 / 2.42 ( 612) link_BETA1-6 : bond 0.00863 / 0.62 ( 68) link_BETA1-6 : angle 1.93266 / 1.30 ( 204) link_MAN-SER : bond 0.00314 / 0.21 ( 20) link_MAN-SER : angle 1.06925 / 0.70 ( 40) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 8 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7894 (t0) cc_final: 0.7494 (m-30) REVERT: A 426 ASP cc_start: 0.7777 (t0) cc_final: 0.7318 (m-30) outliers start: 16 outliers final: 16 residues processed: 24 average time/residue: 0.0622 time to fit residues: 2.7888 Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 8 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095107 restraints weight = 26928.386| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.42 r_work: 0.3256 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13819 Z= 0.262 Angle : 2.038 16.313 20185 Z= 0.687 Chirality : 0.063 0.640 4876 Planarity : 0.002 0.009 555 Dihedral : 13.363 113.040 17519 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.90 % Allowed : 31.25 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.38), residues: 342 helix: None (None), residues: 0 sheet: -1.36 (0.46), residues: 130 loop : -2.34 (0.30), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.008 0.002 TYR A 123 PHE 0.002 0.001 PHE A 109 TRP 0.014 0.003 TRP A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (12851) covalent geometry : angle 1.65667 / 0.56 (17401) SS BOND : bond 0.00992 / 0.50 ( 4) SS BOND : angle 2.11680 / 1.00 ( 8) hydrogen bonds : bond 0.03089 / 2.10 ( 86) hydrogen bonds : angle 6.76978 / 4.80 ( 228) glycosidic custom : bond 0.00786 / 0.56 ( 28) glycosidic custom : angle 2.12315 / 1.39 ( 84) Misc. bond : bond 0.00084 / 0.06 ( 32) link_ALPHA1-2 : bond 0.00826 / 0.58 ( 20) link_ALPHA1-2 : angle 2.49099 / 1.56 ( 60) link_ALPHA1-3 : bond 0.01332 / 0.90 ( 64) link_ALPHA1-3 : angle 3.43140 / 2.20 ( 192) link_ALPHA1-4 : bond 0.01416 / 1.09 ( 48) link_ALPHA1-4 : angle 2.54043 / 1.63 ( 144) link_ALPHA1-6 : bond 0.00358 / 0.20 ( 12) link_ALPHA1-6 : angle 1.80300 / 1.08 ( 36) link_BETA1-2 : bond 0.01103 / 0.74 ( 244) link_BETA1-2 : angle 4.23705 / 2.82 ( 732) link_BETA1-3 : bond 0.00981 / 0.72 ( 224) link_BETA1-3 : angle 3.94591 / 2.64 ( 672) link_BETA1-4 : bond 0.00867 / 0.61 ( 204) link_BETA1-4 : angle 3.51864 / 2.37 ( 612) link_BETA1-6 : bond 0.00865 / 0.62 ( 68) link_BETA1-6 : angle 1.89946 / 1.28 ( 204) link_MAN-SER : bond 0.00280 / 0.19 ( 20) link_MAN-SER : angle 1.11161 / 0.71 ( 40) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.17 seconds wall clock time: 38 minutes 12.35 seconds (2292.35 seconds total)