Starting phenix.real_space_refine on Sat Jun 28 12:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.map" model { file = "/net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev0_19990/06_2025/9ev0_19990.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 21150 2.51 5 N 5130 2.21 5 O 7260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.78s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33540 Number of models: 1 Model: "" Number of chains: 120 Chain: "G" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "M" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "P" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "S" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "V" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "Y" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "b" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "B" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "E" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "N" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "Q" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "T" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "W" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "Z" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "c" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "I" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "C" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "L" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "O" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "R" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "U" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "X" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "d" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1001 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "AA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "BA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "GA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "HA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "IA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "KA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "LA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "NA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "OA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "PA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "QA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "RA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "SA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "TA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "UA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "VA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "WA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "XA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "YA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "ZA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "aA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "bA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "cA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "dA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "eA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "fA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "gA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "hA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "iA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "jA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "kA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "lA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "mA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "nA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "oA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "pA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "qA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "rA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "sA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "tA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "uA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "vA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "wA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "xA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "yA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "zA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 23.54, per 1000 atoms: 0.70 Number of scatterers: 33540 At special positions: 0 Unit cell: (114.204, 114.204, 242.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 7260 8.00 N 5130 7.00 C 21150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM33318 O5 NAG0A 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM33084 O5 NAGuA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32382 O5 NAGcA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32850 O5 NAGoA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32616 O5 NAGiA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32733 O5 NAGlA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM33435 O5 NAG3A 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32967 O5 NAGrA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32499 O5 NAGfA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM33201 O5 NAGxA 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " NAG 0 2 " - " MAN 0 3 " " NAG 1 2 " - " MAN 1 3 " " NAG 2 2 " - " MAN 2 3 " " NAG 3 2 " - " MAN 3 3 " " NAG 4 2 " - " MAN 4 3 " " NAG 5 2 " - " MAN 5 3 " " NAG 6 2 " - " MAN 6 3 " " NAG 7 2 " - " MAN 7 3 " " NAG 8 2 " - " MAN 8 3 " " NAG 9 2 " - " MAN 9 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG h 2 " - " MAN h 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " " NAG k 2 " - " MAN k 3 " " NAG l 2 " - " MAN l 3 " " NAG m 2 " - " MAN m 3 " " NAG n 2 " - " MAN n 3 " " NAG o 2 " - " MAN o 3 " " NAG p 2 " - " MAN p 3 " " NAG q 2 " - " MAN q 3 " " NAG r 2 " - " MAN r 3 " " NAG s 2 " - " MAN s 3 " " NAG t 2 " - " MAN t 3 " " NAG u 2 " - " MAN u 3 " " NAG v 2 " - " MAN v 3 " " NAG w 2 " - " MAN w 3 " " NAG x 2 " - " MAN x 3 " " NAG y 2 " - " MAN y 3 " " NAG z 2 " - " MAN z 3 " " NAG0A 2 " - " MAN0A 3 " " NAG1A 2 " - " MAN1A 3 " " NAG2A 2 " - " MAN2A 3 " " NAG3A 2 " - " MAN3A 3 " " NAG4A 2 " - " MAN4A 3 " " NAG5A 2 " - " MAN5A 3 " " NAGAA 2 " - " MANAA 3 " " NAGBA 2 " - " MANBA 3 " " NAGCA 2 " - " MANCA 3 " " NAGDA 2 " - " MANDA 3 " " NAGEA 2 " - " MANEA 3 " " NAGFA 2 " - " MANFA 3 " " NAGGA 2 " - " MANGA 3 " " NAGHA 2 " - " MANHA 3 " " NAGIA 2 " - " MANIA 3 " " NAGJA 2 " - " MANJA 3 " " NAGKA 2 " - " MANKA 3 " " NAGLA 2 " - " MANLA 3 " " NAGMA 2 " - " MANMA 3 " " NAGNA 2 " - " MANNA 3 " " NAGOA 2 " - " MANOA 3 " " NAGPA 2 " - " MANPA 3 " " NAGQA 2 " - " MANQA 3 " " NAGRA 2 " - " MANRA 3 " " NAGSA 2 " - " MANSA 3 " " NAGTA 2 " - " MANTA 3 " " NAGUA 2 " - " MANUA 3 " " NAGVA 2 " - " MANVA 3 " " NAGWA 2 " - " MANWA 3 " " NAGXA 2 " - " MANXA 3 " " NAGYA 2 " - " MANYA 3 " " NAGZA 2 " - " MANZA 3 " " NAGaA 2 " - " MANaA 3 " " NAGbA 2 " - " MANbA 3 " " NAGcA 2 " - " MANcA 3 " " NAGdA 2 " - " MANdA 3 " " NAGeA 2 " - " MANeA 3 " " NAGfA 2 " - " MANfA 3 " " NAGgA 2 " - " MANgA 3 " " NAGhA 2 " - " MANhA 3 " " NAGiA 2 " - " MANiA 3 " " NAGjA 2 " - " MANjA 3 " " NAGkA 2 " - " MANkA 3 " " NAGlA 2 " - " MANlA 3 " " NAGmA 2 " - " MANmA 3 " " NAGnA 2 " - " MANnA 3 " " NAGoA 2 " - " MANoA 3 " " NAGpA 2 " - " MANpA 3 " " NAGqA 2 " - " MANqA 3 " " NAGrA 2 " - " MANrA 3 " " NAGsA 2 " - " MANsA 3 " " NAGtA 2 " - " MANtA 3 " " NAGuA 2 " - " MANuA 3 " " NAGvA 2 " - " MANvA 3 " " NAGwA 2 " - " MANwA 3 " " NAGxA 2 " - " MANxA 3 " " NAGyA 2 " - " MANyA 3 " " NAGzA 2 " - " MANzA 3 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG0A 1 " - " NAG0A 2 " " NAG1A 1 " - " NAG1A 2 " " NAG2A 1 " - " NAG2A 2 " " NAG3A 1 " - " NAG3A 2 " " NAG4A 1 " - " NAG4A 2 " " NAG5A 1 " - " NAG5A 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGQA 1 " - " NAGQA 2 " " NAGRA 1 " - " NAGRA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGTA 1 " - " NAGTA 2 " " NAGUA 1 " - " NAGUA 2 " " NAGVA 1 " - " NAGVA 2 " " NAGWA 1 " - " NAGWA 2 " " NAGXA 1 " - " NAGXA 2 " " NAGYA 1 " - " NAGYA 2 " " NAGZA 1 " - " NAGZA 2 " " NAGaA 1 " - " NAGaA 2 " " NAGbA 1 " - " NAGbA 2 " " NAGcA 1 " - " NAGcA 2 " " NAGdA 1 " - " NAGdA 2 " " NAGeA 1 " - " NAGeA 2 " " NAGfA 1 " - " NAGfA 2 " " NAGgA 1 " - " NAGgA 2 " " NAGhA 1 " - " NAGhA 2 " " NAGiA 1 " - " NAGiA 2 " " NAGjA 1 " - " NAGjA 2 " " NAGkA 1 " - " NAGkA 2 " " NAGlA 1 " - " NAGlA 2 " " NAGmA 1 " - " NAGmA 2 " " NAGnA 1 " - " NAGnA 2 " " NAGoA 1 " - " NAGoA 2 " " NAGpA 1 " - " NAGpA 2 " " NAGqA 1 " - " NAGqA 2 " " NAGrA 1 " - " NAGrA 2 " " NAGsA 1 " - " NAGsA 2 " " NAGtA 1 " - " NAGtA 2 " " NAGuA 1 " - " NAGuA 2 " " NAGvA 1 " - " NAGvA 2 " " NAGwA 1 " - " NAGwA 2 " " NAGxA 1 " - " NAGxA 2 " " NAGyA 1 " - " NAGyA 2 " " NAGzA 1 " - " NAGzA 2 " NAG-ASN " NAG 0 1 " - " ASN V 75 " " NAG 1 1 " - " ASN V 103 " " NAG 2 1 " - " ASN Y 63 " " NAG 3 1 " - " ASN Y 75 " " NAG 4 1 " - " ASN Y 103 " " NAG 5 1 " - " ASN b 63 " " NAG 6 1 " - " ASN b 75 " " NAG 7 1 " - " ASN b 103 " " NAG 8 1 " - " ASN H 63 " " NAG 9 1 " - " ASN H 75 " " NAG e 1 " - " ASN G 63 " " NAG f 1 " - " ASN G 75 " " NAG g 1 " - " ASN G 103 " " NAG h 1 " - " ASN A 63 " " NAG i 1 " - " ASN A 75 " " NAG j 1 " - " ASN A 103 " " NAG k 1 " - " ASN D 63 " " NAG l 1 " - " ASN D 75 " " NAG m 1 " - " ASN D 103 " " NAG n 1 " - " ASN J 63 " " NAG o 1 " - " ASN J 75 " " NAG p 1 " - " ASN J 103 " " NAG q 1 " - " ASN M 63 " " NAG r 1 " - " ASN M 75 " " NAG s 1 " - " ASN M 103 " " NAG t 1 " - " ASN P 63 " " NAG u 1 " - " ASN P 75 " " NAG v 1 " - " ASN P 103 " " NAG w 1 " - " ASN S 63 " " NAG x 1 " - " ASN S 75 " " NAG y 1 " - " ASN S 103 " " NAG z 1 " - " ASN V 63 " " NAG0A 1 " - " ASN a 63 " " NAG1A 1 " - " ASN a 75 " " NAG2A 1 " - " ASN a 103 " " NAG3A 1 " - " ASN d 63 " " NAG4A 1 " - " ASN d 75 " " NAG5A 1 " - " ASN d 103 " " NAGAA 1 " - " ASN H 103 " " NAGBA 1 " - " ASN B 63 " " NAGCA 1 " - " ASN B 75 " " NAGDA 1 " - " ASN B 103 " " NAGEA 1 " - " ASN E 63 " " NAGFA 1 " - " ASN E 75 " " NAGGA 1 " - " ASN E 103 " " NAGHA 1 " - " ASN K 63 " " NAGIA 1 " - " ASN K 75 " " NAGJA 1 " - " ASN K 103 " " NAGKA 1 " - " ASN N 63 " " NAGLA 1 " - " ASN N 75 " " NAGMA 1 " - " ASN N 103 " " NAGNA 1 " - " ASN Q 63 " " NAGOA 1 " - " ASN Q 75 " " NAGPA 1 " - " ASN Q 103 " " NAGQA 1 " - " ASN T 63 " " NAGRA 1 " - " ASN T 75 " " NAGSA 1 " - " ASN T 103 " " NAGTA 1 " - " ASN W 63 " " NAGUA 1 " - " ASN W 75 " " NAGVA 1 " - " ASN W 103 " " NAGWA 1 " - " ASN Z 63 " " NAGXA 1 " - " ASN Z 75 " " NAGYA 1 " - " ASN Z 103 " " NAGZA 1 " - " ASN c 63 " " NAGaA 1 " - " ASN c 75 " " NAGbA 1 " - " ASN c 103 " " NAGcA 1 " - " ASN I 63 " " NAGdA 1 " - " ASN I 75 " " NAGeA 1 " - " ASN I 103 " " NAGfA 1 " - " ASN C 63 " " NAGgA 1 " - " ASN C 75 " " NAGhA 1 " - " ASN C 103 " " NAGiA 1 " - " ASN F 63 " " NAGjA 1 " - " ASN F 75 " " NAGkA 1 " - " ASN F 103 " " NAGlA 1 " - " ASN L 63 " " NAGmA 1 " - " ASN L 75 " " NAGnA 1 " - " ASN L 103 " " NAGoA 1 " - " ASN O 63 " " NAGpA 1 " - " ASN O 75 " " NAGqA 1 " - " ASN O 103 " " NAGrA 1 " - " ASN R 63 " " NAGsA 1 " - " ASN R 75 " " NAGtA 1 " - " ASN R 103 " " NAGuA 1 " - " ASN U 63 " " NAGvA 1 " - " ASN U 75 " " NAGwA 1 " - " ASN U 103 " " NAGxA 1 " - " ASN X 63 " " NAGyA 1 " - " ASN X 75 " " NAGzA 1 " - " ASN X 103 " Time building additional restraints: 14.41 Conformation dependent library (CDL) restraints added in 4.4 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 23.7% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'G' and resid 16 through 48 removed outlier: 3.802A pdb=" N ILE G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 4.102A pdb=" N SER G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'A' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.102A pdb=" N SER A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'D' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.102A pdb=" N SER D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'J' and resid 17 through 48 removed outlier: 4.172A pdb=" N ILE J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Proline residue: J 45 - end of helix removed outlier: 4.102A pdb=" N SER J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'M' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Proline residue: M 45 - end of helix removed outlier: 4.103A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'P' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Proline residue: P 45 - end of helix removed outlier: 4.102A pdb=" N SER P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'S' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Proline residue: S 45 - end of helix removed outlier: 4.102A pdb=" N SER S 48 " --> pdb=" O ILE S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 51 No H-bonds generated for 'chain 'S' and resid 49 through 51' Processing helix chain 'V' and resid 17 through 48 removed outlier: 4.173A pdb=" N ILE V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) Proline residue: V 45 - end of helix removed outlier: 4.102A pdb=" N SER V 48 " --> pdb=" O ILE V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'Y' and resid 17 through 48 removed outlier: 4.172A pdb=" N ILE Y 44 " --> pdb=" O ALA Y 40 " (cutoff:3.500A) Proline residue: Y 45 - end of helix removed outlier: 4.102A pdb=" N SER Y 48 " --> pdb=" O ILE Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 51 No H-bonds generated for 'chain 'Y' and resid 49 through 51' Processing helix chain 'b' and resid 17 through 48 removed outlier: 4.172A pdb=" N ILE b 44 " --> pdb=" O ALA b 40 " (cutoff:3.500A) Proline residue: b 45 - end of helix removed outlier: 4.102A pdb=" N SER b 48 " --> pdb=" O ILE b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'H' and resid 17 through 49 removed outlier: 4.357A pdb=" N ILE H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix removed outlier: 3.540A pdb=" N SER H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 49 removed outlier: 4.357A pdb=" N ILE B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 3.540A pdb=" N SER B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 49 removed outlier: 4.358A pdb=" N ILE E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 3.541A pdb=" N SER E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 49 removed outlier: 4.357A pdb=" N ILE K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Proline residue: K 45 - end of helix removed outlier: 3.541A pdb=" N SER K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN K 49 " --> pdb=" O PRO K 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 49 removed outlier: 4.357A pdb=" N ILE N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Proline residue: N 45 - end of helix removed outlier: 3.540A pdb=" N SER N 48 " --> pdb=" O ILE N 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 49 removed outlier: 4.357A pdb=" N ILE Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) Proline residue: Q 45 - end of helix removed outlier: 3.540A pdb=" N SER Q 48 " --> pdb=" O ILE Q 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN Q 49 " --> pdb=" O PRO Q 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 49 removed outlier: 4.356A pdb=" N ILE T 44 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Proline residue: T 45 - end of helix removed outlier: 3.540A pdb=" N SER T 48 " --> pdb=" O ILE T 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN T 49 " --> pdb=" O PRO T 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 49 removed outlier: 4.358A pdb=" N ILE W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Proline residue: W 45 - end of helix removed outlier: 3.540A pdb=" N SER W 48 " --> pdb=" O ILE W 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN W 49 " --> pdb=" O PRO W 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 49 removed outlier: 4.358A pdb=" N ILE Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) Proline residue: Z 45 - end of helix removed outlier: 3.541A pdb=" N SER Z 48 " --> pdb=" O ILE Z 44 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN Z 49 " --> pdb=" O PRO Z 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 49 removed outlier: 4.356A pdb=" N ILE c 44 " --> pdb=" O ALA c 40 " (cutoff:3.500A) Proline residue: c 45 - end of helix removed outlier: 3.540A pdb=" N SER c 48 " --> pdb=" O ILE c 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN c 49 " --> pdb=" O PRO c 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Proline residue: I 45 - end of helix Processing helix chain 'C' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Proline residue: C 45 - end of helix Processing helix chain 'F' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'L' and resid 17 through 48 removed outlier: 3.800A pdb=" N ILE L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Proline residue: L 45 - end of helix Processing helix chain 'O' and resid 17 through 48 removed outlier: 3.800A pdb=" N ILE O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Proline residue: O 45 - end of helix Processing helix chain 'R' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Proline residue: R 45 - end of helix Processing helix chain 'U' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Proline residue: U 45 - end of helix Processing helix chain 'X' and resid 17 through 48 removed outlier: 3.800A pdb=" N ILE X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Proline residue: X 45 - end of helix Processing helix chain 'a' and resid 17 through 48 removed outlier: 3.801A pdb=" N ILE a 44 " --> pdb=" O ALA a 40 " (cutoff:3.500A) Proline residue: a 45 - end of helix Processing helix chain 'd' and resid 17 through 48 removed outlier: 3.802A pdb=" N ILE d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) Proline residue: d 45 - end of helix Processing sheet with id=AA1, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR G 141 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE G 93 " --> pdb=" O THR G 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR G 139 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE G 95 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR G 137 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN G 146 " --> pdb=" O PHE G 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY G 147 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL G 55 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY G 57 " --> pdb=" O PRO G 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR G 151 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR G 79 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER G 58 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR G 77 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR G 60 " --> pdb=" O ASN G 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN G 75 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE G 93 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE G 102 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR G 91 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR A 141 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 93 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 139 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE A 95 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 137 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY A 147 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 55 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY A 57 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR A 151 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER A 58 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR A 77 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR A 60 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN A 75 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 93 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE A 102 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR A 91 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR D 141 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE D 93 " --> pdb=" O THR D 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR D 139 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE D 95 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 137 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY D 147 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL D 55 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY D 57 " --> pdb=" O PRO D 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR D 151 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR D 79 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER D 58 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR D 77 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR D 60 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN D 75 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 93 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE D 102 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR D 91 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR J 141 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE J 93 " --> pdb=" O THR J 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR J 139 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE J 95 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR J 137 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN J 146 " --> pdb=" O PHE J 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY J 147 " --> pdb=" O ILE J 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL J 55 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY J 57 " --> pdb=" O PRO J 149 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR J 151 " --> pdb=" O GLY J 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR J 79 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER J 58 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR J 77 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR J 60 " --> pdb=" O ASN J 75 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN J 75 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE J 93 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE J 102 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR J 91 " --> pdb=" O ILE J 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR M 141 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE M 93 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR M 139 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE M 95 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR M 137 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY M 147 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL M 55 " --> pdb=" O GLY M 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY M 57 " --> pdb=" O PRO M 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 151 " --> pdb=" O GLY M 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR M 79 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER M 58 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR M 77 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR M 60 " --> pdb=" O ASN M 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN M 75 " --> pdb=" O THR M 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE M 93 " --> pdb=" O PHE M 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE M 102 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR M 91 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR P 141 " --> pdb=" O THR P 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE P 93 " --> pdb=" O THR P 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR P 139 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE P 95 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR P 137 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN P 146 " --> pdb=" O PHE P 142 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY P 147 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL P 55 " --> pdb=" O GLY P 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY P 57 " --> pdb=" O PRO P 149 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR P 151 " --> pdb=" O GLY P 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR P 79 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER P 58 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR P 77 " --> pdb=" O SER P 58 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR P 60 " --> pdb=" O ASN P 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN P 75 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE P 93 " --> pdb=" O PHE P 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE P 102 " --> pdb=" O THR P 91 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR P 91 " --> pdb=" O ILE P 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR S 141 " --> pdb=" O THR S 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE S 93 " --> pdb=" O THR S 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR S 139 " --> pdb=" O ILE S 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE S 95 " --> pdb=" O THR S 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR S 137 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN S 146 " --> pdb=" O PHE S 142 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY S 147 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL S 55 " --> pdb=" O GLY S 147 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLY S 57 " --> pdb=" O PRO S 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR S 151 " --> pdb=" O GLY S 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR S 79 " --> pdb=" O LEU S 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER S 58 " --> pdb=" O THR S 77 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR S 77 " --> pdb=" O SER S 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR S 60 " --> pdb=" O ASN S 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN S 75 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE S 93 " --> pdb=" O PHE S 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE S 102 " --> pdb=" O THR S 91 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR S 91 " --> pdb=" O ILE S 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR V 141 " --> pdb=" O THR V 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE V 93 " --> pdb=" O THR V 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR V 139 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE V 95 " --> pdb=" O THR V 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR V 137 " --> pdb=" O ILE V 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN V 146 " --> pdb=" O PHE V 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY V 147 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL V 55 " --> pdb=" O GLY V 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY V 57 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR V 151 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR V 79 " --> pdb=" O LEU V 56 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER V 58 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR V 77 " --> pdb=" O SER V 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR V 60 " --> pdb=" O ASN V 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN V 75 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE V 93 " --> pdb=" O PHE V 100 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE V 102 " --> pdb=" O THR V 91 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR V 91 " --> pdb=" O ILE V 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 108 through 109 removed outlier: 6.844A pdb=" N TYR Y 141 " --> pdb=" O THR Y 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE Y 93 " --> pdb=" O THR Y 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR Y 139 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE Y 95 " --> pdb=" O THR Y 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR Y 137 " --> pdb=" O ILE Y 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN Y 146 " --> pdb=" O PHE Y 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY Y 147 " --> pdb=" O ILE Y 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL Y 55 " --> pdb=" O GLY Y 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY Y 57 " --> pdb=" O PRO Y 149 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR Y 151 " --> pdb=" O GLY Y 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR Y 79 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER Y 58 " --> pdb=" O THR Y 77 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR Y 77 " --> pdb=" O SER Y 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR Y 60 " --> pdb=" O ASN Y 75 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN Y 75 " --> pdb=" O THR Y 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE Y 93 " --> pdb=" O PHE Y 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE Y 102 " --> pdb=" O THR Y 91 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR Y 91 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 108 through 109 removed outlier: 6.843A pdb=" N TYR b 141 " --> pdb=" O THR b 91 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE b 93 " --> pdb=" O THR b 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR b 139 " --> pdb=" O ILE b 93 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE b 95 " --> pdb=" O THR b 137 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR b 137 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN b 146 " --> pdb=" O PHE b 142 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLY b 147 " --> pdb=" O ILE b 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL b 55 " --> pdb=" O GLY b 147 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY b 57 " --> pdb=" O PRO b 149 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR b 151 " --> pdb=" O GLY b 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR b 79 " --> pdb=" O LEU b 56 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER b 58 " --> pdb=" O THR b 77 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR b 77 " --> pdb=" O SER b 58 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR b 60 " --> pdb=" O ASN b 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN b 75 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE b 93 " --> pdb=" O PHE b 100 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE b 102 " --> pdb=" O THR b 91 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR b 91 " --> pdb=" O ILE b 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 108 through 109 removed outlier: 6.975A pdb=" N TYR H 141 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE H 93 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR H 139 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE H 95 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR H 137 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY H 147 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL H 55 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY H 57 " --> pdb=" O PRO H 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR H 151 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR H 79 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER H 58 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR H 77 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR H 60 " --> pdb=" O ASN H 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN H 75 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE H 93 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE H 102 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR H 91 " --> pdb=" O ILE H 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR B 141 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 93 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 139 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 95 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 137 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY B 147 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B 55 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY B 57 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR B 151 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER B 58 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR B 77 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR B 60 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN B 75 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 93 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 102 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N THR B 91 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR E 141 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE E 93 " --> pdb=" O THR E 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR E 139 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE E 95 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR E 137 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY E 147 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL E 55 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY E 57 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR E 151 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR E 79 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER E 58 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR E 77 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR E 60 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN E 75 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE E 93 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE E 102 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR E 91 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR K 141 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE K 93 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR K 139 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE K 95 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR K 137 " --> pdb=" O ILE K 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY K 147 " --> pdb=" O ILE K 53 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL K 55 " --> pdb=" O GLY K 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY K 57 " --> pdb=" O PRO K 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR K 151 " --> pdb=" O GLY K 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR K 79 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER K 58 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR K 77 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR K 60 " --> pdb=" O ASN K 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN K 75 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE K 93 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE K 102 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N THR K 91 " --> pdb=" O ILE K 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 108 through 109 removed outlier: 6.975A pdb=" N TYR N 141 " --> pdb=" O THR N 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE N 93 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR N 139 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE N 95 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR N 137 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY N 147 " --> pdb=" O ILE N 53 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL N 55 " --> pdb=" O GLY N 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY N 57 " --> pdb=" O PRO N 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR N 151 " --> pdb=" O GLY N 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR N 79 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER N 58 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR N 77 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR N 60 " --> pdb=" O ASN N 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN N 75 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE N 93 " --> pdb=" O PHE N 100 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE N 102 " --> pdb=" O THR N 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR N 91 " --> pdb=" O ILE N 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 108 through 109 removed outlier: 6.975A pdb=" N TYR Q 141 " --> pdb=" O THR Q 91 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE Q 93 " --> pdb=" O THR Q 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR Q 139 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE Q 95 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR Q 137 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY Q 147 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL Q 55 " --> pdb=" O GLY Q 147 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY Q 57 " --> pdb=" O PRO Q 149 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR Q 151 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR Q 79 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER Q 58 " --> pdb=" O THR Q 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR Q 77 " --> pdb=" O SER Q 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR Q 60 " --> pdb=" O ASN Q 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN Q 75 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE Q 93 " --> pdb=" O PHE Q 100 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE Q 102 " --> pdb=" O THR Q 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR Q 91 " --> pdb=" O ILE Q 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 108 through 109 removed outlier: 6.975A pdb=" N TYR T 141 " --> pdb=" O THR T 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE T 93 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR T 139 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE T 95 " --> pdb=" O THR T 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR T 137 " --> pdb=" O ILE T 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY T 147 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL T 55 " --> pdb=" O GLY T 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY T 57 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR T 151 " --> pdb=" O GLY T 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR T 79 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER T 58 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR T 77 " --> pdb=" O SER T 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR T 60 " --> pdb=" O ASN T 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN T 75 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE T 93 " --> pdb=" O PHE T 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE T 102 " --> pdb=" O THR T 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR T 91 " --> pdb=" O ILE T 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR W 141 " --> pdb=" O THR W 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE W 93 " --> pdb=" O THR W 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR W 139 " --> pdb=" O ILE W 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE W 95 " --> pdb=" O THR W 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR W 137 " --> pdb=" O ILE W 95 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY W 147 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL W 55 " --> pdb=" O GLY W 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY W 57 " --> pdb=" O PRO W 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR W 151 " --> pdb=" O GLY W 57 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR W 79 " --> pdb=" O LEU W 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER W 58 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR W 77 " --> pdb=" O SER W 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR W 60 " --> pdb=" O ASN W 75 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASN W 75 " --> pdb=" O THR W 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE W 93 " --> pdb=" O PHE W 100 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE W 102 " --> pdb=" O THR W 91 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N THR W 91 " --> pdb=" O ILE W 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR Z 141 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE Z 93 " --> pdb=" O THR Z 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR Z 139 " --> pdb=" O ILE Z 93 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE Z 95 " --> pdb=" O THR Z 137 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR Z 137 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY Z 147 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL Z 55 " --> pdb=" O GLY Z 147 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY Z 57 " --> pdb=" O PRO Z 149 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR Z 151 " --> pdb=" O GLY Z 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR Z 79 " --> pdb=" O LEU Z 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER Z 58 " --> pdb=" O THR Z 77 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR Z 77 " --> pdb=" O SER Z 58 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR Z 60 " --> pdb=" O ASN Z 75 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN Z 75 " --> pdb=" O THR Z 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE Z 93 " --> pdb=" O PHE Z 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE Z 102 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR Z 91 " --> pdb=" O ILE Z 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 108 through 109 removed outlier: 6.974A pdb=" N TYR c 141 " --> pdb=" O THR c 91 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE c 93 " --> pdb=" O THR c 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR c 139 " --> pdb=" O ILE c 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE c 95 " --> pdb=" O THR c 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR c 137 " --> pdb=" O ILE c 95 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY c 147 " --> pdb=" O ILE c 53 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL c 55 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY c 57 " --> pdb=" O PRO c 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR c 151 " --> pdb=" O GLY c 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR c 79 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER c 58 " --> pdb=" O THR c 77 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N THR c 77 " --> pdb=" O SER c 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR c 60 " --> pdb=" O ASN c 75 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN c 75 " --> pdb=" O THR c 60 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE c 93 " --> pdb=" O PHE c 100 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE c 102 " --> pdb=" O THR c 91 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N THR c 91 " --> pdb=" O ILE c 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 108 through 109 removed outlier: 6.818A pdb=" N TYR I 141 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE I 93 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR I 139 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE I 95 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR I 137 " --> pdb=" O ILE I 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY I 147 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL I 55 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY I 57 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR I 151 " --> pdb=" O GLY I 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR I 79 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER I 58 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR I 77 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR I 60 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN I 75 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE I 93 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE I 102 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR I 91 " --> pdb=" O ILE I 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.819A pdb=" N TYR C 141 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 93 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 139 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE C 95 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR C 137 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY C 147 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 55 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY C 57 " --> pdb=" O PRO C 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR C 151 " --> pdb=" O GLY C 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR C 79 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER C 58 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR C 77 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 60 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 75 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 93 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE C 102 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR C 91 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 removed outlier: 6.818A pdb=" N TYR F 141 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE F 93 " --> pdb=" O THR F 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR F 139 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE F 95 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR F 137 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY F 147 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL F 55 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY F 57 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR F 151 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR F 79 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER F 58 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR F 77 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR F 60 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN F 75 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE F 93 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE F 102 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR F 91 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 108 through 109 removed outlier: 6.818A pdb=" N TYR L 141 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE L 93 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR L 139 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE L 95 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR L 137 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY L 147 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL L 55 " --> pdb=" O GLY L 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY L 57 " --> pdb=" O PRO L 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR L 151 " --> pdb=" O GLY L 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR L 79 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER L 58 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR L 77 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR L 60 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN L 75 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE L 93 " --> pdb=" O PHE L 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE L 102 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR L 91 " --> pdb=" O ILE L 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 108 through 109 removed outlier: 6.818A pdb=" N TYR O 141 " --> pdb=" O THR O 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE O 93 " --> pdb=" O THR O 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR O 139 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE O 95 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR O 137 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY O 147 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL O 55 " --> pdb=" O GLY O 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY O 57 " --> pdb=" O PRO O 149 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR O 151 " --> pdb=" O GLY O 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR O 79 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER O 58 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR O 77 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR O 60 " --> pdb=" O ASN O 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN O 75 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE O 93 " --> pdb=" O PHE O 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE O 102 " --> pdb=" O THR O 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR O 91 " --> pdb=" O ILE O 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 108 through 109 removed outlier: 6.817A pdb=" N TYR R 141 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE R 93 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR R 139 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE R 95 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR R 137 " --> pdb=" O ILE R 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY R 147 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL R 55 " --> pdb=" O GLY R 147 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY R 57 " --> pdb=" O PRO R 149 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR R 151 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR R 79 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER R 58 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR R 77 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR R 60 " --> pdb=" O ASN R 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN R 75 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE R 93 " --> pdb=" O PHE R 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE R 102 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR R 91 " --> pdb=" O ILE R 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 108 through 109 removed outlier: 6.819A pdb=" N TYR U 141 " --> pdb=" O THR U 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE U 93 " --> pdb=" O THR U 139 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR U 139 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE U 95 " --> pdb=" O THR U 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR U 137 " --> pdb=" O ILE U 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY U 147 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL U 55 " --> pdb=" O GLY U 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY U 57 " --> pdb=" O PRO U 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR U 151 " --> pdb=" O GLY U 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR U 79 " --> pdb=" O LEU U 56 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER U 58 " --> pdb=" O THR U 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR U 77 " --> pdb=" O SER U 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR U 60 " --> pdb=" O ASN U 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN U 75 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE U 93 " --> pdb=" O PHE U 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE U 102 " --> pdb=" O THR U 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR U 91 " --> pdb=" O ILE U 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 108 through 109 removed outlier: 6.818A pdb=" N TYR X 141 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE X 93 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR X 139 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE X 95 " --> pdb=" O THR X 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR X 137 " --> pdb=" O ILE X 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY X 147 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL X 55 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY X 57 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR X 151 " --> pdb=" O GLY X 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR X 79 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER X 58 " --> pdb=" O THR X 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR X 77 " --> pdb=" O SER X 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR X 60 " --> pdb=" O ASN X 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN X 75 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE X 93 " --> pdb=" O PHE X 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE X 102 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR X 91 " --> pdb=" O ILE X 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 108 through 109 removed outlier: 6.817A pdb=" N TYR a 141 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE a 93 " --> pdb=" O THR a 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR a 139 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE a 95 " --> pdb=" O THR a 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR a 137 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY a 147 " --> pdb=" O ILE a 53 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL a 55 " --> pdb=" O GLY a 147 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY a 57 " --> pdb=" O PRO a 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR a 151 " --> pdb=" O GLY a 57 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR a 79 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER a 58 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR a 77 " --> pdb=" O SER a 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR a 60 " --> pdb=" O ASN a 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN a 75 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE a 93 " --> pdb=" O PHE a 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE a 102 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR a 91 " --> pdb=" O ILE a 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 108 through 109 removed outlier: 6.819A pdb=" N TYR d 141 " --> pdb=" O THR d 91 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE d 93 " --> pdb=" O THR d 139 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR d 139 " --> pdb=" O ILE d 93 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE d 95 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR d 137 " --> pdb=" O ILE d 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY d 147 " --> pdb=" O ILE d 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL d 55 " --> pdb=" O GLY d 147 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY d 57 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR d 151 " --> pdb=" O GLY d 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR d 79 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER d 58 " --> pdb=" O THR d 77 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR d 77 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR d 60 " --> pdb=" O ASN d 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN d 75 " --> pdb=" O THR d 60 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE d 93 " --> pdb=" O PHE d 100 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE d 102 " --> pdb=" O THR d 91 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR d 91 " --> pdb=" O ILE d 102 " (cutoff:3.500A) 1550 hydrogen bonds defined for protein. 4380 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: 18.75 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 4980 1.28 - 1.35: 4737 1.35 - 1.42: 2605 1.42 - 1.49: 6850 1.49 - 1.56: 14908 Bond restraints: 34080 Sorted by residual: bond pdb=" C2 MAN 3 3 " pdb=" O2 MAN 3 3 " ideal model delta sigma weight residual 1.407 1.490 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C2 MAN o 3 " pdb=" O2 MAN o 3 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C2 MAN 6 3 " pdb=" O2 MAN 6 3 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C2 MAN r 3 " pdb=" O2 MAN r 3 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C2 MAN i 3 " pdb=" O2 MAN i 3 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 34075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 43982 2.99 - 5.97: 2609 5.97 - 8.96: 79 8.96 - 11.94: 20 11.94 - 14.93: 20 Bond angle restraints: 46710 Sorted by residual: angle pdb=" CA ASN J 63 " pdb=" CB ASN J 63 " pdb=" CG ASN J 63 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASN b 63 " pdb=" CB ASN b 63 " pdb=" CG ASN b 63 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA ASN P 63 " pdb=" CB ASN P 63 " pdb=" CG ASN P 63 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" CA ASN D 63 " pdb=" CB ASN D 63 " pdb=" CG ASN D 63 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" CA ASN V 63 " pdb=" CB ASN V 63 " pdb=" CG ASN V 63 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.00e+00 1.00e+00 3.12e+01 ... (remaining 46705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 22415 24.72 - 49.44: 655 49.44 - 74.15: 250 74.15 - 98.87: 50 98.87 - 123.59: 30 Dihedral angle restraints: 23400 sinusoidal: 11640 harmonic: 11760 Sorted by residual: dihedral pdb=" CA GLY O 51 " pdb=" C GLY O 51 " pdb=" N SER O 52 " pdb=" CA SER O 52 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLY L 51 " pdb=" C GLY L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta harmonic sigma weight residual -180.00 -152.97 -27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY I 51 " pdb=" C GLY I 51 " pdb=" N SER I 52 " pdb=" CA SER I 52 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 23397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 6590 0.297 - 0.595: 60 0.595 - 0.892: 20 0.892 - 1.190: 10 1.190 - 1.487: 10 Chirality restraints: 6690 Sorted by residual: chirality pdb=" C1 MAN3A 3 " pdb=" O6 NAG3A 2 " pdb=" C2 MAN3A 3 " pdb=" O5 MAN3A 3 " both_signs ideal model delta sigma weight residual False 2.40 1.79 0.61 2.00e-02 2.50e+03 9.22e+02 chirality pdb=" C1 MANlA 3 " pdb=" O6 NAGlA 2 " pdb=" C2 MANlA 3 " pdb=" O5 MANlA 3 " both_signs ideal model delta sigma weight residual False 2.40 1.79 0.61 2.00e-02 2.50e+03 9.20e+02 chirality pdb=" C1 MANxA 3 " pdb=" O6 NAGxA 2 " pdb=" C2 MANxA 3 " pdb=" O5 MANxA 3 " both_signs ideal model delta sigma weight residual False 2.40 1.79 0.61 2.00e-02 2.50e+03 9.19e+02 ... (remaining 6687 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 2 " -0.317 2.00e-02 2.50e+03 2.76e-01 9.50e+02 pdb=" C7 NAG l 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG l 2 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG l 2 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG l 2 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " -0.317 2.00e-02 2.50e+03 2.76e-01 9.49e+02 pdb=" C7 NAG i 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " -0.143 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " -0.317 2.00e-02 2.50e+03 2.76e-01 9.49e+02 pdb=" C7 NAG 6 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " -0.111 2.00e-02 2.50e+03 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 10 2.17 - 2.85: 9874 2.85 - 3.53: 46396 3.53 - 4.22: 82282 4.22 - 4.90: 136612 Nonbonded interactions: 275174 Sorted by model distance: nonbonded pdb=" OH TYR U 74 " pdb=" O7 NAGuA 1 " model vdw 1.484 3.040 nonbonded pdb=" OH TYR O 74 " pdb=" O7 NAGoA 1 " model vdw 1.484 3.040 nonbonded pdb=" OH TYR X 74 " pdb=" O7 NAGxA 1 " model vdw 1.485 3.040 nonbonded pdb=" OH TYR d 74 " pdb=" O7 NAG3A 1 " model vdw 1.485 3.040 nonbonded pdb=" OH TYR I 74 " pdb=" O7 NAGcA 1 " model vdw 1.485 3.040 ... (remaining 275169 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'GA' selection = chain 'HA' selection = chain 'IA' selection = chain 'JA' selection = chain 'KA' selection = chain 'LA' selection = chain 'MA' selection = chain 'NA' selection = chain 'OA' selection = chain 'PA' selection = chain 'QA' selection = chain 'RA' selection = chain 'SA' selection = chain 'TA' selection = chain 'UA' selection = chain 'VA' selection = chain 'WA' selection = chain 'XA' selection = chain 'YA' selection = chain 'ZA' selection = chain 'aA' selection = chain 'bA' selection = chain 'cA' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.250 Set scattering table: 0.360 Process input model: 91.830 Find NCS groups from input model: 1.760 Set up NCS constraints: 1.770 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: 0.020 Load rotamer database and sin/cos tables:39.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.010 0.083 34350 Z= 0.634 Angle : 1.795 27.614 47520 Z= 0.996 Chirality : 0.122 1.487 6690 Planarity : 0.016 0.276 5550 Dihedral : 14.390 123.589 15960 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.30 % Allowed : 3.03 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 4170 helix: 0.67 (0.14), residues: 880 sheet: 0.19 (0.13), residues: 1230 loop : -0.38 (0.11), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.007 PHE M 130 TYR 0.090 0.018 TYR U 154 ARG 0.007 0.001 ARG V 113 Details of bonding type rmsd link_NAG-ASN : bond 0.02259 ( 90) link_NAG-ASN : angle 9.44654 ( 270) link_ALPHA1-6 : bond 0.02646 ( 90) link_ALPHA1-6 : angle 4.65059 ( 270) link_BETA1-4 : bond 0.02345 ( 90) link_BETA1-4 : angle 6.11828 ( 270) hydrogen bonds : bond 0.13095 ( 1550) hydrogen bonds : angle 7.21007 ( 4380) covalent geometry : bond 0.01000 (34080) covalent geometry : angle 1.55561 (46710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 461 time to evaluate : 4.745 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: J 140 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9124 (mm) REVERT: P 115 GLN cc_start: 0.8306 (mt0) cc_final: 0.8059 (mt0) REVERT: S 129 ASN cc_start: 0.8194 (m-40) cc_final: 0.7984 (m110) REVERT: H 103 ASN cc_start: 0.7351 (t0) cc_final: 0.7122 (t0) REVERT: E 41 PHE cc_start: 0.8661 (m-80) cc_final: 0.8451 (m-80) REVERT: E 103 ASN cc_start: 0.7515 (t0) cc_final: 0.7213 (t0) REVERT: K 50 GLN cc_start: 0.9069 (tp40) cc_final: 0.8865 (tp40) REVERT: K 103 ASN cc_start: 0.7397 (t0) cc_final: 0.7161 (t0) REVERT: Z 103 ASN cc_start: 0.6916 (t0) cc_final: 0.6623 (t0) REVERT: c 103 ASN cc_start: 0.6715 (t0) cc_final: 0.6351 (t0) REVERT: C 50 GLN cc_start: 0.8306 (tt0) cc_final: 0.7603 (mp10) REVERT: a 129 ASN cc_start: 0.7899 (m110) cc_final: 0.7518 (m110) REVERT: d 129 ASN cc_start: 0.7887 (m110) cc_final: 0.7521 (m-40) outliers start: 10 outliers final: 1 residues processed: 471 average time/residue: 1.9639 time to fit residues: 1078.8274 Evaluate side-chains 364 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 381 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN D 54 GLN D 101 ASN D 115 GLN M 115 GLN P 49 ASN S 54 GLN V 49 ASN V 115 GLN Y 101 ASN H 144 ASN B 115 GLN K 115 GLN N 144 ASN W 115 GLN W 144 ASN c 54 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 ASN a 144 ASN a 155 GLN d 54 GLN d 129 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053629 restraints weight = 68743.895| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.52 r_work: 0.2549 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 34350 Z= 0.246 Angle : 0.877 15.078 47520 Z= 0.385 Chirality : 0.053 0.758 6690 Planarity : 0.005 0.041 5550 Dihedral : 11.942 92.212 9904 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.21 % Allowed : 7.33 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4170 helix: 2.58 (0.15), residues: 940 sheet: -0.00 (0.13), residues: 1270 loop : 0.17 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE E 41 TYR 0.017 0.002 TYR V 141 ARG 0.008 0.001 ARG S 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00874 ( 90) link_NAG-ASN : angle 4.28661 ( 270) link_ALPHA1-6 : bond 0.00662 ( 90) link_ALPHA1-6 : angle 1.90618 ( 270) link_BETA1-4 : bond 0.00646 ( 90) link_BETA1-4 : angle 1.87356 ( 270) hydrogen bonds : bond 0.05091 ( 1550) hydrogen bonds : angle 5.31712 ( 4380) covalent geometry : bond 0.00572 (34080) covalent geometry : angle 0.79663 (46710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: G 140 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9123 (mm) REVERT: A 50 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: A 140 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9084 (mm) REVERT: J 140 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9208 (mp) REVERT: M 50 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: P 140 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9146 (mm) REVERT: S 50 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: S 81 LYS cc_start: 0.9128 (tttm) cc_final: 0.8739 (tttm) REVERT: V 50 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: V 71 ARG cc_start: 0.7699 (mmm160) cc_final: 0.6858 (tpm170) REVERT: Y 50 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: Y 71 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7062 (tpm170) REVERT: Y 101 ASN cc_start: 0.8589 (m-40) cc_final: 0.8381 (m-40) REVERT: b 74 TYR cc_start: 0.8382 (m-80) cc_final: 0.8159 (m-80) REVERT: b 120 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6739 (mm-30) REVERT: K 81 LYS cc_start: 0.9303 (ttmm) cc_final: 0.9023 (ttmt) REVERT: T 113 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8374 (tpp80) REVERT: T 127 LYS cc_start: 0.9465 (tppp) cc_final: 0.8974 (tppt) REVERT: W 120 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8056 (mm-30) REVERT: W 127 LYS cc_start: 0.9452 (tppp) cc_final: 0.9062 (tppt) REVERT: Z 81 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8631 (ttpp) REVERT: c 103 ASN cc_start: 0.7162 (t0) cc_final: 0.6944 (t0) REVERT: I 71 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8074 (ptm-80) REVERT: F 71 ARG cc_start: 0.8338 (ptm-80) cc_final: 0.8054 (ptm-80) REVERT: F 115 GLN cc_start: 0.8473 (mt0) cc_final: 0.8244 (mt0) REVERT: F 120 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8126 (mm-30) REVERT: L 113 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8329 (mmm-85) REVERT: R 127 LYS cc_start: 0.9079 (pptt) cc_final: 0.8878 (pptt) REVERT: U 50 GLN cc_start: 0.8581 (tt0) cc_final: 0.8234 (mt0) REVERT: U 144 ASN cc_start: 0.8968 (m110) cc_final: 0.8758 (m-40) REVERT: X 71 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7495 (ttp-170) REVERT: X 103 ASN cc_start: 0.7633 (t0) cc_final: 0.7413 (t0) REVERT: X 127 LYS cc_start: 0.8963 (pptt) cc_final: 0.8733 (pptt) REVERT: a 71 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7575 (ttp-170) REVERT: d 71 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: d 74 TYR cc_start: 0.8202 (m-80) cc_final: 0.7871 (m-80) REVERT: d 103 ASN cc_start: 0.6799 (t0) cc_final: 0.6543 (t0) REVERT: d 120 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7492 (mm-30) REVERT: d 129 ASN cc_start: 0.8648 (m-40) cc_final: 0.8335 (m-40) outliers start: 73 outliers final: 30 residues processed: 402 average time/residue: 2.1689 time to fit residues: 1007.9123 Evaluate side-chains 383 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain Q residue 144 ASN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 115 GLN Chi-restraints excluded: chain d residue 49 ASN Chi-restraints excluded: chain d residue 65 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 235 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 369 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 283 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN J 54 GLN M 54 GLN M 115 GLN P 49 ASN P 115 GLN S 115 GLN Y 115 GLN b 54 GLN b 101 ASN H 50 GLN B 50 GLN B 115 GLN K 115 GLN c 54 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN L 144 ASN O 115 GLN O 129 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 ASN ** U 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 115 GLN ** a 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 144 ASN d 54 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.054272 restraints weight = 68990.404| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.57 r_work: 0.2567 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34350 Z= 0.170 Angle : 0.784 14.316 47520 Z= 0.340 Chirality : 0.048 0.604 6690 Planarity : 0.005 0.044 5550 Dihedral : 10.838 88.861 9904 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.18 % Allowed : 8.52 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 4170 helix: 3.21 (0.15), residues: 940 sheet: 0.09 (0.13), residues: 1220 loop : 0.46 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE T 119 TYR 0.011 0.001 TYR V 141 ARG 0.008 0.001 ARG M 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 90) link_NAG-ASN : angle 3.65734 ( 270) link_ALPHA1-6 : bond 0.00657 ( 90) link_ALPHA1-6 : angle 1.71033 ( 270) link_BETA1-4 : bond 0.00511 ( 90) link_BETA1-4 : angle 1.78477 ( 270) hydrogen bonds : bond 0.04427 ( 1550) hydrogen bonds : angle 4.86972 ( 4380) covalent geometry : bond 0.00387 (34080) covalent geometry : angle 0.71655 (46710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 386 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 140 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 50 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: D 113 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8279 (mmm-85) REVERT: J 140 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9096 (mm) REVERT: P 140 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9096 (mm) REVERT: S 81 LYS cc_start: 0.9149 (tttm) cc_final: 0.8682 (tttm) REVERT: S 127 LYS cc_start: 0.9320 (ptpp) cc_final: 0.8955 (ptmm) REVERT: V 50 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: V 71 ARG cc_start: 0.7662 (mmm160) cc_final: 0.6903 (tpm170) REVERT: Y 50 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: Y 71 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7085 (tpm170) REVERT: Y 81 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8459 (tttp) REVERT: Y 98 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7732 (mm110) REVERT: Y 101 ASN cc_start: 0.8484 (m-40) cc_final: 0.8218 (m-40) REVERT: Y 120 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7942 (mm-30) REVERT: b 120 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6897 (mm-30) REVERT: N 127 LYS cc_start: 0.9389 (tppp) cc_final: 0.8968 (tppt) REVERT: T 113 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8410 (tpp80) REVERT: W 120 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8051 (mm-30) REVERT: W 127 LYS cc_start: 0.9444 (tppp) cc_final: 0.9079 (tppt) REVERT: Z 81 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8664 (ttpp) REVERT: c 103 ASN cc_start: 0.7273 (t0) cc_final: 0.7008 (t0) REVERT: c 113 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8275 (tpp80) REVERT: I 71 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8079 (ptm-80) REVERT: I 127 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8868 (pptt) REVERT: F 120 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8260 (mm-30) REVERT: L 113 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8336 (mmm-85) REVERT: O 120 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8658 (mm-30) REVERT: U 50 GLN cc_start: 0.8453 (tt0) cc_final: 0.8202 (mt0) REVERT: U 113 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8276 (mmm-85) REVERT: X 71 ARG cc_start: 0.7787 (ptm-80) cc_final: 0.7513 (ptt180) REVERT: X 103 ASN cc_start: 0.7715 (t0) cc_final: 0.7412 (t0) REVERT: X 127 LYS cc_start: 0.8986 (pptt) cc_final: 0.8693 (pptt) REVERT: a 71 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7715 (ttp-170) REVERT: a 127 LYS cc_start: 0.9050 (pptt) cc_final: 0.8777 (pptt) REVERT: a 129 ASN cc_start: 0.8256 (m-40) cc_final: 0.7848 (m-40) REVERT: d 74 TYR cc_start: 0.8112 (m-80) cc_final: 0.7683 (m-80) REVERT: d 101 ASN cc_start: 0.8934 (m110) cc_final: 0.8696 (m-40) REVERT: d 103 ASN cc_start: 0.6911 (t0) cc_final: 0.6592 (t0) REVERT: d 120 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7417 (mm-30) REVERT: d 127 LYS cc_start: 0.8829 (pptt) cc_final: 0.8621 (pptt) outliers start: 72 outliers final: 34 residues processed: 406 average time/residue: 1.8042 time to fit residues: 848.1192 Evaluate side-chains 394 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 98 GLN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain Q residue 144 ASN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 144 ASN Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain d residue 49 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 270 optimal weight: 20.0000 chunk 282 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 417 optimal weight: 20.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN M 50 GLN P 49 ASN V 115 GLN Y 115 GLN b 50 GLN b 54 GLN b 101 ASN B 115 GLN K 115 GLN I 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN O 115 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN ** a 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.052630 restraints weight = 69443.044| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.50 r_work: 0.2515 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 34350 Z= 0.268 Angle : 0.774 12.134 47520 Z= 0.345 Chirality : 0.049 0.695 6690 Planarity : 0.005 0.050 5550 Dihedral : 9.811 87.991 9904 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.64 % Allowed : 9.39 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.12), residues: 4170 helix: 3.21 (0.15), residues: 940 sheet: -0.01 (0.13), residues: 1220 loop : 0.51 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE L 142 TYR 0.015 0.002 TYR L 141 ARG 0.010 0.001 ARG M 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 90) link_NAG-ASN : angle 3.47016 ( 270) link_ALPHA1-6 : bond 0.00541 ( 90) link_ALPHA1-6 : angle 1.58171 ( 270) link_BETA1-4 : bond 0.00556 ( 90) link_BETA1-4 : angle 1.78802 ( 270) hydrogen bonds : bond 0.04714 ( 1550) hydrogen bonds : angle 4.83344 ( 4380) covalent geometry : bond 0.00625 (34080) covalent geometry : angle 0.71209 (46710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 354 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 140 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9152 (mm) REVERT: D 50 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: P 140 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9188 (mm) REVERT: S 50 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: S 71 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7232 (tpm170) REVERT: S 127 LYS cc_start: 0.9338 (ptpp) cc_final: 0.8993 (ptmm) REVERT: V 50 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: Y 50 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: Y 71 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7202 (tpm170) REVERT: Y 98 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: b 120 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6942 (mm-30) REVERT: N 127 LYS cc_start: 0.9453 (tppp) cc_final: 0.9026 (tppt) REVERT: T 113 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8417 (tpp80) REVERT: T 127 LYS cc_start: 0.9474 (tppp) cc_final: 0.8972 (tppt) REVERT: W 120 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8060 (mm-30) REVERT: W 127 LYS cc_start: 0.9473 (tppp) cc_final: 0.9171 (tptp) REVERT: Z 44 ILE cc_start: 0.9328 (mt) cc_final: 0.9114 (mp) REVERT: Z 81 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8697 (ttpp) REVERT: Z 113 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8307 (tpp80) REVERT: Z 144 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8378 (p0) REVERT: c 71 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8329 (ptp-170) REVERT: c 103 ASN cc_start: 0.7167 (t0) cc_final: 0.6929 (t0) REVERT: I 127 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8927 (pptt) REVERT: C 71 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7506 (ptt180) REVERT: F 120 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8234 (mm-30) REVERT: L 71 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (ptm160) REVERT: L 113 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8358 (mmm-85) REVERT: O 120 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8668 (mm-30) REVERT: U 71 ARG cc_start: 0.7934 (ptm-80) cc_final: 0.7396 (ptt180) REVERT: X 71 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7493 (ptt180) REVERT: X 103 ASN cc_start: 0.7739 (t0) cc_final: 0.7401 (t0) REVERT: X 127 LYS cc_start: 0.9045 (pptt) cc_final: 0.8824 (pptt) REVERT: a 71 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7743 (ttp-170) REVERT: d 71 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7357 (ptt-90) REVERT: d 74 TYR cc_start: 0.8116 (m-80) cc_final: 0.7737 (m-80) REVERT: d 101 ASN cc_start: 0.8913 (m110) cc_final: 0.8677 (m-40) REVERT: d 103 ASN cc_start: 0.6975 (t0) cc_final: 0.6551 (t0) REVERT: d 120 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7392 (mm-30) REVERT: d 127 LYS cc_start: 0.8886 (pptt) cc_final: 0.8650 (pptt) outliers start: 87 outliers final: 48 residues processed: 386 average time/residue: 1.8460 time to fit residues: 822.9302 Evaluate side-chains 397 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 98 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain Q residue 144 ASN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 144 ASN Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 144 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain c residue 144 ASN Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 144 ASN Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 144 ASN Chi-restraints excluded: chain d residue 49 ASN Chi-restraints excluded: chain d residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 344 optimal weight: 0.8980 chunk 372 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 135 optimal weight: 0.0070 chunk 298 optimal weight: 0.0070 chunk 200 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 115 GLN J 115 GLN M 50 GLN P 49 ASN b 101 ASN B 115 GLN K 115 GLN Q 50 GLN I 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN L 115 GLN L 144 ASN O 115 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN R 144 ASN a 115 GLN d 54 GLN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055191 restraints weight = 68625.532| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.57 r_work: 0.2597 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34350 Z= 0.133 Angle : 0.736 17.587 47520 Z= 0.320 Chirality : 0.048 1.042 6690 Planarity : 0.005 0.058 5550 Dihedral : 9.150 85.738 9902 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.33 % Allowed : 10.39 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4170 helix: 3.18 (0.15), residues: 940 sheet: 0.06 (0.14), residues: 1220 loop : 0.56 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE R 142 TYR 0.010 0.001 TYR V 141 ARG 0.012 0.002 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 90) link_NAG-ASN : angle 3.68252 ( 270) link_ALPHA1-6 : bond 0.00646 ( 90) link_ALPHA1-6 : angle 1.44358 ( 270) link_BETA1-4 : bond 0.00694 ( 90) link_BETA1-4 : angle 1.80326 ( 270) hydrogen bonds : bond 0.03934 ( 1550) hydrogen bonds : angle 4.62085 ( 4380) covalent geometry : bond 0.00287 (34080) covalent geometry : angle 0.66420 (46710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 376 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 140 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8843 (mm) REVERT: M 71 ARG cc_start: 0.7570 (mmm160) cc_final: 0.7212 (tpm170) REVERT: M 140 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8905 (mm) REVERT: P 71 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7344 (tpm170) REVERT: S 71 ARG cc_start: 0.7597 (mmm160) cc_final: 0.7286 (tpm170) REVERT: S 81 LYS cc_start: 0.9151 (tttm) cc_final: 0.8606 (tttm) REVERT: S 127 LYS cc_start: 0.9309 (ptpp) cc_final: 0.8986 (ptmm) REVERT: V 50 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: V 78 ILE cc_start: 0.8990 (pt) cc_final: 0.8703 (tp) REVERT: Y 50 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: Y 71 ARG cc_start: 0.7610 (mmm160) cc_final: 0.7240 (tpm170) REVERT: Y 81 LYS cc_start: 0.8607 (tttp) cc_final: 0.8243 (tmmm) REVERT: b 120 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7110 (mm-30) REVERT: K 120 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8351 (mm-30) REVERT: T 113 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8349 (tpp80) REVERT: T 127 LYS cc_start: 0.9406 (tppp) cc_final: 0.8933 (tppt) REVERT: W 98 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8343 (mm-40) REVERT: W 120 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8012 (mm-30) REVERT: W 127 LYS cc_start: 0.9433 (tppp) cc_final: 0.9139 (tptp) REVERT: Z 44 ILE cc_start: 0.9291 (mt) cc_final: 0.9062 (mp) REVERT: Z 50 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8949 (mm-40) REVERT: Z 81 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8733 (ttpp) REVERT: Z 113 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8346 (tpp80) REVERT: c 81 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (ttmm) REVERT: C 71 ARG cc_start: 0.8240 (ptm-80) cc_final: 0.7512 (ptt180) REVERT: F 113 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8316 (mmm-85) REVERT: F 120 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8299 (mm-30) REVERT: L 113 ARG cc_start: 0.8824 (ttm-80) cc_final: 0.8359 (mmm-85) REVERT: U 71 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7444 (ptt180) REVERT: U 113 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8377 (mmm-85) REVERT: U 144 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8701 (p0) REVERT: X 71 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7510 (ptt180) REVERT: X 103 ASN cc_start: 0.7724 (t0) cc_final: 0.7407 (t0) REVERT: X 113 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8434 (mmm160) REVERT: X 127 LYS cc_start: 0.9060 (pptt) cc_final: 0.8660 (pptt) REVERT: a 71 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7762 (ttp-170) REVERT: a 127 LYS cc_start: 0.9143 (pptt) cc_final: 0.8936 (pptt) REVERT: a 129 ASN cc_start: 0.8216 (m-40) cc_final: 0.7969 (m-40) REVERT: d 71 ARG cc_start: 0.7595 (ttp-170) cc_final: 0.7367 (ptt-90) REVERT: d 74 TYR cc_start: 0.8097 (m-80) cc_final: 0.7733 (m-80) REVERT: d 103 ASN cc_start: 0.6928 (t0) cc_final: 0.6509 (t0) REVERT: d 113 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8511 (tpp80) REVERT: d 120 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7317 (mm-30) REVERT: d 127 LYS cc_start: 0.8892 (pptt) cc_final: 0.8652 (pptt) outliers start: 77 outliers final: 39 residues processed: 410 average time/residue: 1.7836 time to fit residues: 847.1301 Evaluate side-chains 387 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 342 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain Q residue 144 ASN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 144 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain d residue 49 ASN Chi-restraints excluded: chain d residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 323 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 316 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 366 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 115 GLN M 50 GLN P 49 ASN V 115 GLN b 115 GLN B 115 GLN K 115 GLN N 50 GLN Z 98 GLN I 115 GLN C 115 GLN F 115 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN O 144 ASN R 115 GLN R 144 ASN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 ASN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054697 restraints weight = 69112.599| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.57 r_work: 0.2582 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34350 Z= 0.155 Angle : 0.730 23.035 47520 Z= 0.320 Chirality : 0.046 0.586 6690 Planarity : 0.005 0.057 5550 Dihedral : 8.901 83.469 9902 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.42 % Allowed : 10.94 % Favored : 86.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.13), residues: 4170 helix: 3.24 (0.15), residues: 940 sheet: 0.15 (0.13), residues: 1320 loop : 0.53 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE L 142 TYR 0.012 0.001 TYR R 141 ARG 0.014 0.001 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 90) link_NAG-ASN : angle 3.69486 ( 270) link_ALPHA1-6 : bond 0.00545 ( 90) link_ALPHA1-6 : angle 1.49546 ( 270) link_BETA1-4 : bond 0.00600 ( 90) link_BETA1-4 : angle 1.93044 ( 270) hydrogen bonds : bond 0.03961 ( 1550) hydrogen bonds : angle 4.52801 ( 4380) covalent geometry : bond 0.00351 (34080) covalent geometry : angle 0.65465 (46710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: G 140 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8987 (mm) REVERT: D 71 ARG cc_start: 0.7670 (ttp-170) cc_final: 0.7438 (ttm170) REVERT: M 117 ILE cc_start: 0.8889 (mm) cc_final: 0.8525 (pt) REVERT: P 71 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7446 (tpm170) REVERT: P 140 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9026 (mm) REVERT: S 50 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: S 71 ARG cc_start: 0.7582 (mmm160) cc_final: 0.7332 (tpm170) REVERT: S 127 LYS cc_start: 0.9312 (ptpp) cc_final: 0.8998 (ptmm) REVERT: V 50 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: V 78 ILE cc_start: 0.8985 (pt) cc_final: 0.8740 (tp) REVERT: V 140 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8710 (mm) REVERT: Y 50 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: Y 71 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7303 (tpm170) REVERT: Y 81 LYS cc_start: 0.8677 (tttp) cc_final: 0.8297 (tmmm) REVERT: b 120 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7111 (mm-30) REVERT: K 144 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8443 (p0) REVERT: N 127 LYS cc_start: 0.9405 (tppp) cc_final: 0.8933 (tppt) REVERT: T 113 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8347 (tpp80) REVERT: T 127 LYS cc_start: 0.9435 (tppp) cc_final: 0.8962 (tppt) REVERT: W 98 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8386 (mm-40) REVERT: W 120 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7980 (mm-30) REVERT: W 127 LYS cc_start: 0.9441 (tppp) cc_final: 0.9156 (tptp) REVERT: Z 44 ILE cc_start: 0.9287 (mt) cc_final: 0.9041 (mp) REVERT: Z 81 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8743 (ttpp) REVERT: Z 113 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8316 (tpp80) REVERT: c 81 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (ttmm) REVERT: C 71 ARG cc_start: 0.8260 (ptm-80) cc_final: 0.7521 (ptt180) REVERT: F 120 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8221 (mm-30) REVERT: L 50 GLN cc_start: 0.8585 (tt0) cc_final: 0.8333 (mt0) REVERT: L 113 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8368 (mmm-85) REVERT: U 71 ARG cc_start: 0.8027 (ptm-80) cc_final: 0.7519 (ptt180) REVERT: U 120 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8514 (mm-30) REVERT: X 71 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7602 (ptt180) REVERT: X 103 ASN cc_start: 0.7712 (t0) cc_final: 0.7428 (t0) REVERT: X 113 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8425 (mmm160) REVERT: X 127 LYS cc_start: 0.9075 (pptt) cc_final: 0.8631 (pptt) REVERT: a 71 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7831 (ttp-170) REVERT: a 113 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8308 (mmm-85) REVERT: a 127 LYS cc_start: 0.9166 (pptt) cc_final: 0.8793 (pptt) REVERT: d 71 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7403 (ptt-90) REVERT: d 74 TYR cc_start: 0.8052 (m-80) cc_final: 0.7664 (m-80) REVERT: d 103 ASN cc_start: 0.6934 (t0) cc_final: 0.6514 (t0) REVERT: d 113 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8441 (tpp80) REVERT: d 120 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7260 (mm-30) REVERT: d 127 LYS cc_start: 0.8898 (pptt) cc_final: 0.8636 (pptt) outliers start: 80 outliers final: 45 residues processed: 387 average time/residue: 1.7546 time to fit residues: 784.7933 Evaluate side-chains 391 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain d residue 49 ASN Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 115 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN J 115 GLN M 50 GLN P 49 ASN P 115 GLN b 101 ASN K 115 GLN C 115 GLN F 115 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 GLN O 144 ASN R 144 ASN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.085962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051495 restraints weight = 69473.322| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.58 r_work: 0.2508 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 34350 Z= 0.286 Angle : 0.757 15.230 47520 Z= 0.343 Chirality : 0.048 0.505 6690 Planarity : 0.005 0.068 5550 Dihedral : 8.927 80.388 9902 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.42 % Allowed : 11.39 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.12), residues: 4170 helix: 3.15 (0.15), residues: 940 sheet: 0.10 (0.13), residues: 1310 loop : 0.41 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE R 142 TYR 0.017 0.002 TYR L 141 ARG 0.015 0.002 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 90) link_NAG-ASN : angle 3.47934 ( 270) link_ALPHA1-6 : bond 0.00448 ( 90) link_ALPHA1-6 : angle 1.56276 ( 270) link_BETA1-4 : bond 0.00532 ( 90) link_BETA1-4 : angle 1.64804 ( 270) hydrogen bonds : bond 0.04679 ( 1550) hydrogen bonds : angle 4.76343 ( 4380) covalent geometry : bond 0.00667 (34080) covalent geometry : angle 0.69542 (46710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 332 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 ASN cc_start: 0.9165 (m110) cc_final: 0.8859 (m-40) REVERT: G 140 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9112 (mm) REVERT: D 50 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: P 71 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7510 (tpm170) REVERT: P 140 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9131 (mm) REVERT: S 50 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: S 71 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7461 (tpm170) REVERT: S 127 LYS cc_start: 0.9335 (ptpp) cc_final: 0.9013 (ptmm) REVERT: V 50 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: V 140 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8859 (mm) REVERT: Y 50 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: Y 71 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7358 (tpm170) REVERT: Y 81 LYS cc_start: 0.8701 (tttp) cc_final: 0.8219 (tmmm) REVERT: b 120 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7176 (mm-30) REVERT: N 127 LYS cc_start: 0.9480 (tppp) cc_final: 0.9000 (tppt) REVERT: Q 127 LYS cc_start: 0.9425 (tppp) cc_final: 0.8927 (tppt) REVERT: T 113 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8247 (tpp80) REVERT: T 127 LYS cc_start: 0.9489 (tppp) cc_final: 0.9021 (tppt) REVERT: W 98 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8437 (mm-40) REVERT: W 120 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8009 (mm-30) REVERT: W 127 LYS cc_start: 0.9463 (tppp) cc_final: 0.9213 (tptp) REVERT: Z 44 ILE cc_start: 0.9326 (mt) cc_final: 0.9069 (mp) REVERT: Z 113 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8329 (tpp80) REVERT: c 81 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8370 (ttmm) REVERT: C 71 ARG cc_start: 0.8248 (ptm-80) cc_final: 0.7587 (ptt180) REVERT: C 113 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8200 (mmm-85) REVERT: F 50 GLN cc_start: 0.8623 (tt0) cc_final: 0.8361 (mt0) REVERT: F 113 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8267 (mmm-85) REVERT: F 120 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8235 (mm-30) REVERT: L 50 GLN cc_start: 0.8778 (tt0) cc_final: 0.8492 (mt0) REVERT: L 113 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8374 (mmm-85) REVERT: O 120 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8630 (mm-30) REVERT: R 50 GLN cc_start: 0.8818 (tt0) cc_final: 0.8548 (mt0) REVERT: R 113 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8346 (mmm-85) REVERT: U 71 ARG cc_start: 0.8038 (ptm-80) cc_final: 0.7551 (ptt180) REVERT: U 113 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8269 (mmm-85) REVERT: U 120 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8471 (mm-30) REVERT: X 71 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7564 (ptt180) REVERT: X 103 ASN cc_start: 0.7753 (t0) cc_final: 0.7368 (t0) REVERT: X 113 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8429 (mmm160) REVERT: X 127 LYS cc_start: 0.9087 (pptt) cc_final: 0.8661 (pptt) REVERT: a 71 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7811 (ttp-170) REVERT: a 113 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8288 (mmm-85) REVERT: a 127 LYS cc_start: 0.9215 (pptt) cc_final: 0.9015 (pptt) REVERT: d 71 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7400 (ptt-90) REVERT: d 74 TYR cc_start: 0.8070 (m-80) cc_final: 0.7787 (m-80) REVERT: d 103 ASN cc_start: 0.6968 (t0) cc_final: 0.6533 (t0) REVERT: d 113 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8566 (tpp80) REVERT: d 120 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7432 (mm-30) REVERT: d 127 LYS cc_start: 0.8935 (pptt) cc_final: 0.8665 (pptt) outliers start: 80 outliers final: 47 residues processed: 371 average time/residue: 1.8876 time to fit residues: 809.3909 Evaluate side-chains 372 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain X residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain d residue 49 ASN Chi-restraints excluded: chain d residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 344 optimal weight: 0.8980 chunk 334 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 234 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 370 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 GLN M 50 GLN P 49 ASN V 54 GLN Y 115 GLN b 50 GLN b 101 ASN B 115 GLN K 115 GLN L 115 GLN L 144 ASN R 144 ASN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.088276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054571 restraints weight = 69068.572| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.52 r_work: 0.2584 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34350 Z= 0.136 Angle : 0.692 14.841 47520 Z= 0.302 Chirality : 0.046 0.477 6690 Planarity : 0.005 0.070 5550 Dihedral : 8.607 76.882 9902 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 12.12 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4170 helix: 3.16 (0.15), residues: 940 sheet: 0.16 (0.14), residues: 1310 loop : 0.49 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE R 142 TYR 0.010 0.001 TYR J 141 ARG 0.017 0.001 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 90) link_NAG-ASN : angle 3.31792 ( 270) link_ALPHA1-6 : bond 0.00550 ( 90) link_ALPHA1-6 : angle 1.45295 ( 270) link_BETA1-4 : bond 0.00513 ( 90) link_BETA1-4 : angle 1.60891 ( 270) hydrogen bonds : bond 0.03924 ( 1550) hydrogen bonds : angle 4.53561 ( 4380) covalent geometry : bond 0.00308 (34080) covalent geometry : angle 0.63006 (46710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 347 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: G 117 ILE cc_start: 0.8856 (mm) cc_final: 0.8398 (pt) REVERT: G 140 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 117 ILE cc_start: 0.8793 (mm) cc_final: 0.8472 (pt) REVERT: J 117 ILE cc_start: 0.8749 (mm) cc_final: 0.8355 (pt) REVERT: M 117 ILE cc_start: 0.8822 (mm) cc_final: 0.8476 (pt) REVERT: M 140 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8894 (mm) REVERT: P 71 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7494 (tpm170) REVERT: S 50 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8557 (mp10) REVERT: S 127 LYS cc_start: 0.9319 (ptpp) cc_final: 0.9006 (ptmm) REVERT: V 50 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: V 78 ILE cc_start: 0.9033 (pt) cc_final: 0.8740 (tp) REVERT: V 140 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8691 (mm) REVERT: Y 50 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: Y 71 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7345 (tpm170) REVERT: Y 81 LYS cc_start: 0.8694 (tttp) cc_final: 0.8227 (tmmm) REVERT: Y 127 LYS cc_start: 0.8988 (ptmm) cc_final: 0.8223 (tptp) REVERT: b 74 TYR cc_start: 0.8357 (m-80) cc_final: 0.8095 (m-80) REVERT: b 120 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7172 (mm-30) REVERT: b 127 LYS cc_start: 0.9060 (ptmm) cc_final: 0.8459 (tptp) REVERT: K 144 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8436 (p0) REVERT: N 127 LYS cc_start: 0.9456 (tppp) cc_final: 0.8964 (tppt) REVERT: Q 50 GLN cc_start: 0.9260 (tp40) cc_final: 0.9049 (tp40) REVERT: Q 127 LYS cc_start: 0.9390 (tppp) cc_final: 0.8955 (tppt) REVERT: T 113 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8224 (tpp80) REVERT: T 127 LYS cc_start: 0.9440 (tppp) cc_final: 0.8918 (tppt) REVERT: W 71 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7996 (mtm180) REVERT: W 98 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8334 (mm-40) REVERT: W 120 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7823 (mm-30) REVERT: W 127 LYS cc_start: 0.9450 (tppp) cc_final: 0.9193 (tptp) REVERT: Z 44 ILE cc_start: 0.9280 (mt) cc_final: 0.9032 (mp) REVERT: Z 113 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8311 (tpp80) REVERT: c 81 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: C 71 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7597 (ptt180) REVERT: C 113 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8226 (mmm-85) REVERT: F 50 GLN cc_start: 0.8324 (tt0) cc_final: 0.8110 (mt0) REVERT: F 113 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8391 (mmm-85) REVERT: F 120 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8221 (mm-30) REVERT: L 50 GLN cc_start: 0.8448 (tt0) cc_final: 0.8234 (mt0) REVERT: L 113 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8388 (mmm-85) REVERT: O 120 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8629 (mm-30) REVERT: R 50 GLN cc_start: 0.8553 (tt0) cc_final: 0.8251 (mt0) REVERT: R 113 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8309 (mmm-85) REVERT: U 71 ARG cc_start: 0.8020 (ptm-80) cc_final: 0.7554 (ptt180) REVERT: U 120 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8480 (mm-30) REVERT: U 127 LYS cc_start: 0.9189 (pttm) cc_final: 0.8854 (pptt) REVERT: X 71 ARG cc_start: 0.7795 (ptm-80) cc_final: 0.7488 (ptt180) REVERT: X 103 ASN cc_start: 0.7725 (t0) cc_final: 0.7387 (t0) REVERT: X 113 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8449 (mmm160) REVERT: X 127 LYS cc_start: 0.9094 (pptt) cc_final: 0.8713 (pptt) REVERT: a 71 ARG cc_start: 0.8066 (ttp-170) cc_final: 0.7806 (ttp-170) REVERT: a 113 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8315 (mmm-85) REVERT: a 127 LYS cc_start: 0.9224 (pptt) cc_final: 0.8716 (pptt) REVERT: d 74 TYR cc_start: 0.8004 (m-80) cc_final: 0.7760 (m-80) REVERT: d 103 ASN cc_start: 0.6882 (t0) cc_final: 0.6464 (t0) REVERT: d 113 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8487 (tpp80) REVERT: d 120 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7369 (mm-30) REVERT: d 127 LYS cc_start: 0.8968 (pptt) cc_final: 0.8740 (pptt) outliers start: 64 outliers final: 38 residues processed: 380 average time/residue: 1.8092 time to fit residues: 794.0058 Evaluate side-chains 379 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 144 ASN Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 144 ASN Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain d residue 65 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 291 optimal weight: 0.9980 chunk 247 optimal weight: 0.0270 chunk 228 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 339 optimal weight: 0.7980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN M 50 GLN P 49 ASN Y 115 GLN b 54 GLN B 115 GLN K 115 GLN L 115 GLN O 115 GLN R 144 ASN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055793 restraints weight = 69154.447| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.53 r_work: 0.2615 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34350 Z= 0.118 Angle : 0.665 14.881 47520 Z= 0.290 Chirality : 0.045 0.446 6690 Planarity : 0.005 0.077 5550 Dihedral : 8.433 72.717 9902 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.82 % Allowed : 12.30 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.13), residues: 4170 helix: 3.24 (0.15), residues: 940 sheet: 0.23 (0.14), residues: 1310 loop : 0.55 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE R 142 TYR 0.008 0.001 TYR J 141 ARG 0.019 0.002 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 90) link_NAG-ASN : angle 3.07124 ( 270) link_ALPHA1-6 : bond 0.00533 ( 90) link_ALPHA1-6 : angle 1.45696 ( 270) link_BETA1-4 : bond 0.00485 ( 90) link_BETA1-4 : angle 1.55417 ( 270) hydrogen bonds : bond 0.03637 ( 1550) hydrogen bonds : angle 4.37360 ( 4380) covalent geometry : bond 0.00267 (34080) covalent geometry : angle 0.60788 (46710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 361 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: G 117 ILE cc_start: 0.8806 (mm) cc_final: 0.8525 (pt) REVERT: G 140 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 113 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7931 (mtp85) REVERT: D 71 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7436 (ptp-170) REVERT: D 117 ILE cc_start: 0.8783 (mm) cc_final: 0.8564 (pt) REVERT: J 71 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7465 (mmm-85) REVERT: J 117 ILE cc_start: 0.8754 (mm) cc_final: 0.8444 (pt) REVERT: M 117 ILE cc_start: 0.8734 (mm) cc_final: 0.8510 (pt) REVERT: M 140 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8881 (mm) REVERT: P 71 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7451 (tpm170) REVERT: P 81 LYS cc_start: 0.9170 (tttt) cc_final: 0.8902 (ttmt) REVERT: P 117 ILE cc_start: 0.8748 (mm) cc_final: 0.8355 (pt) REVERT: S 50 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: S 71 ARG cc_start: 0.7403 (tpm170) cc_final: 0.7067 (tpm170) REVERT: S 127 LYS cc_start: 0.9338 (ptpp) cc_final: 0.9010 (ptmm) REVERT: V 50 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: V 71 ARG cc_start: 0.7293 (tpm170) cc_final: 0.6831 (tpm170) REVERT: V 78 ILE cc_start: 0.8982 (pt) cc_final: 0.8749 (tp) REVERT: V 140 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8632 (mm) REVERT: Y 50 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: Y 81 LYS cc_start: 0.8703 (tttp) cc_final: 0.8272 (tmmm) REVERT: Y 113 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: Y 127 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8246 (tptp) REVERT: b 120 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7220 (mm-30) REVERT: N 127 LYS cc_start: 0.9447 (tppp) cc_final: 0.8967 (tppt) REVERT: Q 50 GLN cc_start: 0.9257 (tp40) cc_final: 0.9040 (tp40) REVERT: Q 127 LYS cc_start: 0.9350 (tppp) cc_final: 0.8933 (tppt) REVERT: T 113 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8258 (tpp80) REVERT: T 127 LYS cc_start: 0.9424 (tppp) cc_final: 0.8928 (tppt) REVERT: W 71 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8014 (mtm180) REVERT: W 120 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7782 (mm-30) REVERT: W 127 LYS cc_start: 0.9447 (tppp) cc_final: 0.9196 (tptp) REVERT: Z 44 ILE cc_start: 0.9284 (mt) cc_final: 0.9051 (mp) REVERT: Z 113 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8322 (tpp80) REVERT: c 71 ARG cc_start: 0.8507 (ptp-170) cc_final: 0.7957 (ptm160) REVERT: c 81 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8379 (ttmm) REVERT: C 71 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.7634 (ptt180) REVERT: C 113 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8271 (mmm-85) REVERT: F 71 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8020 (ptt180) REVERT: F 113 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8363 (mmm-85) REVERT: F 120 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8263 (mm-30) REVERT: L 113 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8416 (mmm-85) REVERT: O 120 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8625 (mm-30) REVERT: R 50 GLN cc_start: 0.8547 (tt0) cc_final: 0.8220 (mt0) REVERT: R 113 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8347 (mmm-85) REVERT: U 49 ASN cc_start: 0.9143 (p0) cc_final: 0.8938 (p0) REVERT: U 71 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7531 (ptt180) REVERT: U 113 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8331 (mmm-85) REVERT: U 120 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8466 (mm-30) REVERT: U 127 LYS cc_start: 0.9172 (pttm) cc_final: 0.8833 (pptt) REVERT: X 50 GLN cc_start: 0.8527 (mt0) cc_final: 0.8175 (mt0) REVERT: X 71 ARG cc_start: 0.7804 (ptm-80) cc_final: 0.7501 (ptt180) REVERT: X 103 ASN cc_start: 0.7753 (t0) cc_final: 0.7446 (t0) REVERT: X 113 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8512 (mmm160) REVERT: X 127 LYS cc_start: 0.9093 (pptt) cc_final: 0.8713 (pptt) REVERT: X 155 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8732 (mm110) REVERT: a 71 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7883 (ttp-170) REVERT: a 113 ARG cc_start: 0.8847 (ttm-80) cc_final: 0.8328 (mmm-85) REVERT: a 120 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8376 (mm-30) REVERT: a 127 LYS cc_start: 0.9250 (pptt) cc_final: 0.8726 (pptt) REVERT: d 103 ASN cc_start: 0.6870 (t0) cc_final: 0.6636 (t0) REVERT: d 113 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8429 (tpp80) REVERT: d 120 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7438 (mm-30) REVERT: d 127 LYS cc_start: 0.9006 (pptt) cc_final: 0.8805 (pptt) outliers start: 60 outliers final: 39 residues processed: 393 average time/residue: 1.8661 time to fit residues: 853.1761 Evaluate side-chains 381 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain L residue 144 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain X residue 146 GLN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 146 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 31 optimal weight: 2.9990 chunk 305 optimal weight: 0.1980 chunk 246 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 GLN D 115 GLN M 50 GLN P 49 ASN b 50 GLN b 54 GLN b 101 ASN K 115 GLN C 129 ASN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054872 restraints weight = 68978.731| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.56 r_work: 0.2600 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34350 Z= 0.138 Angle : 0.665 14.879 47520 Z= 0.293 Chirality : 0.045 0.450 6690 Planarity : 0.005 0.092 5550 Dihedral : 8.354 68.910 9902 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.64 % Allowed : 12.79 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.13), residues: 4170 helix: 3.28 (0.15), residues: 940 sheet: 0.25 (0.14), residues: 1310 loop : 0.57 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE K 41 TYR 0.013 0.001 TYR V 141 ARG 0.021 0.002 ARG M 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 90) link_NAG-ASN : angle 2.96656 ( 270) link_ALPHA1-6 : bond 0.00511 ( 90) link_ALPHA1-6 : angle 1.46625 ( 270) link_BETA1-4 : bond 0.00473 ( 90) link_BETA1-4 : angle 1.55526 ( 270) hydrogen bonds : bond 0.03744 ( 1550) hydrogen bonds : angle 4.37343 ( 4380) covalent geometry : bond 0.00321 (34080) covalent geometry : angle 0.61068 (46710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 ILE cc_start: 0.8839 (mm) cc_final: 0.8571 (pt) REVERT: G 140 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 113 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7903 (mtp85) REVERT: D 71 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7401 (ptp-170) REVERT: D 117 ILE cc_start: 0.8773 (mm) cc_final: 0.8566 (pt) REVERT: J 71 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7435 (mmm-85) REVERT: J 117 ILE cc_start: 0.8811 (mm) cc_final: 0.8509 (pt) REVERT: M 140 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8863 (mm) REVERT: P 71 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7417 (tpm170) REVERT: P 81 LYS cc_start: 0.9170 (tttt) cc_final: 0.8893 (ttmt) REVERT: P 117 ILE cc_start: 0.8783 (mm) cc_final: 0.8389 (pt) REVERT: P 140 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9000 (mm) REVERT: S 50 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: S 71 ARG cc_start: 0.7440 (tpm170) cc_final: 0.7113 (tpm170) REVERT: S 81 LYS cc_start: 0.9168 (tttm) cc_final: 0.8826 (ttpp) REVERT: S 117 ILE cc_start: 0.8542 (mm) cc_final: 0.8253 (pt) REVERT: S 127 LYS cc_start: 0.9334 (ptpp) cc_final: 0.9011 (ptmm) REVERT: V 50 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: V 71 ARG cc_start: 0.7335 (tpm170) cc_final: 0.6913 (tpm170) REVERT: V 78 ILE cc_start: 0.8960 (pt) cc_final: 0.8730 (tp) REVERT: V 127 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8313 (tptp) REVERT: V 140 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8665 (mm) REVERT: Y 50 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: Y 81 LYS cc_start: 0.8704 (tttp) cc_final: 0.8261 (tmmm) REVERT: Y 113 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8235 (mmm-85) REVERT: Y 127 LYS cc_start: 0.9012 (ptmm) cc_final: 0.8298 (tptp) REVERT: b 120 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7255 (mm-30) REVERT: N 127 LYS cc_start: 0.9454 (tppp) cc_final: 0.8976 (tppt) REVERT: Q 50 GLN cc_start: 0.9267 (tp40) cc_final: 0.9065 (tp40) REVERT: Q 127 LYS cc_start: 0.9365 (tppp) cc_final: 0.8934 (tppt) REVERT: T 127 LYS cc_start: 0.9431 (tppp) cc_final: 0.8954 (tppt) REVERT: W 71 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7783 (mtm180) REVERT: W 120 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7749 (mm-30) REVERT: W 127 LYS cc_start: 0.9442 (tppp) cc_final: 0.9204 (tptp) REVERT: Z 44 ILE cc_start: 0.9281 (mt) cc_final: 0.9047 (mp) REVERT: Z 81 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8728 (ttpp) REVERT: Z 113 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8280 (tpp80) REVERT: c 71 ARG cc_start: 0.8514 (ptp-170) cc_final: 0.7979 (ptm160) REVERT: c 81 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8381 (ttmm) REVERT: C 71 ARG cc_start: 0.8217 (ptm-80) cc_final: 0.7606 (ptt180) REVERT: C 113 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8227 (mmm-85) REVERT: F 50 GLN cc_start: 0.8660 (mt0) cc_final: 0.8402 (mt0) REVERT: F 71 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7898 (ptt180) REVERT: F 113 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8328 (mmm-85) REVERT: F 120 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8298 (mm-30) REVERT: L 50 GLN cc_start: 0.8847 (mt0) cc_final: 0.8639 (mt0) REVERT: L 113 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8382 (mmm-85) REVERT: O 120 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8635 (mm-30) REVERT: R 50 GLN cc_start: 0.8646 (tt0) cc_final: 0.8369 (mt0) REVERT: R 113 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8311 (mmm-85) REVERT: R 120 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8519 (mm-30) REVERT: U 49 ASN cc_start: 0.9153 (p0) cc_final: 0.8941 (p0) REVERT: U 71 ARG cc_start: 0.8038 (ptm-80) cc_final: 0.7550 (ptt180) REVERT: U 120 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8499 (mm-30) REVERT: X 50 GLN cc_start: 0.8566 (mt0) cc_final: 0.8211 (mt0) REVERT: X 71 ARG cc_start: 0.7812 (ptm-80) cc_final: 0.7506 (ptt180) REVERT: X 103 ASN cc_start: 0.7754 (t0) cc_final: 0.7442 (t0) REVERT: X 113 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8494 (mmm160) REVERT: X 127 LYS cc_start: 0.9077 (pptt) cc_final: 0.8680 (pptt) REVERT: X 155 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8705 (mm110) REVERT: a 113 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8313 (mmm-85) REVERT: a 120 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8119 (mm-30) REVERT: a 127 LYS cc_start: 0.9247 (pptt) cc_final: 0.8726 (pptt) REVERT: d 103 ASN cc_start: 0.6752 (t0) cc_final: 0.6518 (t0) REVERT: d 113 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8438 (tpp80) REVERT: d 120 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7448 (mm-30) outliers start: 54 outliers final: 37 residues processed: 364 average time/residue: 1.8928 time to fit residues: 789.4515 Evaluate side-chains 371 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 103 ASN Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 81 LYS Chi-restraints excluded: chain c residue 121 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain X residue 146 GLN Chi-restraints excluded: chain a residue 49 ASN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 103 ASN Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 146 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 185 optimal weight: 6.9990 chunk 364 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 361 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 50 GLN P 49 ASN P 115 GLN b 54 GLN B 49 ASN K 115 GLN ** X 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055129 restraints weight = 68968.282| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.52 r_work: 0.2605 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34350 Z= 0.137 Angle : 0.666 14.867 47520 Z= 0.293 Chirality : 0.045 0.440 6690 Planarity : 0.005 0.067 5550 Dihedral : 8.315 66.310 9902 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.52 % Allowed : 13.00 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.13), residues: 4170 helix: 3.26 (0.15), residues: 940 sheet: 0.26 (0.14), residues: 1310 loop : 0.59 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE B 41 TYR 0.013 0.001 TYR V 141 ARG 0.016 0.002 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 90) link_NAG-ASN : angle 2.96341 ( 270) link_ALPHA1-6 : bond 0.00512 ( 90) link_ALPHA1-6 : angle 1.45925 ( 270) link_BETA1-4 : bond 0.00476 ( 90) link_BETA1-4 : angle 1.54452 ( 270) hydrogen bonds : bond 0.03727 ( 1550) hydrogen bonds : angle 4.35145 ( 4380) covalent geometry : bond 0.00318 (34080) covalent geometry : angle 0.61186 (46710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27326.39 seconds wall clock time: 470 minutes 40.82 seconds (28240.82 seconds total)