Starting phenix.real_space_refine on Sat Jun 28 01:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.map" model { file = "/net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osy_20189/06_2025/6osy_20189.cif" } resolution = 4.3 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= 0.006 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 20328 2.51 5 N 5316 2.21 5 O 6645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32463 Number of models: 1 Model: "" Number of chains: 78 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "K" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "O" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Q" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "S" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "IA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 18.60, per 1000 atoms: 0.57 Number of scatterers: 32463 At special positions: 0 Unit cell: (157.768, 157.768, 154.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 6645 8.00 N 5316 7.00 C 20328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.01 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.05 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.05 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 100A" distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.02 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.01 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.05 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 98 " - pdb=" SG CYS P 100A" distance=2.02 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " distance=2.01 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN q 4 " - " MAN q 5 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 3 3 " - " MAN 3 5 " " BMA 9 3 " - " MAN 9 4 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 6 " " BMA e 3 " - " MAN e 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 9 " " BMA m 3 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN K 133 " " NAG 1 1 " - " ASN K 137 " " NAG 2 635 " - " ASN 2 355 " " NAG 3 1 " - " ASN K 156 " " NAG 4 1 " - " ASN K 160 " " NAG 9 1 " - " ASN K 197 " " NAG A 701 " - " ASN A 637 " " NAG A 702 " - " ASN A 611 " " NAG B 635 " - " ASN B 355 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 611 " " NAG K 635 " - " ASN K 355 " " NAG Q 701 " - " ASN Q 637 " " NAG Q 702 " - " ASN Q 611 " " NAG T 1 " - " ASN 2 88 " " NAG U 1 " - " ASN 2 133 " " NAG V 1 " - " ASN 2 137 " " NAG W 1 " - " ASN 2 156 " " NAG X 1 " - " ASN 2 160 " " NAG Y 1 " - " ASN 2 197 " " NAG Z 1 " - " ASN 2 234 " " NAG a 1 " - " ASN 2 262 " " NAG b 1 " - " ASN 2 295 " " NAG c 1 " - " ASN 2 301 " " NAG d 1 " - " ASN 2 363 " " NAG e 1 " - " ASN 2 386 " " NAG f 1 " - " ASN 2 392 " " NAG g 1 " - " ASN 2 332 " " NAG h 1 " - " ASN 2 448 " " NAG i 1 " - " ASN 2 276 " " NAG j 1 " - " ASN B 88 " " NAG k 1 " - " ASN B 133 " " NAG l 1 " - " ASN B 137 " " NAG m 1 " - " ASN B 156 " " NAG n 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 197 " " NAG p 1 " - " ASN B 234 " " NAG q 1 " - " ASN B 262 " " NAG r 1 " - " ASN B 295 " " NAG s 1 " - " ASN B 301 " " NAG t 1 " - " ASN B 363 " " NAG u 1 " - " ASN B 386 " " NAG v 1 " - " ASN B 392 " " NAG w 1 " - " ASN B 332 " " NAG x 1 " - " ASN B 448 " " NAG y 1 " - " ASN B 276 " " NAG z 1 " - " ASN K 88 " " NAGAA 1 " - " ASN K 234 " " NAGBA 1 " - " ASN K 262 " " NAGCA 1 " - " ASN K 295 " " NAGDA 1 " - " ASN K 301 " " NAGEA 1 " - " ASN K 363 " " NAGFA 1 " - " ASN K 386 " " NAGGA 1 " - " ASN K 392 " " NAGHA 1 " - " ASN K 332 " " NAGIA 1 " - " ASN K 448 " " NAGJA 1 " - " ASN K 276 " Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 3.7 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 14.1% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain '2' and resid 58 through 62 removed outlier: 3.565A pdb=" N GLU 2 62 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 removed outlier: 3.505A pdb=" N MET 2 104 " --> pdb=" O MET 2 100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 4.012A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 351 through 353 No H-bonds generated for 'chain '2' and resid 351 through 353' Processing helix chain '2' and resid 368 through 373 removed outlier: 3.836A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR 2 373 " --> pdb=" O LEU 2 369 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 368 through 373' Processing helix chain '2' and resid 387 through 390 removed outlier: 3.795A pdb=" N LEU 2 390 " --> pdb=" O THR 2 387 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 387 through 390' Processing helix chain '2' and resid 474 through 479 removed outlier: 3.882A pdb=" N ASP 2 477 " --> pdb=" O ASP 2 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 2 478 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 86 Processing helix chain '5' and resid 100D through 100H removed outlier: 3.921A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '6' and resid 79 through 83 Processing helix chain '7' and resid 78 through 82 removed outlier: 3.762A pdb=" N ASP 7 81 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE 7 82 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 78 through 82' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.669A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY A 516 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 517 " --> pdb=" O GLY A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.490A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.537A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.573A pdb=" N GLU B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.633A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.653A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.845A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.807A pdb=" N LEU B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 100D through 100H removed outlier: 3.916A pdb=" N PHE C 100G" --> pdb=" O VAL C 100D" (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'F' and resid 61 through 64 removed outlier: 4.073A pdb=" N GLN F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.713A pdb=" N THR F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY G 516 " --> pdb=" O VAL G 513 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA G 517 " --> pdb=" O GLY G 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 517' Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 570 through 595 removed outlier: 3.729A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.710A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 641 through 661 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.692A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.084A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.646A pdb=" N GLN I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.024A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR I 87 " --> pdb=" O ASP I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.145A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.587A pdb=" N GLU K 62 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 115 removed outlier: 3.541A pdb=" N MET K 104 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 removed outlier: 4.006A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 198 Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.657A pdb=" N THR K 372 " --> pdb=" O ASP K 368 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 368 through 373' Processing helix chain 'K' and resid 387 through 390 removed outlier: 3.821A pdb=" N LEU K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 387 through 390' Processing helix chain 'K' and resid 475 through 479 removed outlier: 3.534A pdb=" N ASN K 478 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.213A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H removed outlier: 3.984A pdb=" N PHE M 100G" --> pdb=" O VAL M 100D" (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.123A pdb=" N GLN P 64 " --> pdb=" O ARG P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.731A pdb=" N THR P 87 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 517 removed outlier: 3.545A pdb=" N GLY Q 516 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Q 517 " --> pdb=" O GLY Q 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 513 through 517' Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 570 through 595 removed outlier: 3.728A pdb=" N LYS Q 574 " --> pdb=" O VAL Q 570 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 616 removed outlier: 4.362A pdb=" N SER Q 615 " --> pdb=" O ASN Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 624 Processing helix chain 'Q' and resid 627 through 635 Processing helix chain 'Q' and resid 641 through 661 Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLN R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.971A pdb=" N ASP R 86 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR R 87 " --> pdb=" O ASP R 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 83 through 87' Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.184A pdb=" N ILE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 6.045A pdb=" N VAL 2 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 4.022A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 7.002A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 260 through 261 removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain '2' and resid 359 through 361 removed outlier: 3.647A pdb=" N ILE 2 359 " --> pdb=" O TRP 2 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 11 through 12 removed outlier: 3.834A pdb=" N VAL 5 12 " --> pdb=" O THR 5 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 17 through 22 Processing sheet with id=AB4, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AB5, first strand: chain '6' and resid 9 through 13 removed outlier: 3.689A pdb=" N THR 6 102 " --> pdb=" O TYR 6 86 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 18 through 23 removed outlier: 3.643A pdb=" N CYS 6 23 " --> pdb=" O ALA 6 71 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 7 44 " --> pdb=" O GLN 7 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR 8 102 " --> pdb=" O ARG 8 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 495 through 499 removed outlier: 6.009A pdb=" N VAL B 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR G 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS G 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.067A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.019A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 424 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.825A pdb=" N VAL C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 33 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 17 through 22 Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 100A Processing sheet with id=AD5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.739A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.557A pdb=" N CYS D 23 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.678A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.935A pdb=" N THR J 53 " --> pdb=" O HIS J 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU J 33 " --> pdb=" O HIS J 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 495 through 499 removed outlier: 6.061A pdb=" N VAL K 36 " --> pdb=" O THR Q 606 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR Q 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS Q 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.112A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AF5, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AF6, first strand: chain 'K' and resid 202 through 203 removed outlier: 7.045A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 260 through 261 removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.646A pdb=" N ILE K 359 " --> pdb=" O TRP K 395 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER K 393 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.961A pdb=" N THR L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS M 96 " --> pdb=" O TYR M 100O" (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR M 100M" --> pdb=" O GLY M 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 17 through 22 Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.706A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.673A pdb=" N CYS N 23 " --> pdb=" O ALA N 71 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 10 through 13 removed outlier: 5.852A pdb=" N GLN O 36 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU O 45 " --> pdb=" O GLN O 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AH2, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH3, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'S' and resid 53 through 54 removed outlier: 4.017A pdb=" N THR S 53 " --> pdb=" O HIS S 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS S 49 " --> pdb=" O THR S 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU S 33 " --> pdb=" O HIS S 49 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2652 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: 13.63 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9656 1.34 - 1.46: 9036 1.46 - 1.59: 14218 1.59 - 1.71: 29 1.71 - 1.83: 229 Bond restraints: 33168 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG y 1 " pdb=" O5 NAG y 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C1 MAN y 4 " pdb=" C2 MAN y 4 " ideal model delta sigma weight residual 1.526 1.646 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1 MAN i 4 " pdb=" C2 MAN i 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C1 MANJA 4 " pdb=" C2 MANJA 4 " ideal model delta sigma weight residual 1.526 1.632 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 33163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 43716 3.83 - 7.67: 1221 7.67 - 11.50: 123 11.50 - 15.34: 15 15.34 - 19.17: 6 Bond angle restraints: 45081 Sorted by residual: angle pdb=" C ILE 8 48 " pdb=" N GLY 8 49 " pdb=" CA GLY 8 49 " ideal model delta sigma weight residual 121.35 113.60 7.75 1.03e+00 9.43e-01 5.66e+01 angle pdb=" C ASP 7 49 " pdb=" N THR 7 50 " pdb=" CA THR 7 50 " ideal model delta sigma weight residual 121.54 135.61 -14.07 1.91e+00 2.74e-01 5.42e+01 angle pdb=" C ASP E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta sigma weight residual 121.54 135.45 -13.91 1.91e+00 2.74e-01 5.31e+01 angle pdb=" C ASP O 49 " pdb=" N THR O 50 " pdb=" CA THR O 50 " ideal model delta sigma weight residual 121.54 135.44 -13.90 1.91e+00 2.74e-01 5.30e+01 angle pdb=" N VAL A 570 " pdb=" CA VAL A 570 " pdb=" C VAL A 570 " ideal model delta sigma weight residual 113.47 106.69 6.78 1.01e+00 9.80e-01 4.50e+01 ... (remaining 45076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 19515 22.25 - 44.51: 1816 44.51 - 66.76: 354 66.76 - 89.01: 195 89.01 - 111.26: 134 Dihedral angle restraints: 22014 sinusoidal: 11013 harmonic: 11001 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 -178.63 -88.37 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA CYS B 201 " pdb=" C CYS B 201 " pdb=" N THR B 202 " pdb=" CA THR B 202 " ideal model delta harmonic sigma weight residual -180.00 -140.39 -39.61 0 5.00e+00 4.00e-02 6.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.40 -69.40 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 22011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 5168 0.157 - 0.314: 344 0.314 - 0.470: 29 0.470 - 0.627: 3 0.627 - 0.784: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAGJA 1 " pdb=" ND2 ASN K 276 " pdb=" C2 NAGJA 1 " pdb=" O5 NAGJA 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C1 NAG y 1 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG y 1 " pdb=" O5 NAG y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN 2 276 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 5544 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO 8 100E" -0.210 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.063 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 100D" 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO P 100E" -0.207 5.00e-02 4.00e+02 pdb=" CA PRO P 100E" 0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 100E" 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 100D" -0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO F 100E" 0.182 5.00e-02 4.00e+02 pdb=" CA PRO F 100E" -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 100E" -0.058 5.00e-02 4.00e+02 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9960 2.81 - 3.33: 26013 3.33 - 3.86: 54732 3.86 - 4.38: 55599 4.38 - 4.90: 96473 Nonbonded interactions: 242777 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP 5 56 " pdb=" O2 BMA V 3 " model vdw 2.301 3.040 nonbonded pdb=" OD1 ASP C 56 " pdb=" O2 BMA l 3 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASP M 56 " pdb=" O2 BMA 1 3 " model vdw 2.306 3.040 nonbonded pdb=" OG SER K 334 " pdb=" OG1 THR K 337 " model vdw 2.307 3.040 ... (remaining 242772 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 'AA' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'IA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain '9' selection = chain 'JA' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain '3' selection = chain 'FA' selection = chain 'W' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain '4' selection = chain 'EA' selection = chain 'X' selection = chain 'd' selection = chain 'n' selection = chain 't' } ncs_group { reference = chain '5' selection = chain 'C' selection = chain 'M' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'N' } ncs_group { reference = chain '7' selection = chain 'E' selection = chain 'O' } ncs_group { reference = chain '8' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'BA' selection = chain 'a' selection = chain 'q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'HA' selection = chain 'g' selection = chain 'w' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'S' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.350 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 73.610 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.014 0.140 33405 Z= 0.665 Angle : 1.606 19.169 45741 Z= 0.807 Chirality : 0.087 0.784 5547 Planarity : 0.010 0.121 5469 Dihedral : 20.537 111.262 14817 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.64 % Allowed : 17.57 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.58 (0.11), residues: 3768 helix: -4.26 (0.12), residues: 396 sheet: -1.27 (0.14), residues: 1188 loop : -2.75 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP 8 50 HIS 0.015 0.003 HIS H 100 PHE 0.047 0.006 PHE 2 288 TYR 0.035 0.004 TYR F 59 ARG 0.016 0.001 ARG 8 61 Details of bonding type rmsd link_NAG-ASN : bond 0.01971 ( 57) link_NAG-ASN : angle 5.35792 ( 171) link_ALPHA1-6 : bond 0.01175 ( 18) link_ALPHA1-6 : angle 2.10318 ( 54) link_BETA1-4 : bond 0.01346 ( 78) link_BETA1-4 : angle 4.93681 ( 234) link_ALPHA1-2 : bond 0.00689 ( 9) link_ALPHA1-2 : angle 2.49075 ( 27) link_ALPHA1-3 : bond 0.01367 ( 24) link_ALPHA1-3 : angle 3.52516 ( 72) hydrogen bonds : bond 0.14380 ( 976) hydrogen bonds : angle 7.68635 ( 2652) SS BOND : bond 0.01102 ( 51) SS BOND : angle 3.81195 ( 102) covalent geometry : bond 0.01439 (33168) covalent geometry : angle 1.52363 (45081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 605 time to evaluate : 3.660 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: 2 271 MET cc_start: 0.8001 (mtm) cc_final: 0.7790 (mtm) REVERT: 2 504 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7762 (ttp-110) REVERT: 5 44 GLN cc_start: 0.8772 (pm20) cc_final: 0.8555 (pm20) REVERT: 5 103 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8444 (mtmm) REVERT: 6 28 LEU cc_start: 0.8987 (mt) cc_final: 0.8776 (mt) REVERT: 6 42 GLN cc_start: 0.8730 (mt0) cc_final: 0.8489 (mp10) REVERT: 7 17 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8417 (mp0) REVERT: 7 48 TYR cc_start: 0.6710 (p90) cc_final: 0.3931 (p90) REVERT: 7 53 ARG cc_start: 0.7337 (ptm-80) cc_final: 0.6628 (ptt-90) REVERT: A 530 MET cc_start: 0.8087 (mtm) cc_final: 0.7211 (mtm) REVERT: A 584 GLU cc_start: 0.7869 (tt0) cc_final: 0.7593 (tt0) REVERT: B 261 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (pp) REVERT: B 289 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8616 (p0) REVERT: B 479 TRP cc_start: 0.8595 (m-10) cc_final: 0.8242 (m-90) REVERT: C 44 GLN cc_start: 0.8541 (pm20) cc_final: 0.8318 (pm20) REVERT: D 70 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8105 (m) REVERT: F 51 ILE cc_start: 0.9200 (tt) cc_final: 0.8980 (mp) REVERT: G 530 MET cc_start: 0.8552 (mtm) cc_final: 0.7714 (mtm) REVERT: G 571 TRP cc_start: 0.8531 (m100) cc_final: 0.8278 (m-10) REVERT: H 4 LEU cc_start: 0.8917 (mm) cc_final: 0.8643 (mt) REVERT: H 12 MET cc_start: 0.7053 (mtp) cc_final: 0.6095 (ttm) REVERT: H 36 TRP cc_start: 0.7753 (m100) cc_final: 0.7131 (m100) REVERT: H 48 ILE cc_start: 0.7379 (mt) cc_final: 0.7129 (mp) REVERT: H 52 TYR cc_start: 0.7104 (m-80) cc_final: 0.6836 (m-80) REVERT: I 4 LEU cc_start: 0.8686 (mt) cc_final: 0.8256 (mm) REVERT: I 12 MET cc_start: 0.6146 (mtp) cc_final: 0.5732 (ttm) REVERT: I 78 PHE cc_start: 0.6919 (t80) cc_final: 0.6573 (t80) REVERT: J 5 THR cc_start: 0.6959 (m) cc_final: 0.6671 (m) REVERT: J 30 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7430 (mtmt) REVERT: J 59 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: K 427 TRP cc_start: 0.8763 (m-90) cc_final: 0.8125 (m-90) REVERT: L 5 THR cc_start: 0.7110 (m) cc_final: 0.6207 (m) REVERT: L 59 PRO cc_start: 0.8344 (Cg_exo) cc_final: 0.7697 (Cg_endo) REVERT: M 75 LYS cc_start: 0.8749 (mttt) cc_final: 0.8480 (mtpt) REVERT: N 104 LEU cc_start: 0.9031 (mm) cc_final: 0.8713 (tp) REVERT: O 59 ASP cc_start: 0.8571 (p0) cc_final: 0.8283 (t0) REVERT: P 102 TYR cc_start: 0.6789 (m-80) cc_final: 0.6547 (m-80) REVERT: Q 530 MET cc_start: 0.8474 (mtt) cc_final: 0.7759 (mtt) REVERT: R 4 LEU cc_start: 0.8426 (mt) cc_final: 0.7833 (mm) REVERT: R 36 TRP cc_start: 0.7810 (m100) cc_final: 0.7213 (m100) REVERT: R 52 TYR cc_start: 0.7154 (m-80) cc_final: 0.6871 (m-80) REVERT: R 102 LEU cc_start: 0.8026 (mt) cc_final: 0.7757 (mt) REVERT: S 5 THR cc_start: 0.7198 (m) cc_final: 0.6300 (m) REVERT: S 59 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7507 (Cg_endo) outliers start: 88 outliers final: 46 residues processed: 684 average time/residue: 0.5148 time to fit residues: 546.6336 Evaluate side-chains 448 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 66 HIS 2 94 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 287 GLN 2 302 ASN 2 348 GLN 2 352 HIS 8 6 GLN ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 101 GLN A 577 GLN B 66 HIS B 94 ASN B 287 GLN B 348 GLN B 374 HIS F 6 GLN G 577 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS K 94 ASN K 99 ASN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN K 348 GLN L 49 HIS P 6 GLN ** P 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 577 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078734 restraints weight = 95445.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078084 restraints weight = 76221.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078799 restraints weight = 63929.002| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33405 Z= 0.202 Angle : 0.927 14.509 45741 Z= 0.435 Chirality : 0.051 0.259 5547 Planarity : 0.006 0.098 5469 Dihedral : 16.410 106.501 7896 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.39 % Allowed : 5.41 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.73 (0.12), residues: 3768 helix: -2.23 (0.22), residues: 396 sheet: -0.97 (0.14), residues: 1173 loop : -2.28 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 100F HIS 0.010 0.002 HIS B 374 PHE 0.027 0.002 PHE P 100D TYR 0.023 0.002 TYR K 484 ARG 0.016 0.001 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 57) link_NAG-ASN : angle 3.24297 ( 171) link_ALPHA1-6 : bond 0.00809 ( 18) link_ALPHA1-6 : angle 1.96618 ( 54) link_BETA1-4 : bond 0.00735 ( 78) link_BETA1-4 : angle 2.93593 ( 234) link_ALPHA1-2 : bond 0.00538 ( 9) link_ALPHA1-2 : angle 2.25796 ( 27) link_ALPHA1-3 : bond 0.01153 ( 24) link_ALPHA1-3 : angle 2.53484 ( 72) hydrogen bonds : bond 0.04521 ( 976) hydrogen bonds : angle 6.35192 ( 2652) SS BOND : bond 0.00416 ( 51) SS BOND : angle 2.60729 ( 102) covalent geometry : bond 0.00450 (33168) covalent geometry : angle 0.86796 (45081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 541 time to evaluate : 3.562 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: 5 100 MET cc_start: 0.8930 (mpp) cc_final: 0.8496 (mmp) REVERT: 7 89 GLN cc_start: 0.7727 (pm20) cc_final: 0.7096 (pm20) REVERT: 8 51 ILE cc_start: 0.9184 (tt) cc_final: 0.8808 (mp) REVERT: 8 59 TYR cc_start: 0.7741 (m-80) cc_final: 0.7478 (m-80) REVERT: 8 75 GLN cc_start: 0.8770 (mp10) cc_final: 0.8548 (pm20) REVERT: 8 81 GLU cc_start: 0.7981 (pt0) cc_final: 0.7663 (pm20) REVERT: 8 82 LEU cc_start: 0.9347 (mt) cc_final: 0.9113 (mt) REVERT: A 530 MET cc_start: 0.8154 (mtm) cc_final: 0.7287 (mtm) REVERT: A 619 LEU cc_start: 0.9293 (pp) cc_final: 0.9040 (tt) REVERT: B 475 MET cc_start: 0.7950 (mmt) cc_final: 0.7714 (mmt) REVERT: C 100 MET cc_start: 0.8776 (mpp) cc_final: 0.8335 (mmp) REVERT: E 84 VAL cc_start: 0.8673 (t) cc_final: 0.8472 (m) REVERT: E 89 GLN cc_start: 0.8046 (pm20) cc_final: 0.7718 (pm20) REVERT: F 51 ILE cc_start: 0.9134 (tt) cc_final: 0.8831 (mp) REVERT: G 530 MET cc_start: 0.8647 (mtm) cc_final: 0.7639 (mtm) REVERT: G 571 TRP cc_start: 0.8505 (m100) cc_final: 0.8222 (m-10) REVERT: G 584 GLU cc_start: 0.7937 (tt0) cc_final: 0.7525 (tm-30) REVERT: G 591 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8674 (tm-30) REVERT: H 4 LEU cc_start: 0.9042 (mm) cc_final: 0.8792 (mm) REVERT: H 12 MET cc_start: 0.6702 (mtp) cc_final: 0.6345 (ttp) REVERT: H 46 GLU cc_start: 0.8461 (tp30) cc_final: 0.7967 (tp30) REVERT: I 11 VAL cc_start: 0.8451 (m) cc_final: 0.8150 (m) REVERT: I 46 GLU cc_start: 0.8259 (tp30) cc_final: 0.7846 (tp30) REVERT: I 77 HIS cc_start: 0.6859 (m-70) cc_final: 0.6630 (m-70) REVERT: I 78 PHE cc_start: 0.7171 (t80) cc_final: 0.6789 (t80) REVERT: J 5 THR cc_start: 0.6735 (m) cc_final: 0.6166 (m) REVERT: K 287 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: K 479 TRP cc_start: 0.8396 (m-90) cc_final: 0.8191 (m-90) REVERT: M 75 LYS cc_start: 0.8762 (mttt) cc_final: 0.8474 (mmmt) REVERT: M 100 MET cc_start: 0.8825 (mpp) cc_final: 0.8290 (mmp) REVERT: M 100 ASP cc_start: 0.8795 (p0) cc_final: 0.8542 (p0) REVERT: O 70 PHE cc_start: 0.8338 (m-80) cc_final: 0.8114 (m-10) REVERT: O 89 GLN cc_start: 0.7799 (pm20) cc_final: 0.7327 (pm20) REVERT: P 51 ILE cc_start: 0.9205 (tt) cc_final: 0.8974 (mp) REVERT: P 82 LEU cc_start: 0.9505 (mt) cc_final: 0.9294 (mt) REVERT: P 102 TYR cc_start: 0.6852 (m-80) cc_final: 0.6560 (m-80) REVERT: Q 530 MET cc_start: 0.8537 (mtm) cc_final: 0.7919 (mtt) REVERT: Q 619 LEU cc_start: 0.9416 (pp) cc_final: 0.9106 (tt) REVERT: R 4 LEU cc_start: 0.8616 (mt) cc_final: 0.8240 (mm) REVERT: R 46 GLU cc_start: 0.8312 (tp30) cc_final: 0.7681 (tp30) outliers start: 13 outliers final: 3 residues processed: 554 average time/residue: 0.5817 time to fit residues: 517.1884 Evaluate side-chains 393 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 389 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 72 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 231 optimal weight: 0.0040 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 203 GLN ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN B 66 HIS H 77 HIS J 6 GLN J 38 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN M 76 ASN P 6 GLN R 100 HIS S 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080641 restraints weight = 95037.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080728 restraints weight = 71372.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081671 restraints weight = 58317.532| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33405 Z= 0.140 Angle : 0.844 16.845 45741 Z= 0.389 Chirality : 0.049 0.216 5547 Planarity : 0.005 0.087 5469 Dihedral : 13.954 105.163 7896 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.29 (0.13), residues: 3768 helix: -0.82 (0.27), residues: 357 sheet: -0.97 (0.14), residues: 1209 loop : -2.02 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 8 100F HIS 0.007 0.001 HIS 2 85 PHE 0.035 0.002 PHE R 78 TYR 0.029 0.001 TYR 2 217 ARG 0.006 0.001 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 57) link_NAG-ASN : angle 3.11990 ( 171) link_ALPHA1-6 : bond 0.00786 ( 18) link_ALPHA1-6 : angle 1.82489 ( 54) link_BETA1-4 : bond 0.00714 ( 78) link_BETA1-4 : angle 2.74962 ( 234) link_ALPHA1-2 : bond 0.00788 ( 9) link_ALPHA1-2 : angle 2.28356 ( 27) link_ALPHA1-3 : bond 0.01254 ( 24) link_ALPHA1-3 : angle 1.99520 ( 72) hydrogen bonds : bond 0.03954 ( 976) hydrogen bonds : angle 5.83829 ( 2652) SS BOND : bond 0.00468 ( 51) SS BOND : angle 2.27241 ( 102) covalent geometry : bond 0.00302 (33168) covalent geometry : angle 0.78800 (45081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 557 time to evaluate : 3.318 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: 2 271 MET cc_start: 0.7634 (mtm) cc_final: 0.7284 (mtm) REVERT: 2 377 ASN cc_start: 0.8437 (t0) cc_final: 0.8136 (t0) REVERT: 2 504 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7522 (ttp-110) REVERT: 5 13 LYS cc_start: 0.7884 (pttp) cc_final: 0.7553 (tppt) REVERT: 5 34 TRP cc_start: 0.8125 (m100) cc_final: 0.7893 (m100) REVERT: 5 100 ASP cc_start: 0.8788 (p0) cc_final: 0.8562 (p0) REVERT: 7 89 GLN cc_start: 0.7515 (pm20) cc_final: 0.7283 (pm20) REVERT: 8 51 ILE cc_start: 0.9117 (tt) cc_final: 0.8636 (mp) REVERT: 8 59 TYR cc_start: 0.7572 (m-80) cc_final: 0.6584 (m-80) REVERT: 8 81 GLU cc_start: 0.8034 (pt0) cc_final: 0.7540 (pm20) REVERT: 8 82 LEU cc_start: 0.9316 (mt) cc_final: 0.8922 (mt) REVERT: A 530 MET cc_start: 0.8118 (mtm) cc_final: 0.7387 (mtm) REVERT: A 595 ILE cc_start: 0.9170 (pt) cc_final: 0.8860 (mm) REVERT: A 619 LEU cc_start: 0.9231 (pp) cc_final: 0.8956 (tt) REVERT: A 658 GLN cc_start: 0.8656 (tt0) cc_final: 0.7316 (tp40) REVERT: B 122 LEU cc_start: 0.9527 (mt) cc_final: 0.9319 (mm) REVERT: B 377 ASN cc_start: 0.8577 (t0) cc_final: 0.8297 (t0) REVERT: B 475 MET cc_start: 0.7781 (mmt) cc_final: 0.7547 (mmt) REVERT: B 479 TRP cc_start: 0.8231 (m-90) cc_final: 0.7933 (m-90) REVERT: C 44 GLN cc_start: 0.8505 (pm20) cc_final: 0.8226 (pm20) REVERT: C 100 MET cc_start: 0.8861 (mpp) cc_final: 0.8488 (mmp) REVERT: D 67 SER cc_start: 0.8644 (m) cc_final: 0.8198 (t) REVERT: D 90 ILE cc_start: 0.9271 (pt) cc_final: 0.9038 (mm) REVERT: E 84 VAL cc_start: 0.8467 (t) cc_final: 0.8260 (m) REVERT: F 51 ILE cc_start: 0.9038 (tt) cc_final: 0.8598 (mp) REVERT: G 530 MET cc_start: 0.8440 (mtm) cc_final: 0.7521 (mtm) REVERT: G 591 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8746 (tm-30) REVERT: H 12 MET cc_start: 0.6634 (mtp) cc_final: 0.6309 (ttp) REVERT: H 46 GLU cc_start: 0.8383 (tp30) cc_final: 0.7799 (tp30) REVERT: H 52 TYR cc_start: 0.7633 (m-80) cc_final: 0.7425 (m-80) REVERT: I 16 GLU cc_start: 0.4787 (mm-30) cc_final: 0.4531 (mm-30) REVERT: I 46 GLU cc_start: 0.8243 (tp30) cc_final: 0.7800 (tp30) REVERT: I 52 TYR cc_start: 0.7521 (m-80) cc_final: 0.7082 (m-80) REVERT: J 4 MET cc_start: 0.7675 (tpt) cc_final: 0.7165 (tpp) REVERT: J 88 CYS cc_start: 0.4671 (p) cc_final: 0.3260 (p) REVERT: K 479 TRP cc_start: 0.8306 (m-90) cc_final: 0.8005 (m-90) REVERT: K 484 TYR cc_start: 0.8987 (p90) cc_final: 0.8740 (p90) REVERT: M 34 TRP cc_start: 0.8086 (m100) cc_final: 0.7771 (m100) REVERT: M 75 LYS cc_start: 0.8714 (mttt) cc_final: 0.8454 (mmmt) REVERT: M 100 MET cc_start: 0.8816 (mpp) cc_final: 0.8112 (mmt) REVERT: N 52 ASN cc_start: 0.7900 (m-40) cc_final: 0.7256 (m-40) REVERT: P 59 TYR cc_start: 0.7335 (m-80) cc_final: 0.6504 (m-80) REVERT: P 82 LEU cc_start: 0.9320 (mt) cc_final: 0.9071 (mt) REVERT: Q 530 MET cc_start: 0.8533 (mtm) cc_final: 0.7783 (mtt) REVERT: Q 591 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8833 (tm-30) REVERT: Q 595 ILE cc_start: 0.9271 (pt) cc_final: 0.8595 (mm) REVERT: Q 619 LEU cc_start: 0.9376 (pp) cc_final: 0.9011 (tt) REVERT: Q 638 TYR cc_start: 0.8212 (m-10) cc_final: 0.7706 (m-10) REVERT: R 46 GLU cc_start: 0.8310 (tp30) cc_final: 0.7727 (tp30) outliers start: 5 outliers final: 3 residues processed: 561 average time/residue: 0.4526 time to fit residues: 404.0402 Evaluate side-chains 404 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 22 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 287 GLN 2 374 HIS 2 478 ASN 5 32 ASN 8 6 GLN ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 103 GLN F 64 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 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 = 0.3639 r_free = 0.3639 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076079 restraints weight = 96647.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075926 restraints weight = 74272.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076563 restraints weight = 61481.745| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 33405 Z= 0.291 Angle : 0.947 14.979 45741 Z= 0.441 Chirality : 0.051 0.286 5547 Planarity : 0.006 0.090 5469 Dihedral : 12.953 101.261 7896 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.18 (0.13), residues: 3768 helix: -0.79 (0.26), residues: 378 sheet: -0.74 (0.15), residues: 1134 loop : -2.02 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 8 100F HIS 0.008 0.002 HIS 2 85 PHE 0.021 0.003 PHE K 288 TYR 0.024 0.002 TYR C 100B ARG 0.006 0.001 ARG P 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 57) link_NAG-ASN : angle 3.29254 ( 171) link_ALPHA1-6 : bond 0.00909 ( 18) link_ALPHA1-6 : angle 2.03563 ( 54) link_BETA1-4 : bond 0.00651 ( 78) link_BETA1-4 : angle 2.82024 ( 234) link_ALPHA1-2 : bond 0.00751 ( 9) link_ALPHA1-2 : angle 2.46654 ( 27) link_ALPHA1-3 : bond 0.01094 ( 24) link_ALPHA1-3 : angle 2.60828 ( 72) hydrogen bonds : bond 0.04613 ( 976) hydrogen bonds : angle 5.79528 ( 2652) SS BOND : bond 0.00724 ( 51) SS BOND : angle 2.78407 ( 102) covalent geometry : bond 0.00658 (33168) covalent geometry : angle 0.88884 (45081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 470 time to evaluate : 3.419 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: 2 100 MET cc_start: 0.8279 (ptm) cc_final: 0.7918 (ttm) REVERT: 2 111 LEU cc_start: 0.9068 (pp) cc_final: 0.8861 (tt) REVERT: 2 271 MET cc_start: 0.7729 (mtm) cc_final: 0.7498 (mtm) REVERT: 2 504 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7597 (ttp-110) REVERT: 5 100 MET cc_start: 0.8905 (mpp) cc_final: 0.8533 (mmp) REVERT: 5 100 ASP cc_start: 0.8812 (p0) cc_final: 0.8609 (p0) REVERT: 6 60 ASP cc_start: 0.8100 (t0) cc_final: 0.7852 (t0) REVERT: 7 89 GLN cc_start: 0.7712 (pm20) cc_final: 0.7235 (pm20) REVERT: 8 59 TYR cc_start: 0.8073 (m-80) cc_final: 0.6800 (m-80) REVERT: 8 81 GLU cc_start: 0.8116 (pt0) cc_final: 0.7561 (pm20) REVERT: 8 82 LEU cc_start: 0.9394 (mt) cc_final: 0.8913 (mt) REVERT: A 530 MET cc_start: 0.8148 (mtm) cc_final: 0.7617 (mtm) REVERT: A 619 LEU cc_start: 0.9295 (pp) cc_final: 0.8995 (tt) REVERT: A 658 GLN cc_start: 0.8724 (tt0) cc_final: 0.7399 (tp40) REVERT: B 122 LEU cc_start: 0.9561 (mt) cc_final: 0.9338 (mm) REVERT: B 377 ASN cc_start: 0.8506 (t0) cc_final: 0.8272 (t0) REVERT: C 44 GLN cc_start: 0.8547 (pm20) cc_final: 0.8177 (pm20) REVERT: C 100 TYR cc_start: 0.8599 (p90) cc_final: 0.8323 (p90) REVERT: C 100 ASP cc_start: 0.8785 (p0) cc_final: 0.8583 (p0) REVERT: E 70 PHE cc_start: 0.8230 (m-10) cc_final: 0.7934 (m-10) REVERT: E 89 GLN cc_start: 0.7877 (pm20) cc_final: 0.7527 (pm20) REVERT: F 82 LEU cc_start: 0.9499 (mt) cc_final: 0.9257 (mt) REVERT: G 530 MET cc_start: 0.8618 (mtm) cc_final: 0.7588 (mtm) REVERT: G 591 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8808 (tm-30) REVERT: H 12 MET cc_start: 0.6933 (mtp) cc_final: 0.6618 (ttp) REVERT: H 46 GLU cc_start: 0.8329 (tp30) cc_final: 0.7741 (tp30) REVERT: I 16 GLU cc_start: 0.4863 (mm-30) cc_final: 0.4620 (mm-30) REVERT: I 46 GLU cc_start: 0.8371 (tp30) cc_final: 0.7855 (tp30) REVERT: I 78 PHE cc_start: 0.7306 (t80) cc_final: 0.7067 (t80) REVERT: J 70 GLU cc_start: 0.7414 (tp30) cc_final: 0.7203 (tp30) REVERT: M 100 ASP cc_start: 0.8820 (p0) cc_final: 0.8606 (p0) REVERT: N 52 ASN cc_start: 0.7998 (m-40) cc_final: 0.7375 (m-40) REVERT: P 51 ILE cc_start: 0.9339 (tt) cc_final: 0.9113 (mp) REVERT: P 82 LEU cc_start: 0.9377 (mt) cc_final: 0.9090 (mt) REVERT: Q 530 MET cc_start: 0.8572 (mtm) cc_final: 0.7974 (mtt) REVERT: Q 619 LEU cc_start: 0.9398 (pp) cc_final: 0.8978 (tt) REVERT: Q 638 TYR cc_start: 0.8160 (m-10) cc_final: 0.7491 (m-10) REVERT: R 46 GLU cc_start: 0.8199 (tp30) cc_final: 0.7737 (tp30) outliers start: 2 outliers final: 0 residues processed: 472 average time/residue: 0.4777 time to fit residues: 362.0365 Evaluate side-chains 367 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 202 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 333 optimal weight: 0.0000 chunk 84 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 478 ASN ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 89 HIS ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS H 77 HIS J 6 GLN K 352 HIS L 6 GLN ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS S 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080196 restraints weight = 94829.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080419 restraints weight = 72063.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080868 restraints weight = 60529.505| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33405 Z= 0.145 Angle : 0.822 14.085 45741 Z= 0.380 Chirality : 0.049 0.399 5547 Planarity : 0.005 0.138 5469 Dihedral : 11.456 100.271 7896 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.90 (0.13), residues: 3768 helix: -0.33 (0.28), residues: 378 sheet: -0.50 (0.15), residues: 1155 loop : -1.93 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 8 100F HIS 0.009 0.001 HIS P 35 PHE 0.017 0.002 PHE E 70 TYR 0.021 0.001 TYR B 484 ARG 0.008 0.000 ARG O 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 57) link_NAG-ASN : angle 2.82254 ( 171) link_ALPHA1-6 : bond 0.00910 ( 18) link_ALPHA1-6 : angle 1.78291 ( 54) link_BETA1-4 : bond 0.00593 ( 78) link_BETA1-4 : angle 2.58337 ( 234) link_ALPHA1-2 : bond 0.00893 ( 9) link_ALPHA1-2 : angle 2.11414 ( 27) link_ALPHA1-3 : bond 0.01183 ( 24) link_ALPHA1-3 : angle 2.13115 ( 72) hydrogen bonds : bond 0.03779 ( 976) hydrogen bonds : angle 5.49702 ( 2652) SS BOND : bond 0.00629 ( 51) SS BOND : angle 2.30974 ( 102) covalent geometry : bond 0.00323 (33168) covalent geometry : angle 0.77179 (45081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 520 time to evaluate : 3.585 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: 2 100 MET cc_start: 0.8124 (ptm) cc_final: 0.7766 (ttm) REVERT: 2 377 ASN cc_start: 0.8504 (t0) cc_final: 0.8211 (t0) REVERT: 2 504 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7560 (ttp-110) REVERT: 5 100 TYR cc_start: 0.8882 (p90) cc_final: 0.8648 (p90) REVERT: 5 100 ASP cc_start: 0.8765 (p0) cc_final: 0.8512 (p0) REVERT: 7 89 GLN cc_start: 0.7337 (pm20) cc_final: 0.6965 (pm20) REVERT: 8 51 ILE cc_start: 0.9041 (tt) cc_final: 0.8728 (mp) REVERT: 8 59 TYR cc_start: 0.7744 (m-80) cc_final: 0.6433 (m-80) REVERT: 8 81 GLU cc_start: 0.8000 (pt0) cc_final: 0.7665 (pm20) REVERT: 8 82 LEU cc_start: 0.9231 (mt) cc_final: 0.8900 (mt) REVERT: A 530 MET cc_start: 0.8053 (mtm) cc_final: 0.7298 (mtm) REVERT: A 595 ILE cc_start: 0.9364 (pt) cc_final: 0.9047 (mm) REVERT: A 619 LEU cc_start: 0.9258 (pp) cc_final: 0.8932 (tt) REVERT: A 658 GLN cc_start: 0.8609 (tt0) cc_final: 0.7237 (tp40) REVERT: B 161 MET cc_start: 0.9007 (tpp) cc_final: 0.8791 (tpp) REVERT: C 44 GLN cc_start: 0.8539 (pm20) cc_final: 0.8160 (pm20) REVERT: C 100 TYR cc_start: 0.8679 (p90) cc_final: 0.8409 (p90) REVERT: C 100 ASP cc_start: 0.8757 (p0) cc_final: 0.8470 (p0) REVERT: E 70 PHE cc_start: 0.8078 (m-80) cc_final: 0.7614 (m-10) REVERT: F 51 ILE cc_start: 0.9048 (tt) cc_final: 0.8825 (mp) REVERT: F 59 TYR cc_start: 0.7499 (m-80) cc_final: 0.6750 (m-80) REVERT: F 82 LEU cc_start: 0.9463 (mt) cc_final: 0.9233 (mt) REVERT: G 530 MET cc_start: 0.8392 (mtm) cc_final: 0.7815 (mtt) REVERT: G 584 GLU cc_start: 0.7866 (tt0) cc_final: 0.7652 (tm-30) REVERT: G 591 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8802 (tm-30) REVERT: G 638 TYR cc_start: 0.8108 (m-80) cc_final: 0.7488 (m-10) REVERT: H 12 MET cc_start: 0.6990 (mtp) cc_final: 0.6720 (ttp) REVERT: H 16 GLU cc_start: 0.4949 (mm-30) cc_final: 0.4675 (mm-30) REVERT: H 46 GLU cc_start: 0.8368 (tp30) cc_final: 0.7697 (tp30) REVERT: H 77 HIS cc_start: 0.6916 (m-70) cc_final: 0.6659 (m90) REVERT: I 46 GLU cc_start: 0.8305 (tp30) cc_final: 0.7785 (tp30) REVERT: I 78 PHE cc_start: 0.7321 (t80) cc_final: 0.6951 (t80) REVERT: J 5 THR cc_start: 0.6817 (m) cc_final: 0.6529 (m) REVERT: K 122 LEU cc_start: 0.9414 (mt) cc_final: 0.9130 (mm) REVERT: K 484 TYR cc_start: 0.8969 (p90) cc_final: 0.8752 (p90) REVERT: M 34 TRP cc_start: 0.7940 (m100) cc_final: 0.7680 (m100) REVERT: M 100 TYR cc_start: 0.8940 (p90) cc_final: 0.8739 (p90) REVERT: M 100 MET cc_start: 0.8750 (mpp) cc_final: 0.8064 (mmt) REVERT: M 100 ASP cc_start: 0.8814 (p0) cc_final: 0.8610 (p0) REVERT: N 52 ASN cc_start: 0.8025 (m-40) cc_final: 0.7622 (m-40) REVERT: P 59 TYR cc_start: 0.7647 (m-80) cc_final: 0.7120 (m-80) REVERT: P 82 LEU cc_start: 0.9352 (mt) cc_final: 0.9056 (mt) REVERT: P 101 GLN cc_start: 0.8005 (tt0) cc_final: 0.7688 (tp40) REVERT: Q 530 MET cc_start: 0.8580 (mtm) cc_final: 0.8034 (mtm) REVERT: Q 595 ILE cc_start: 0.9291 (pt) cc_final: 0.8947 (mm) REVERT: Q 619 LEU cc_start: 0.9415 (pp) cc_final: 0.9088 (tt) REVERT: Q 638 TYR cc_start: 0.8165 (m-80) cc_final: 0.7559 (m-10) REVERT: R 46 GLU cc_start: 0.8489 (tp30) cc_final: 0.8081 (tp30) outliers start: 1 outliers final: 0 residues processed: 521 average time/residue: 0.4460 time to fit residues: 371.9206 Evaluate side-chains 387 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 248 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 351 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 215 optimal weight: 40.0000 chunk 291 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 203 GLN 2 478 ASN 6 51 ASN ** 8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 287 GLN C 32 ASN F 6 GLN J 6 GLN K 374 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN S 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076951 restraints weight = 98357.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076900 restraints weight = 79485.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077859 restraints weight = 64004.661| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33405 Z= 0.214 Angle : 0.861 15.735 45741 Z= 0.399 Chirality : 0.049 0.302 5547 Planarity : 0.005 0.087 5469 Dihedral : 10.982 98.545 7896 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.77 (0.14), residues: 3768 helix: -0.00 (0.29), residues: 363 sheet: -0.37 (0.16), residues: 1131 loop : -1.89 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP 8 100F HIS 0.011 0.001 HIS 8 35 PHE 0.017 0.002 PHE O 70 TYR 0.021 0.002 TYR B 484 ARG 0.007 0.000 ARG D 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 57) link_NAG-ASN : angle 3.16144 ( 171) link_ALPHA1-6 : bond 0.00948 ( 18) link_ALPHA1-6 : angle 1.96721 ( 54) link_BETA1-4 : bond 0.00579 ( 78) link_BETA1-4 : angle 2.58274 ( 234) link_ALPHA1-2 : bond 0.00723 ( 9) link_ALPHA1-2 : angle 2.05463 ( 27) link_ALPHA1-3 : bond 0.01109 ( 24) link_ALPHA1-3 : angle 2.34086 ( 72) hydrogen bonds : bond 0.04067 ( 976) hydrogen bonds : angle 5.46921 ( 2652) SS BOND : bond 0.00513 ( 51) SS BOND : angle 2.44334 ( 102) covalent geometry : bond 0.00489 (33168) covalent geometry : angle 0.80641 (45081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 4.021 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: 2 100 MET cc_start: 0.8161 (ptm) cc_final: 0.7892 (ttm) REVERT: 2 103 GLN cc_start: 0.7916 (pp30) cc_final: 0.7433 (pp30) REVERT: 2 504 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7615 (ttp-110) REVERT: 5 34 TRP cc_start: 0.8319 (m100) cc_final: 0.8026 (m100) REVERT: 5 100 MET cc_start: 0.8890 (mpp) cc_final: 0.8461 (mmp) REVERT: 5 100 ASP cc_start: 0.8819 (p0) cc_final: 0.8578 (p0) REVERT: 7 89 GLN cc_start: 0.7524 (pm20) cc_final: 0.7104 (pm20) REVERT: 8 51 ILE cc_start: 0.9190 (tt) cc_final: 0.8833 (mp) REVERT: 8 59 TYR cc_start: 0.7807 (m-80) cc_final: 0.6113 (m-80) REVERT: 8 81 GLU cc_start: 0.7970 (pt0) cc_final: 0.7535 (pm20) REVERT: 8 82 LEU cc_start: 0.9381 (mt) cc_final: 0.8890 (mt) REVERT: A 530 MET cc_start: 0.8213 (mtm) cc_final: 0.7471 (mtm) REVERT: A 595 ILE cc_start: 0.9357 (pt) cc_final: 0.9010 (mm) REVERT: A 619 LEU cc_start: 0.9288 (pp) cc_final: 0.8937 (tt) REVERT: A 658 GLN cc_start: 0.8660 (tt0) cc_final: 0.7319 (tp40) REVERT: C 44 GLN cc_start: 0.8633 (pm20) cc_final: 0.8244 (pm20) REVERT: C 100 TYR cc_start: 0.8749 (p90) cc_final: 0.8532 (p90) REVERT: C 100 ASP cc_start: 0.8805 (p0) cc_final: 0.8534 (p0) REVERT: E 70 PHE cc_start: 0.8140 (m-80) cc_final: 0.7562 (m-10) REVERT: F 51 ILE cc_start: 0.9124 (tt) cc_final: 0.8820 (mp) REVERT: F 82 LEU cc_start: 0.9470 (mt) cc_final: 0.9202 (mt) REVERT: G 530 MET cc_start: 0.8586 (mtm) cc_final: 0.7621 (mtm) REVERT: G 584 GLU cc_start: 0.7985 (tt0) cc_final: 0.7689 (tm-30) REVERT: G 591 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8836 (tm-30) REVERT: G 638 TYR cc_start: 0.8179 (m-80) cc_final: 0.7508 (m-10) REVERT: H 12 MET cc_start: 0.6905 (mtp) cc_final: 0.6670 (ttp) REVERT: H 46 GLU cc_start: 0.8415 (tp30) cc_final: 0.7784 (tp30) REVERT: H 77 HIS cc_start: 0.6688 (m-70) cc_final: 0.6421 (m90) REVERT: I 46 GLU cc_start: 0.8378 (tp30) cc_final: 0.7818 (tp30) REVERT: K 122 LEU cc_start: 0.9435 (mt) cc_final: 0.9182 (mm) REVERT: M 34 TRP cc_start: 0.8025 (m100) cc_final: 0.7713 (m100) REVERT: M 44 GLN cc_start: 0.8725 (pm20) cc_final: 0.8510 (pm20) REVERT: M 100 MET cc_start: 0.8789 (mpp) cc_final: 0.8124 (mmt) REVERT: N 52 ASN cc_start: 0.7991 (m-40) cc_final: 0.7563 (m-40) REVERT: O 81 ASP cc_start: 0.8028 (m-30) cc_final: 0.7716 (m-30) REVERT: Q 530 MET cc_start: 0.8719 (mtm) cc_final: 0.8240 (mtt) REVERT: Q 591 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9026 (tm-30) REVERT: Q 595 ILE cc_start: 0.9295 (pt) cc_final: 0.8774 (mm) REVERT: Q 619 LEU cc_start: 0.9396 (pp) cc_final: 0.8995 (tt) REVERT: Q 638 TYR cc_start: 0.8241 (m-80) cc_final: 0.7548 (m-10) REVERT: Q 658 GLN cc_start: 0.8725 (tt0) cc_final: 0.7161 (tp40) REVERT: R 12 MET cc_start: 0.5811 (mtp) cc_final: 0.5474 (mtp) REVERT: R 32 TYR cc_start: 0.8542 (m-10) cc_final: 0.8289 (m-10) REVERT: R 46 GLU cc_start: 0.8567 (tp30) cc_final: 0.8114 (tp30) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.5360 time to fit residues: 425.0744 Evaluate side-chains 382 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0936 > 50: distance: 4 - 7: 16.828 distance: 7 - 8: 17.633 distance: 8 - 9: 30.295 distance: 8 - 11: 42.961 distance: 9 - 10: 40.949 distance: 9 - 14: 12.556 distance: 11 - 12: 23.520 distance: 11 - 13: 35.714 distance: 14 - 15: 10.069 distance: 15 - 16: 10.067 distance: 15 - 18: 12.449 distance: 16 - 17: 15.286 distance: 16 - 22: 17.684 distance: 18 - 19: 8.760 distance: 18 - 20: 9.585 distance: 19 - 21: 16.400 distance: 22 - 23: 17.342 distance: 23 - 24: 26.694 distance: 23 - 26: 16.093 distance: 24 - 25: 19.571 distance: 24 - 31: 32.439 distance: 26 - 27: 16.861 distance: 27 - 28: 16.207 distance: 28 - 29: 8.980 distance: 29 - 30: 7.694 distance: 31 - 32: 38.035 distance: 32 - 33: 16.016 distance: 32 - 35: 27.550 distance: 33 - 34: 30.299 distance: 33 - 38: 22.097 distance: 35 - 36: 21.233 distance: 35 - 37: 16.094 distance: 38 - 39: 9.705 distance: 38 - 44: 37.402 distance: 39 - 40: 21.630 distance: 39 - 42: 14.565 distance: 40 - 41: 29.306 distance: 40 - 45: 21.219 distance: 42 - 43: 30.471 distance: 43 - 44: 8.054 distance: 45 - 46: 24.269 distance: 46 - 47: 14.727 distance: 47 - 48: 14.957 distance: 47 - 49: 19.521 distance: 49 - 50: 15.588 distance: 50 - 51: 41.570 distance: 50 - 53: 22.759 distance: 51 - 52: 39.109 distance: 51 - 55: 16.359 distance: 53 - 54: 21.475 distance: 55 - 56: 14.176 distance: 56 - 57: 42.837 distance: 56 - 59: 40.566 distance: 57 - 58: 26.057 distance: 57 - 61: 25.781 distance: 59 - 60: 9.456 distance: 61 - 62: 26.380 distance: 61 - 102: 17.958 distance: 62 - 63: 11.949 distance: 62 - 65: 18.050 distance: 63 - 64: 22.629 distance: 63 - 68: 9.491 distance: 64 - 99: 25.283 distance: 65 - 66: 14.105 distance: 65 - 67: 21.716 distance: 68 - 69: 21.495 distance: 69 - 70: 20.566 distance: 69 - 72: 24.511 distance: 70 - 71: 17.517 distance: 70 - 77: 23.615 distance: 72 - 73: 32.434 distance: 73 - 74: 12.807 distance: 74 - 75: 13.098 distance: 75 - 76: 26.451