Starting phenix.real_space_refine on Fri Jun 27 21:37:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.map" model { file = "/net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot1_20191/06_2025/6ot1_20191.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.106 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 165 5.16 5 C 20226 2.51 5 N 5331 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 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: 32247 Number of models: 1 Model: "" Number of chains: 75 Chain: "B" 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: "G" 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: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} 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: "q" 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: "r" 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: "O" 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: "E" 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: "A" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "F" 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: "I" 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: "J" 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: "K" 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: "D" 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: "P" 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: "M" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "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: 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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: 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: "e" 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: "f" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 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: 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: "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: 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: "z" 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: "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: 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: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 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: 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: "DA" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" 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: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 18.42, per 1000 atoms: 0.57 Number of scatterers: 32247 At special positions: 0 Unit cell: (160.988, 153.475, 155.621, 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 165 16.00 O 6525 8.00 N 5331 7.00 C 20226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 100A" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.02 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.03 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 98 " - pdb=" SG CYS S 100A" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 87 " 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 d 4 " - " MAN d 5 " " MAN w 4 " - " MAN w 5 " " MANBA 4 " - " MANBA 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 8 3 " - " MAN 8 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " BMADA 3 " - " MANDA 4 " " BMAGA 3 " - " MANGA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 3 3 " - " MAN 3 5 " " BMA V 3 " - " MAN V 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 5 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMABA 3 " - " MANBA 6 " " BMADA 3 " - " MANDA 5 " " BMAGA 3 " - " MANGA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " 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 Y 1 " - " NAG Y 2 " " 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 f 2 " - " BMA f 3 " " 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 k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 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 v 1 " - " NAG v 2 " " 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 z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN E 276 " " NAG 2 1 " - " ASN P 88 " " NAG 3 1 " - " ASN P 137 " " NAG 4 1 " - " ASN P 156 " " NAG 5 1 " - " ASN P 160 " " NAG 6 1 " - " ASN P 197 " " NAG 7 1 " - " ASN P 234 " " NAG 8 1 " - " ASN P 262 " " NAG 9 1 " - " ASN P 295 " " NAG B 701 " - " ASN B 637 " " NAG D 701 " - " ASN D 637 " " NAG E 625 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG E 633 " - " ASN E 355 " " NAG G 625 " - " ASN G 133 " " NAG G 632 " - " ASN G 339 " " NAG G 633 " - " ASN G 355 " " NAG O 701 " - " ASN O 637 " " NAG P 625 " - " ASN P 133 " " NAG P 632 " - " ASN P 339 " " NAG P 633 " - " ASN P 355 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 137 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 276 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 137 " " NAG l 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 160 " " NAG p 1 " - " ASN E 197 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 262 " " NAG u 1 " - " ASN E 295 " " NAG v 1 " - " ASN E 301 " " NAG w 1 " - " ASN E 332 " " NAG x 1 " - " ASN E 363 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 392 " " NAGAA 1 " - " ASN P 301 " " NAGBA 1 " - " ASN P 332 " " NAGCA 1 " - " ASN P 363 " " NAGDA 1 " - " ASN P 386 " " NAGEA 1 " - " ASN P 392 " " NAGFA 1 " - " ASN P 448 " " NAGGA 1 " - " ASN P 276 " Time building additional restraints: 9.21 Conformation dependent library (CDL) restraints added in 3.8 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 93 sheets defined 11.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.894A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.588A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 354 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.406A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.089A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.671A pdb=" N ASP m 31 " --> pdb=" O LEU m 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'n' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU n 83 " --> pdb=" O ALA n 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.892A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.607A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 634 " --> pdb=" O GLN O 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER O 636 " --> pdb=" O ASP O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.827A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.408A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.893A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.741A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE P 109 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.881A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 349 removed outlier: 3.690A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.407A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.019A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.518A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.991A pdb=" N THR S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.509A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.563A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AB3, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER H 70 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 89 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS m 92 " --> pdb=" O TRP m 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP m 101 " --> pdb=" O CYS m 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR m 94 " --> pdb=" O ASP m 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'n' and resid 9 through 13 removed outlier: 3.761A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'n' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'n' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS q 35 " --> pdb=" O VAL q 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS q 92 " --> pdb=" O TRP q 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP q 103 " --> pdb=" O CYS q 92 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 94 " --> pdb=" O GLN q 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 17 through 19 Processing sheet with id=AD1, first strand: chain 'q' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER q 58 " --> pdb=" O TRP q 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR r 48 " --> pdb=" O ARG r 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'O' and resid 603 through 609 removed outlier: 7.992A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.507A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AE5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE6, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AE7, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AE8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.559A pdb=" N SER A 70 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 32 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 52 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 89 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR F 33 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS F 92 " --> pdb=" O TRP F 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP F 101 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR F 94 " --> pdb=" O ASP F 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 98 " --> pdb=" O TYR F 100M" (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AF9, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.664A pdb=" N ALA I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 35 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG J 94 " --> pdb=" O GLN J 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.502A pdb=" N SER J 58 " --> pdb=" O TRP J 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR K 48 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG9, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'P' and resid 158 through 162 Processing sheet with id=AH5, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AH6, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AH9, first strand: chain 'P' and resid 304 through 308 Processing sheet with id=AI1, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AI2, first strand: chain 'P' and resid 375 through 378 Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER M 70 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE M 32 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR M 52 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG M 94 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU N 89 " --> pdb=" O HIS N 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR Q 33 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP Q 101 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR Q 94 " --> pdb=" O ASP Q 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY Q 98 " --> pdb=" O TYR Q 100M" (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 18 through 22 Processing sheet with id=AJ2, first strand: chain 'R' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA R 84 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ4, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AJ6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS S 35 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG S 94 " --> pdb=" O GLN S 101 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 17 through 19 Processing sheet with id=AJ9, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER S 58 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AK2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP T 34 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR T 48 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 10 through 13 924 hydrogen bonds defined for protein. 2214 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: 14.73 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9970 1.34 - 1.46: 8484 1.46 - 1.58: 14276 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 32946 Sorted by residual: bond pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.89e+01 bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.63e+01 bond pdb=" C1 NAG 2 1 " pdb=" O5 NAG 2 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 BMA z 3 " pdb=" C2 BMA z 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 42345 1.96 - 3.92: 1975 3.92 - 5.88: 310 5.88 - 7.84: 116 7.84 - 9.80: 44 Bond angle restraints: 44790 Sorted by residual: angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLY N 68 " pdb=" N THR N 69 " pdb=" CA THR N 69 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C CYS J 98 " pdb=" N ASP J 99 " pdb=" CA ASP J 99 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C CYS q 98 " pdb=" N ASP q 99 " pdb=" CA ASP q 99 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 ... (remaining 44785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 19477 21.69 - 43.39: 1540 43.39 - 65.08: 238 65.08 - 86.78: 177 86.78 - 108.47: 99 Dihedral angle restraints: 21531 sinusoidal: 10467 harmonic: 11064 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.91 65.91 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.90 65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 21528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4669 0.087 - 0.175: 688 0.175 - 0.262: 52 0.262 - 0.350: 30 0.350 - 0.437: 6 Chirality restraints: 5445 Sorted by residual: chirality pdb=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" N2 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.05 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C2 NAG 3 1 " pdb=" C1 NAG 3 1 " pdb=" C3 NAG 3 1 " pdb=" N2 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C2 NAG k 1 " pdb=" C1 NAG k 1 " pdb=" C3 NAG k 1 " pdb=" N2 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5442 not shown) Planarity restraints: 5547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 275 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C GLU G 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU G 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 275 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU P 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU P 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN P 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 275 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLU E 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU E 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 276 " -0.016 2.00e-02 2.50e+03 ... (remaining 5544 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 393 2.59 - 3.17: 25306 3.17 - 3.75: 47473 3.75 - 4.32: 64453 4.32 - 4.90: 107153 Nonbonded interactions: 244778 Sorted by model distance: nonbonded pdb=" OE1 GLU O 647 " pdb=" NH2 ARG D 542 " model vdw 2.015 3.120 nonbonded pdb=" NH2 ARG B 542 " pdb=" OE1 GLU D 647 " model vdw 2.021 3.120 nonbonded pdb=" CB ASP q 76B" pdb=" OH TYR E 318 " model vdw 2.032 3.440 nonbonded pdb=" OH TYR G 318 " pdb=" CB ASP S 76B" model vdw 2.048 3.440 nonbonded pdb=" OE1 GLU B 647 " pdb=" NH2 ARG O 542 " model vdw 2.048 3.120 ... (remaining 244773 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: 0.03 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'AA' selection = chain 'FA' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'j' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'DA' selection = chain 'GA' selection = chain 'V' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'CA' selection = chain 'EA' selection = chain 'W' selection = chain 'e' selection = chain 'g' selection = chain 'l' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '8' selection = chain 'a' selection = chain 't' } ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'BA' selection = chain 'd' selection = chain 'w' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'R' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'q' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'r' } 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: 1.860 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: 0.050 Extract box with map and model: 1.220 Check model and map are aligned: 0.250 Set scattering table: 0.270 Process input model: 74.940 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.007 0.059 33159 Z= 0.353 Angle : 1.066 16.616 45372 Z= 0.525 Chirality : 0.063 0.437 5445 Planarity : 0.007 0.064 5490 Dihedral : 18.251 108.471 14274 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.72 % Allowed : 9.69 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.15 (0.11), residues: 3801 helix: -4.64 (0.10), residues: 387 sheet: -2.13 (0.14), residues: 1230 loop : -2.84 (0.10), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 112 HIS 0.006 0.001 HIS F 3 PHE 0.031 0.002 PHE S 100D TYR 0.013 0.002 TYR Q 100M ARG 0.021 0.001 ARG E 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 57) link_NAG-ASN : angle 4.46696 ( 171) link_ALPHA1-6 : bond 0.00393 ( 12) link_ALPHA1-6 : angle 1.60195 ( 36) link_BETA1-4 : bond 0.01035 ( 69) link_BETA1-4 : angle 2.68981 ( 207) link_ALPHA1-2 : bond 0.00041 ( 3) link_ALPHA1-2 : angle 1.75686 ( 9) link_ALPHA1-3 : bond 0.00521 ( 15) link_ALPHA1-3 : angle 2.52274 ( 45) hydrogen bonds : bond 0.26641 ( 870) hydrogen bonds : angle 9.84750 ( 2214) SS BOND : bond 0.00548 ( 57) SS BOND : angle 2.22938 ( 114) covalent geometry : bond 0.00749 (32946) covalent geometry : angle 1.01029 (44790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 434 time to evaluate : 3.605 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: B 519 PHE cc_start: 0.8400 (m-80) cc_final: 0.8016 (m-10) REVERT: B 654 GLU cc_start: 0.8443 (tp30) cc_final: 0.8176 (tp30) REVERT: B 657 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 272 ILE cc_start: 0.8932 (pt) cc_final: 0.8458 (mt) REVERT: G 426 MET cc_start: 0.7357 (mmm) cc_final: 0.7137 (mmt) REVERT: H 36 TRP cc_start: 0.2994 (m100) cc_final: 0.2702 (m100) REVERT: L 50 GLU cc_start: 0.4860 (mt-10) cc_final: 0.4481 (mm-30) REVERT: m 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8096 (mppt) REVERT: r 17 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 32 PHE cc_start: 0.7258 (m-80) cc_final: 0.6722 (m-10) REVERT: C 50 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4727 (mm-30) REVERT: F 13 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7757 (mmmt) REVERT: F 103 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8165 (mppt) REVERT: I 49 TYR cc_start: 0.8377 (p90) cc_final: 0.8108 (p90) REVERT: D 519 PHE cc_start: 0.8575 (m-80) cc_final: 0.8237 (m-10) REVERT: P 439 ILE cc_start: 0.8856 (pt) cc_final: 0.8563 (pt) REVERT: N 50 GLU cc_start: 0.4691 (mt-10) cc_final: 0.4323 (mm-30) REVERT: Q 103 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7945 (mppt) REVERT: T 11 LEU cc_start: 0.9046 (tp) cc_final: 0.8792 (tt) REVERT: T 78 ASP cc_start: 0.8748 (t70) cc_final: 0.8489 (t70) outliers start: 24 outliers final: 8 residues processed: 458 average time/residue: 0.4911 time to fit residues: 347.2287 Evaluate side-chains 303 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN G 67 ASN G 103 GLN G 183 GLN G 203 GLN H 77 GLN L 93 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN n 38 GLN O 575 GLN E 67 ASN E 103 GLN E 183 GLN E 203 GLN A 77 GLN C 93 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 38 GLN D 575 GLN P 67 ASN P 103 GLN P 183 GLN P 203 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 93 GLN ** Q 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 38 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.105336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063964 restraints weight = 81979.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066019 restraints weight = 46878.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067350 restraints weight = 34353.882| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33159 Z= 0.234 Angle : 0.799 12.425 45372 Z= 0.386 Chirality : 0.048 0.295 5445 Planarity : 0.005 0.054 5490 Dihedral : 14.232 84.174 7343 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.42 % Allowed : 15.19 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.40 (0.12), residues: 3801 helix: -3.27 (0.18), residues: 396 sheet: -1.70 (0.14), residues: 1224 loop : -2.44 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 571 HIS 0.004 0.001 HIS E 330 PHE 0.024 0.002 PHE J 100D TYR 0.017 0.001 TYR H 59 ARG 0.012 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 57) link_NAG-ASN : angle 3.21904 ( 171) link_ALPHA1-6 : bond 0.00578 ( 12) link_ALPHA1-6 : angle 1.87763 ( 36) link_BETA1-4 : bond 0.00601 ( 69) link_BETA1-4 : angle 2.13827 ( 207) link_ALPHA1-2 : bond 0.00495 ( 3) link_ALPHA1-2 : angle 2.07555 ( 9) link_ALPHA1-3 : bond 0.00957 ( 15) link_ALPHA1-3 : angle 2.53578 ( 45) hydrogen bonds : bond 0.04678 ( 870) hydrogen bonds : angle 6.69483 ( 2214) SS BOND : bond 0.00645 ( 57) SS BOND : angle 1.93461 ( 114) covalent geometry : bond 0.00527 (32946) covalent geometry : angle 0.75291 (44790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 327 time to evaluate : 3.467 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: B 519 PHE cc_start: 0.8243 (m-80) cc_final: 0.7996 (m-10) REVERT: B 535 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7938 (mtt) REVERT: B 654 GLU cc_start: 0.8562 (tp30) cc_final: 0.8303 (tp30) REVERT: B 657 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8287 (tm-30) REVERT: G 203 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: G 272 ILE cc_start: 0.8897 (pt) cc_final: 0.8471 (mt) REVERT: L 50 GLU cc_start: 0.5019 (mt-10) cc_final: 0.4747 (mm-30) REVERT: m 32 ASN cc_start: 0.8623 (m-40) cc_final: 0.8355 (m110) REVERT: m 103 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8174 (mppt) REVERT: n 87 TYR cc_start: 0.8378 (m-80) cc_final: 0.7888 (m-80) REVERT: q 100 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7679 (t80) REVERT: E 33 ASN cc_start: 0.8010 (p0) cc_final: 0.7584 (p0) REVERT: A 101 ASP cc_start: 0.4820 (p0) cc_final: 0.4566 (p0) REVERT: C 50 GLU cc_start: 0.5055 (mt-10) cc_final: 0.4811 (mm-30) REVERT: F 103 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8194 (mppt) REVERT: K 1 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: K 98 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7551 (tm-30) REVERT: P 33 ASN cc_start: 0.8091 (p0) cc_final: 0.7890 (p0) REVERT: P 255 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8797 (m) REVERT: N 50 GLU cc_start: 0.4899 (mt-10) cc_final: 0.4590 (mm-30) REVERT: Q 32 ASN cc_start: 0.8513 (m-40) cc_final: 0.8260 (m110) REVERT: S 100 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7666 (t80) outliers start: 81 outliers final: 34 residues processed: 393 average time/residue: 0.4713 time to fit residues: 291.1512 Evaluate side-chains 330 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 329 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 377 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 324 optimal weight: 50.0000 chunk 141 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 346 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN M 3 GLN M 5 GLN N 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070210 restraints weight = 82115.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068961 restraints weight = 59812.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069513 restraints weight = 52780.185| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33159 Z= 0.169 Angle : 0.737 11.368 45372 Z= 0.354 Chirality : 0.047 0.287 5445 Planarity : 0.004 0.056 5490 Dihedral : 12.503 80.773 7341 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.75 % Allowed : 16.95 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.05 (0.12), residues: 3801 helix: -2.57 (0.21), residues: 396 sheet: -1.55 (0.14), residues: 1248 loop : -2.24 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 571 HIS 0.006 0.001 HIS Q 3 PHE 0.042 0.002 PHE N 98 TYR 0.015 0.001 TYR A 59 ARG 0.012 0.000 ARG m 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 57) link_NAG-ASN : angle 2.89515 ( 171) link_ALPHA1-6 : bond 0.00533 ( 12) link_ALPHA1-6 : angle 1.75364 ( 36) link_BETA1-4 : bond 0.00513 ( 69) link_BETA1-4 : angle 1.91544 ( 207) link_ALPHA1-2 : bond 0.00525 ( 3) link_ALPHA1-2 : angle 1.88515 ( 9) link_ALPHA1-3 : bond 0.01085 ( 15) link_ALPHA1-3 : angle 1.91196 ( 45) hydrogen bonds : bond 0.03977 ( 870) hydrogen bonds : angle 6.02437 ( 2214) SS BOND : bond 0.00322 ( 57) SS BOND : angle 1.49038 ( 114) covalent geometry : bond 0.00381 (32946) covalent geometry : angle 0.69951 (44790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 309 time to evaluate : 3.288 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: B 654 GLU cc_start: 0.8532 (tp30) cc_final: 0.8215 (tp30) REVERT: B 657 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8301 (tm-30) REVERT: G 272 ILE cc_start: 0.8889 (pt) cc_final: 0.8558 (mt) REVERT: m 32 ASN cc_start: 0.8590 (m-40) cc_final: 0.8379 (m110) REVERT: m 103 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8208 (mppt) REVERT: n 87 TYR cc_start: 0.8331 (m-80) cc_final: 0.7741 (m-80) REVERT: q 76 ASP cc_start: 0.8116 (t0) cc_final: 0.7837 (t0) REVERT: q 100 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7793 (t80) REVERT: O 663 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8854 (pp) REVERT: E 33 ASN cc_start: 0.8280 (p0) cc_final: 0.7874 (p0) REVERT: F 43 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9032 (mtmt) REVERT: F 103 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8255 (mppt) REVERT: K 1 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: K 98 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7764 (tm-30) REVERT: P 255 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (m) REVERT: N 4 MET cc_start: -0.1973 (mmm) cc_final: -0.2355 (mtp) REVERT: Q 32 ASN cc_start: 0.8500 (m-40) cc_final: 0.8102 (m-40) REVERT: S 100 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7759 (t80) REVERT: T 78 ASP cc_start: 0.8228 (t70) cc_final: 0.7878 (t70) outliers start: 92 outliers final: 51 residues processed: 386 average time/residue: 0.4492 time to fit residues: 273.9289 Evaluate side-chains 335 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 279 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 98 CYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 288 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 332 optimal weight: 50.0000 chunk 293 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 214 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 198 optimal weight: 50.0000 chunk 129 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN L 38 GLN r 88 GLN E 203 GLN C 38 GLN F 97 HIS P 33 ASN N 38 GLN Q 97 HIS S 101 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062691 restraints weight = 82638.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064743 restraints weight = 47507.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066013 restraints weight = 34954.704| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33159 Z= 0.278 Angle : 0.801 12.131 45372 Z= 0.382 Chirality : 0.049 0.297 5445 Planarity : 0.004 0.055 5490 Dihedral : 11.464 81.664 7341 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.89 % Allowed : 17.97 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.92 (0.13), residues: 3801 helix: -2.24 (0.23), residues: 399 sheet: -1.52 (0.14), residues: 1290 loop : -2.16 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 36 HIS 0.005 0.001 HIS E 330 PHE 0.039 0.002 PHE L 98 TYR 0.016 0.002 TYR A 59 ARG 0.006 0.000 ARG Q 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 57) link_NAG-ASN : angle 3.00276 ( 171) link_ALPHA1-6 : bond 0.00442 ( 12) link_ALPHA1-6 : angle 1.87143 ( 36) link_BETA1-4 : bond 0.00533 ( 69) link_BETA1-4 : angle 1.93411 ( 207) link_ALPHA1-2 : bond 0.00334 ( 3) link_ALPHA1-2 : angle 2.04626 ( 9) link_ALPHA1-3 : bond 0.01027 ( 15) link_ALPHA1-3 : angle 2.09378 ( 45) hydrogen bonds : bond 0.03861 ( 870) hydrogen bonds : angle 5.87523 ( 2214) SS BOND : bond 0.00576 ( 57) SS BOND : angle 2.05789 ( 114) covalent geometry : bond 0.00639 (32946) covalent geometry : angle 0.76090 (44790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 289 time to evaluate : 5.223 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: B 530 MET cc_start: 0.8449 (mtt) cc_final: 0.8186 (mtt) REVERT: B 654 GLU cc_start: 0.8564 (tp30) cc_final: 0.8353 (tp30) REVERT: B 657 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8288 (tm-30) REVERT: G 161 MET cc_start: 0.7678 (tpp) cc_final: 0.7463 (ttm) REVERT: G 272 ILE cc_start: 0.8930 (pt) cc_final: 0.8522 (mt) REVERT: m 30 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8591 (mtp-110) REVERT: m 103 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8227 (mppt) REVERT: n 49 TYR cc_start: 0.8509 (p90) cc_final: 0.8165 (p90) REVERT: n 87 TYR cc_start: 0.8274 (m-80) cc_final: 0.7665 (m-80) REVERT: q 76 ASP cc_start: 0.8052 (t0) cc_final: 0.7764 (t0) REVERT: q 100 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7785 (t80) REVERT: r 33 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8875 (p) REVERT: O 519 PHE cc_start: 0.8339 (m-10) cc_final: 0.8131 (m-10) REVERT: E 33 ASN cc_start: 0.8036 (p0) cc_final: 0.7767 (p0) REVERT: F 103 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8266 (mppt) REVERT: I 49 TYR cc_start: 0.8480 (p90) cc_final: 0.8136 (p90) REVERT: J 100 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8058 (t80) REVERT: K 1 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: K 32 MET cc_start: 0.8423 (tpt) cc_final: 0.7232 (tpp) REVERT: K 98 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7718 (tm-30) REVERT: P 255 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8874 (m) REVERT: M 4 LEU cc_start: 0.6030 (tp) cc_final: 0.5678 (tp) REVERT: N 4 MET cc_start: -0.0096 (mmm) cc_final: -0.0360 (mtp) REVERT: Q 32 ASN cc_start: 0.8290 (m-40) cc_final: 0.7905 (m-40) REVERT: S 100 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7709 (t80) REVERT: T 78 ASP cc_start: 0.8158 (t70) cc_final: 0.7848 (t70) outliers start: 130 outliers final: 87 residues processed: 399 average time/residue: 0.5872 time to fit residues: 375.8271 Evaluate side-chains 370 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 277 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 434 MET Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 98 CYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 138 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 375 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 32 ASN m 97 HIS n 51 ASN E 203 GLN A 3 GLN C 90 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30EHIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072652 restraints weight = 81444.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070242 restraints weight = 62359.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071124 restraints weight = 50363.194| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33159 Z= 0.124 Angle : 0.698 11.125 45372 Z= 0.333 Chirality : 0.046 0.277 5445 Planarity : 0.004 0.059 5490 Dihedral : 10.328 76.535 7341 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.96 % Allowed : 20.36 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.72 (0.13), residues: 3801 helix: -1.94 (0.24), residues: 414 sheet: -1.48 (0.14), residues: 1263 loop : -1.99 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP M 36 HIS 0.006 0.001 HIS m 3 PHE 0.035 0.001 PHE C 98 TYR 0.017 0.001 TYR A 59 ARG 0.007 0.000 ARG Q 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 57) link_NAG-ASN : angle 2.60728 ( 171) link_ALPHA1-6 : bond 0.00547 ( 12) link_ALPHA1-6 : angle 1.88311 ( 36) link_BETA1-4 : bond 0.00485 ( 69) link_BETA1-4 : angle 1.69935 ( 207) link_ALPHA1-2 : bond 0.00605 ( 3) link_ALPHA1-2 : angle 1.46994 ( 9) link_ALPHA1-3 : bond 0.01095 ( 15) link_ALPHA1-3 : angle 1.83467 ( 45) hydrogen bonds : bond 0.03266 ( 870) hydrogen bonds : angle 5.39610 ( 2214) SS BOND : bond 0.00325 ( 57) SS BOND : angle 1.48145 ( 114) covalent geometry : bond 0.00274 (32946) covalent geometry : angle 0.66495 (44790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 312 time to evaluate : 3.343 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: B 654 GLU cc_start: 0.8409 (tp30) cc_final: 0.8091 (tp30) REVERT: B 657 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8249 (tm-30) REVERT: G 161 MET cc_start: 0.7597 (tpp) cc_final: 0.7370 (ttm) REVERT: G 272 ILE cc_start: 0.8874 (pt) cc_final: 0.8583 (mt) REVERT: G 482 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: H 57 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (tp) REVERT: m 43 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8964 (mtpt) REVERT: m 103 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8243 (mppt) REVERT: n 49 TYR cc_start: 0.8398 (p90) cc_final: 0.8195 (p90) REVERT: q 100 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7718 (t80) REVERT: O 663 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8790 (pp) REVERT: E 33 ASN cc_start: 0.8119 (p0) cc_final: 0.7876 (p0) REVERT: E 95 MET cc_start: 0.8261 (ptm) cc_final: 0.7496 (ttp) REVERT: F 43 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9024 (mtmt) REVERT: F 103 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8251 (mppt) REVERT: I 49 TYR cc_start: 0.8386 (p90) cc_final: 0.8089 (p90) REVERT: J 100 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8177 (t80) REVERT: K 1 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: K 32 MET cc_start: 0.8309 (tpt) cc_final: 0.7104 (tpp) REVERT: K 98 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7707 (tm-30) REVERT: P 255 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8708 (m) REVERT: N 4 MET cc_start: -0.2234 (mmm) cc_final: -0.2849 (mtp) REVERT: Q 13 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8070 (mmmt) REVERT: Q 16 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7041 (tm-30) REVERT: Q 30 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8530 (tpp80) REVERT: Q 32 ASN cc_start: 0.8338 (m-40) cc_final: 0.7949 (m-40) REVERT: Q 43 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8925 (mtpt) REVERT: S 100 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7739 (t80) outliers start: 99 outliers final: 58 residues processed: 397 average time/residue: 0.4437 time to fit residues: 282.0380 Evaluate side-chains 342 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 372 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS E 203 GLN ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061485 restraints weight = 82975.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063490 restraints weight = 48241.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064752 restraints weight = 35817.445| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 33159 Z= 0.361 Angle : 0.862 12.243 45372 Z= 0.410 Chirality : 0.050 0.303 5445 Planarity : 0.005 0.054 5490 Dihedral : 10.526 82.234 7341 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.92 % Allowed : 20.81 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.75 (0.13), residues: 3801 helix: -1.99 (0.23), residues: 420 sheet: -1.42 (0.14), residues: 1290 loop : -2.06 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 36 HIS 0.006 0.001 HIS P 330 PHE 0.029 0.002 PHE J 100D TYR 0.021 0.002 TYR Q 100M ARG 0.012 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00882 ( 57) link_NAG-ASN : angle 3.10769 ( 171) link_ALPHA1-6 : bond 0.00490 ( 12) link_ALPHA1-6 : angle 1.95335 ( 36) link_BETA1-4 : bond 0.00578 ( 69) link_BETA1-4 : angle 2.00312 ( 207) link_ALPHA1-2 : bond 0.00157 ( 3) link_ALPHA1-2 : angle 2.20785 ( 9) link_ALPHA1-3 : bond 0.01027 ( 15) link_ALPHA1-3 : angle 2.13418 ( 45) hydrogen bonds : bond 0.03933 ( 870) hydrogen bonds : angle 5.70602 ( 2214) SS BOND : bond 0.00470 ( 57) SS BOND : angle 1.86223 ( 114) covalent geometry : bond 0.00829 (32946) covalent geometry : angle 0.82413 (44790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 277 time to evaluate : 3.979 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: B 654 GLU cc_start: 0.8652 (tp30) cc_final: 0.8404 (tp30) REVERT: B 657 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8147 (tm-30) REVERT: G 161 MET cc_start: 0.7823 (tpp) cc_final: 0.7527 (ttm) REVERT: G 271 MET cc_start: 0.7909 (mtt) cc_final: 0.7568 (mtt) REVERT: G 272 ILE cc_start: 0.8983 (pt) cc_final: 0.8565 (mt) REVERT: G 482 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: H 32 PHE cc_start: 0.7134 (m-80) cc_final: 0.6850 (m-10) REVERT: H 57 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7891 (tp) REVERT: m 30 ARG cc_start: 0.8909 (mtp-110) cc_final: 0.8366 (mmm160) REVERT: m 103 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8287 (mppt) REVERT: n 49 TYR cc_start: 0.8587 (p90) cc_final: 0.8315 (p90) REVERT: q 76 ASP cc_start: 0.8222 (t0) cc_final: 0.7920 (t0) REVERT: O 626 MET cc_start: 0.8029 (mtp) cc_final: 0.7826 (mtp) REVERT: O 663 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8816 (pp) REVERT: E 33 ASN cc_start: 0.8100 (p0) cc_final: 0.7845 (p0) REVERT: E 95 MET cc_start: 0.8592 (ptm) cc_final: 0.8022 (ttp) REVERT: E 236 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 30 HIS cc_start: 0.2786 (OUTLIER) cc_final: 0.2376 (t70) REVERT: F 30 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8351 (tpp80) REVERT: F 103 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8236 (mppt) REVERT: I 49 TYR cc_start: 0.8586 (p90) cc_final: 0.8286 (p90) REVERT: J 100 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7910 (t80) REVERT: K 1 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: K 98 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7725 (tm-30) REVERT: P 255 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8957 (m) REVERT: N 4 MET cc_start: -0.0299 (mmm) cc_final: -0.0511 (mtp) REVERT: Q 16 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6957 (tm-30) REVERT: Q 32 ASN cc_start: 0.8333 (m-40) cc_final: 0.7893 (m-40) REVERT: S 100 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7767 (t80) REVERT: T 98 GLU cc_start: 0.8686 (tt0) cc_final: 0.8439 (tm-30) outliers start: 131 outliers final: 98 residues processed: 389 average time/residue: 0.4484 time to fit residues: 281.8337 Evaluate side-chains 371 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 264 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 80 MET Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 10 ILE Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain P residue 496 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 107 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 366 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS m 32 ASN E 203 GLN ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.106925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066150 restraints weight = 80708.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068266 restraints weight = 45585.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069600 restraints weight = 33116.550| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33159 Z= 0.126 Angle : 0.705 10.445 45372 Z= 0.338 Chirality : 0.046 0.283 5445 Planarity : 0.004 0.057 5490 Dihedral : 9.843 74.870 7341 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.99 % Allowed : 22.57 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.45 (0.13), residues: 3801 helix: -1.46 (0.25), residues: 402 sheet: -1.22 (0.15), residues: 1221 loop : -1.92 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 36 HIS 0.006 0.001 HIS F 3 PHE 0.020 0.001 PHE J 100D TYR 0.019 0.001 TYR Q 100O ARG 0.017 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 57) link_NAG-ASN : angle 2.54279 ( 171) link_ALPHA1-6 : bond 0.00597 ( 12) link_ALPHA1-6 : angle 1.79340 ( 36) link_BETA1-4 : bond 0.00470 ( 69) link_BETA1-4 : angle 1.58190 ( 207) link_ALPHA1-2 : bond 0.00673 ( 3) link_ALPHA1-2 : angle 1.34786 ( 9) link_ALPHA1-3 : bond 0.01054 ( 15) link_ALPHA1-3 : angle 1.65518 ( 45) hydrogen bonds : bond 0.03177 ( 870) hydrogen bonds : angle 5.16701 ( 2214) SS BOND : bond 0.00451 ( 57) SS BOND : angle 1.38064 ( 114) covalent geometry : bond 0.00279 (32946) covalent geometry : angle 0.67528 (44790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 295 time to evaluate : 3.761 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: G 161 MET cc_start: 0.7719 (tpp) cc_final: 0.7501 (ttm) REVERT: G 272 ILE cc_start: 0.8892 (pt) cc_final: 0.8630 (mt) REVERT: G 302 ASN cc_start: 0.8552 (t0) cc_final: 0.8252 (t0) REVERT: G 482 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: H 32 PHE cc_start: 0.6866 (m-80) cc_final: 0.6520 (m-10) REVERT: H 59 TYR cc_start: 0.5012 (m-10) cc_final: 0.4706 (m-10) REVERT: m 30 ARG cc_start: 0.8816 (mtp-110) cc_final: 0.8446 (mmm-85) REVERT: m 43 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8908 (mtpt) REVERT: m 53 ASP cc_start: 0.8199 (p0) cc_final: 0.7848 (p0) REVERT: O 626 MET cc_start: 0.7968 (mtp) cc_final: 0.7745 (mtp) REVERT: O 663 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8779 (pp) REVERT: E 33 ASN cc_start: 0.7960 (p0) cc_final: 0.7690 (p0) REVERT: E 95 MET cc_start: 0.8427 (ptm) cc_final: 0.7780 (ttp) REVERT: C 36 TYR cc_start: 0.5093 (m-10) cc_final: 0.4883 (m-10) REVERT: F 43 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8946 (mtmt) REVERT: F 103 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8250 (mppt) REVERT: J 100 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8040 (t80) REVERT: K 1 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: K 98 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7699 (tm-30) REVERT: P 255 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8772 (m) REVERT: P 302 ASN cc_start: 0.8673 (t0) cc_final: 0.8410 (t0) REVERT: M 32 PHE cc_start: 0.6922 (m-80) cc_final: 0.6599 (m-80) REVERT: Q 13 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8047 (mmmt) REVERT: Q 16 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6927 (tm-30) REVERT: Q 30 ARG cc_start: 0.8772 (ttp-110) cc_final: 0.8455 (tpp80) REVERT: Q 32 ASN cc_start: 0.8199 (m-40) cc_final: 0.7800 (m-40) REVERT: Q 43 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8896 (mtpt) REVERT: S 100 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7753 (t80) outliers start: 100 outliers final: 66 residues processed: 378 average time/residue: 0.4537 time to fit residues: 274.7963 Evaluate side-chains 350 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 79 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 367 optimal weight: 0.8980 chunk 197 optimal weight: 0.0010 chunk 168 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.106129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065155 restraints weight = 81990.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067233 restraints weight = 46776.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068561 restraints weight = 34170.710| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33159 Z= 0.162 Angle : 0.713 10.566 45372 Z= 0.341 Chirality : 0.046 0.284 5445 Planarity : 0.004 0.057 5490 Dihedral : 9.609 75.118 7341 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.05 % Allowed : 22.63 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.33 (0.13), residues: 3801 helix: -1.29 (0.26), residues: 384 sheet: -1.12 (0.15), residues: 1221 loop : -1.87 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 36 HIS 0.004 0.001 HIS F 3 PHE 0.019 0.001 PHE q 100D TYR 0.024 0.001 TYR Q 100O ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 57) link_NAG-ASN : angle 2.55272 ( 171) link_ALPHA1-6 : bond 0.00569 ( 12) link_ALPHA1-6 : angle 1.76944 ( 36) link_BETA1-4 : bond 0.00480 ( 69) link_BETA1-4 : angle 1.65841 ( 207) link_ALPHA1-2 : bond 0.00421 ( 3) link_ALPHA1-2 : angle 1.70520 ( 9) link_ALPHA1-3 : bond 0.01080 ( 15) link_ALPHA1-3 : angle 1.73530 ( 45) hydrogen bonds : bond 0.03159 ( 870) hydrogen bonds : angle 5.10333 ( 2214) SS BOND : bond 0.00294 ( 57) SS BOND : angle 1.45926 ( 114) covalent geometry : bond 0.00372 (32946) covalent geometry : angle 0.68272 (44790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 279 time to evaluate : 3.921 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: G 161 MET cc_start: 0.7769 (tpp) cc_final: 0.7408 (ttm) REVERT: G 271 MET cc_start: 0.7601 (mtt) cc_final: 0.7238 (mtt) REVERT: G 482 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: H 32 PHE cc_start: 0.6939 (m-80) cc_final: 0.6606 (m-10) REVERT: m 30 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8460 (mmm-85) REVERT: m 43 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8890 (mtpt) REVERT: m 53 ASP cc_start: 0.8251 (p0) cc_final: 0.7922 (p0) REVERT: r 80 GLU cc_start: 0.8391 (pt0) cc_final: 0.8168 (pt0) REVERT: O 663 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8796 (pp) REVERT: E 33 ASN cc_start: 0.7943 (p0) cc_final: 0.7653 (p0) REVERT: E 95 MET cc_start: 0.8420 (ptm) cc_final: 0.7775 (ttp) REVERT: A 4 LEU cc_start: 0.6058 (tt) cc_final: 0.5764 (mp) REVERT: C 30 HIS cc_start: 0.3064 (OUTLIER) cc_final: 0.2496 (t70) REVERT: F 43 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8993 (mtmt) REVERT: F 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8179 (mppt) REVERT: J 100 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8234 (t80) REVERT: K 1 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: K 32 MET cc_start: 0.7907 (tpp) cc_final: 0.7541 (ttt) REVERT: K 98 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7620 (tm-30) REVERT: P 255 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8759 (m) REVERT: Q 16 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6906 (tm-30) REVERT: Q 30 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8517 (tpp80) REVERT: Q 32 ASN cc_start: 0.8150 (m-40) cc_final: 0.7726 (m-40) REVERT: Q 43 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8880 (mtpt) REVERT: S 100 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7974 (t80) REVERT: T 32 MET cc_start: 0.8414 (tpt) cc_final: 0.7591 (tpp) outliers start: 102 outliers final: 75 residues processed: 363 average time/residue: 0.4574 time to fit residues: 264.5859 Evaluate side-chains 351 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 80 MET Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 64 GLN Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 59 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN G 203 GLN P 33 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.107748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065699 restraints weight = 80777.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067735 restraints weight = 46915.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069041 restraints weight = 34756.862| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33159 Z= 0.140 Angle : 0.702 11.589 45372 Z= 0.336 Chirality : 0.046 0.281 5445 Planarity : 0.004 0.056 5490 Dihedral : 9.404 73.397 7341 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.81 % Allowed : 23.26 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.13), residues: 3801 helix: -1.36 (0.25), residues: 402 sheet: -1.04 (0.15), residues: 1215 loop : -1.82 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 36 HIS 0.005 0.001 HIS F 3 PHE 0.018 0.001 PHE q 100D TYR 0.029 0.001 TYR Q 100O ARG 0.010 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 57) link_NAG-ASN : angle 2.43873 ( 171) link_ALPHA1-6 : bond 0.00594 ( 12) link_ALPHA1-6 : angle 1.72990 ( 36) link_BETA1-4 : bond 0.00475 ( 69) link_BETA1-4 : angle 1.57266 ( 207) link_ALPHA1-2 : bond 0.00479 ( 3) link_ALPHA1-2 : angle 1.53869 ( 9) link_ALPHA1-3 : bond 0.01024 ( 15) link_ALPHA1-3 : angle 1.57440 ( 45) hydrogen bonds : bond 0.03061 ( 870) hydrogen bonds : angle 4.90293 ( 2214) SS BOND : bond 0.00267 ( 57) SS BOND : angle 1.50157 ( 114) covalent geometry : bond 0.00323 (32946) covalent geometry : angle 0.67378 (44790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 293 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.7832 (tpp) cc_final: 0.7499 (ttm) REVERT: G 482 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: H 32 PHE cc_start: 0.6932 (m-80) cc_final: 0.6605 (m-10) REVERT: m 30 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8481 (mmm-85) REVERT: m 43 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8915 (mtpt) REVERT: m 53 ASP cc_start: 0.8286 (p0) cc_final: 0.7962 (p0) REVERT: O 663 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (pp) REVERT: E 33 ASN cc_start: 0.7975 (p0) cc_final: 0.7683 (p0) REVERT: E 95 MET cc_start: 0.8411 (ptm) cc_final: 0.7752 (ttp) REVERT: C 30 HIS cc_start: 0.3019 (OUTLIER) cc_final: 0.2478 (t70) REVERT: F 43 LYS cc_start: 0.9287 (mmmm) cc_final: 0.8989 (mtmt) REVERT: F 103 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8255 (mppt) REVERT: J 99 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8183 (t0) REVERT: J 100 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8170 (t80) REVERT: K 1 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: K 98 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7632 (tm-30) REVERT: P 255 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (m) REVERT: Q 16 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6961 (tm-30) REVERT: Q 32 ASN cc_start: 0.8171 (m-40) cc_final: 0.7791 (m-40) REVERT: Q 43 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8923 (mtpt) REVERT: S 100 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8067 (t80) REVERT: T 32 MET cc_start: 0.8369 (tpt) cc_final: 0.7358 (tpp) outliers start: 94 outliers final: 77 residues processed: 369 average time/residue: 0.4406 time to fit residues: 261.3288 Evaluate side-chains 355 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 270 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 80 MET Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 64 GLN Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 271 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 376 optimal weight: 8.9990 chunk 204 optimal weight: 40.0000 chunk 295 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.106949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066264 restraints weight = 80746.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068355 restraints weight = 45565.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069677 restraints weight = 33235.529| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33159 Z= 0.145 Angle : 0.700 10.463 45372 Z= 0.335 Chirality : 0.045 0.279 5445 Planarity : 0.004 0.057 5490 Dihedral : 9.281 72.784 7341 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.75 % Allowed : 23.47 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.21 (0.13), residues: 3801 helix: -1.34 (0.25), residues: 402 sheet: -1.00 (0.15), residues: 1221 loop : -1.79 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 36 HIS 0.004 0.001 HIS F 3 PHE 0.019 0.001 PHE C 98 TYR 0.030 0.001 TYR Q 100O ARG 0.009 0.000 ARG F 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 57) link_NAG-ASN : angle 2.41494 ( 171) link_ALPHA1-6 : bond 0.00594 ( 12) link_ALPHA1-6 : angle 1.70790 ( 36) link_BETA1-4 : bond 0.00480 ( 69) link_BETA1-4 : angle 1.58688 ( 207) link_ALPHA1-2 : bond 0.00434 ( 3) link_ALPHA1-2 : angle 1.59365 ( 9) link_ALPHA1-3 : bond 0.00998 ( 15) link_ALPHA1-3 : angle 1.55894 ( 45) hydrogen bonds : bond 0.03017 ( 870) hydrogen bonds : angle 4.84608 ( 2214) SS BOND : bond 0.00270 ( 57) SS BOND : angle 1.44678 ( 114) covalent geometry : bond 0.00333 (32946) covalent geometry : angle 0.67226 (44790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 286 time to evaluate : 4.666 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: G 161 MET cc_start: 0.7804 (tpp) cc_final: 0.7446 (ttm) REVERT: G 482 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: H 32 PHE cc_start: 0.6831 (m-80) cc_final: 0.6475 (m-10) REVERT: m 30 ARG cc_start: 0.8766 (mtp-110) cc_final: 0.8240 (mmm160) REVERT: O 663 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (pp) REVERT: E 33 ASN cc_start: 0.7896 (p0) cc_final: 0.7607 (p0) REVERT: E 95 MET cc_start: 0.8389 (ptm) cc_final: 0.7734 (ttp) REVERT: E 302 ASN cc_start: 0.8464 (t0) cc_final: 0.8068 (t0) REVERT: C 30 HIS cc_start: 0.3087 (OUTLIER) cc_final: 0.2465 (t70) REVERT: F 13 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7889 (mmmt) REVERT: F 43 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8927 (mtmt) REVERT: F 103 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8247 (mppt) REVERT: J 99 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8111 (t0) REVERT: J 100 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8177 (t80) REVERT: K 98 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7616 (tm-30) REVERT: P 255 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8739 (m) REVERT: Q 16 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6893 (tm-30) REVERT: Q 30 ARG cc_start: 0.8514 (mmt-90) cc_final: 0.8292 (mmt180) REVERT: Q 32 ASN cc_start: 0.8139 (m-40) cc_final: 0.7697 (m-40) REVERT: Q 43 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8914 (mtpt) REVERT: Q 96 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8677 (mmmt) REVERT: R 25 GLU cc_start: 0.7515 (pt0) cc_final: 0.7254 (pt0) REVERT: S 100 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7880 (t80) REVERT: T 32 MET cc_start: 0.8194 (tpt) cc_final: 0.7193 (tpp) outliers start: 92 outliers final: 78 residues processed: 363 average time/residue: 0.4642 time to fit residues: 272.7857 Evaluate side-chains 356 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 271 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 80 MET Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 64 GLN Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 50.4276 > 50: distance: 5 - 8: 3.879 distance: 8 - 9: 7.177 distance: 9 - 10: 4.356 distance: 9 - 12: 4.417 distance: 10 - 11: 10.728 distance: 10 - 15: 8.465 distance: 12 - 13: 6.026 distance: 12 - 14: 8.932 distance: 16 - 17: 3.994 distance: 16 - 19: 8.501 distance: 17 - 18: 12.186 distance: 17 - 23: 6.645 distance: 19 - 20: 3.431 distance: 19 - 21: 7.836 distance: 20 - 22: 12.725 distance: 23 - 24: 19.313 distance: 24 - 25: 11.395 distance: 24 - 27: 22.426 distance: 25 - 26: 8.764 distance: 25 - 32: 11.209 distance: 27 - 28: 3.699 distance: 28 - 29: 10.662 distance: 29 - 30: 17.450 distance: 30 - 31: 15.304 distance: 32 - 33: 8.110 distance: 33 - 34: 14.287 distance: 33 - 36: 12.483 distance: 34 - 35: 20.298 distance: 34 - 39: 11.876 distance: 36 - 37: 16.947 distance: 36 - 38: 16.793 distance: 39 - 40: 5.033 distance: 39 - 45: 19.663 distance: 40 - 41: 8.403 distance: 40 - 43: 4.525 distance: 41 - 42: 4.354 distance: 41 - 46: 5.423 distance: 43 - 44: 19.505 distance: 44 - 45: 16.877 distance: 46 - 47: 17.712 distance: 47 - 48: 10.301 distance: 48 - 49: 13.431 distance: 50 - 51: 4.538 distance: 51 - 52: 3.545 distance: 51 - 54: 7.612 distance: 52 - 53: 11.247 distance: 52 - 56: 18.749 distance: 54 - 55: 13.266 distance: 57 - 58: 21.524 distance: 57 - 60: 7.408 distance: 58 - 59: 11.360 distance: 62 - 63: 11.642 distance: 62 - 106: 16.156 distance: 63 - 64: 14.047 distance: 63 - 66: 10.683 distance: 64 - 65: 14.651 distance: 64 - 69: 8.283 distance: 65 - 103: 16.442 distance: 66 - 67: 21.597 distance: 66 - 68: 31.337 distance: 69 - 70: 10.534 distance: 70 - 71: 17.886 distance: 70 - 73: 7.334 distance: 71 - 72: 33.850 distance: 71 - 78: 22.523 distance: 73 - 74: 12.684 distance: 74 - 75: 15.728 distance: 75 - 76: 18.049 distance: 76 - 77: 12.064