Starting phenix.real_space_refine on Thu May 29 14:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.map" model { file = "/net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mph_9189/05_2025/6mph_9189.cif" } resolution = 3.8 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= 0.014 sd= 0.126 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 20157 2.51 5 N 5316 2.21 5 O 6454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32092 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "2" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "3" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "4" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "6" 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: "A" 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: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 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: "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: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} 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: "X" 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: "Y" 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: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "h" 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: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 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: "K" 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: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 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: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 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: "k" 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" 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: "n" 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: "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: "q" 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: "r" 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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: 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: 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "6" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 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: 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: 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 Time building chain proxies: 17.33, per 1000 atoms: 0.54 Number of scatterers: 32092 At special positions: 0 Unit cell: (157.94, 156.88, 152.64, 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 6454 8.00 N 5316 7.00 C 20157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 598 " - pdb=" SG CYS 6 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 605 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 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 103 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.03 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.03 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " distance=2.03 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 9 3 " - " MAN 9 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA j 3 " - " MAN j 5 " " BMA n 3 " - " MAN n 6 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 5 1 " - " NAG 5 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 9 2 " - " BMA 9 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 5 1 " - " ASN C 295 " " NAG 6 701 " - " ASN 6 637 " " NAG 8 1 " - " ASN C 363 " " NAG 9 1 " - " ASN C 386 " " NAG A 635 " - " ASN A 339 " " NAG A 647 " - " ASN A 88 " " NAG B 634 " - " ASN B 339 " " NAG B 646 " - " ASN B 88 " " NAG C 635 " - " ASN C 339 " " NAG C 647 " - " ASN C 88 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN B 332 " " NAG k 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 295 " " NAG q 1 " - " ASN B 363 " " NAG r 1 " - " ASN B 386 " " NAG s 1 " - " ASN B 392 " " NAG t 1 " - " ASN C 332 " " NAG x 1 " - " ASN C 160 " " NAGAA 1 " - " ASN C 392 " Time building additional restraints: 8.14 Conformation dependent library (CDL) restraints added in 3.2 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 14.5% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain '1' and resid 60 through 64 Processing helix chain '1' and resid 83 through 87 removed outlier: 3.527A pdb=" N THR 1 87 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 83 removed outlier: 3.513A pdb=" N ASP 2 82 " --> pdb=" O GLU 2 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 83 " --> pdb=" O ALA 2 80 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 79 through 83' Processing helix chain '3' and resid 60 through 64 Processing helix chain '3' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR 3 87 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 83 removed outlier: 3.532A pdb=" N ASP 4 82 " --> pdb=" O GLU 4 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 4 83 " --> pdb=" O ALA 4 80 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 79 through 83' Processing helix chain '6' and resid 529 through 534 Processing helix chain '6' and resid 537 through 543 Processing helix chain '6' and resid 570 through 595 removed outlier: 3.673A pdb=" N LYS 6 574 " --> pdb=" O VAL 6 570 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 616 removed outlier: 4.107A pdb=" N SER 6 615 " --> pdb=" O ASN 6 611 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 626 removed outlier: 3.537A pdb=" N ILE 6 622 " --> pdb=" O ASN 6 618 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP 6 623 " --> pdb=" O LEU 6 619 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP 6 624 " --> pdb=" O SER 6 620 " (cutoff:3.500A) Processing helix chain '6' and resid 627 through 635 Processing helix chain '6' and resid 641 through 664 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.690A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.537A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.807A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.680A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 4.184A pdb=" N HIS B 66 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.667A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.166A pdb=" N HIS C 66 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 67' Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.605A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.662A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.110A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.555A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.578A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.654A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.113A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.551A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.536A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.903A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.618A pdb=" N GLN Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.687A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.910A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.936A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'f' and resid 62 through 65 removed outlier: 3.624A pdb=" N GLN f 65 " --> pdb=" O ARG f 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 62 through 65' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.683A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 65 removed outlier: 3.662A pdb=" N GLN g 65 " --> pdb=" O ARG g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 65' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.623A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 11 through 12 removed outlier: 3.812A pdb=" N VAL 1 12 " --> pdb=" O THR 1 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP 1 34 " --> pdb=" O TYR 1 50 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR 1 50 " --> pdb=" O TRP 1 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP 1 36 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain '2' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain '2' and resid 45 through 49 removed outlier: 6.569A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY 2 84 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 2 104 " --> pdb=" O GLY 2 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain '3' and resid 11 through 12 removed outlier: 3.820A pdb=" N VAL 3 12 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP 3 34 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain '4' and resid 45 through 49 removed outlier: 6.558A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY 4 84 " --> pdb=" O VAL 4 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 603 through 609 removed outlier: 3.542A pdb=" N VAL A 38 " --> pdb=" O CYS 6 604 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR 6 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 36 " --> pdb=" O THR 6 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.817A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.759A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.927A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.021A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.149A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 38 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.799A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.761A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 6.950A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.042A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.133A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.803A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.945A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.014A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.749A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.589A pdb=" N VAL N 13 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'N' and resid 19 through 26 removed outlier: 4.135A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.589A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.610A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP R 34 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.738A pdb=" N THR X 95 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.766A pdb=" N THR Y 95 " --> pdb=" O TYR Y 33 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'Z' and resid 12 through 13 removed outlier: 3.579A pdb=" N VAL Z 13 " --> pdb=" O ILE Z 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Z' and resid 19 through 26 removed outlier: 4.067A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.610A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 12 through 13 removed outlier: 3.584A pdb=" N VAL a 13 " --> pdb=" O ILE a 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'a' and resid 19 through 26 removed outlier: 4.087A pdb=" N ALA a 71 " --> pdb=" O CYS a 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.601A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.564A pdb=" N ILE f 34 " --> pdb=" O TRP f 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP f 50 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP f 36 " --> pdb=" O ILE f 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY f 44 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AH8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.563A pdb=" N ILE g 34 " --> pdb=" O TRP g 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP g 50 " --> pdb=" O ILE g 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP g 36 " --> pdb=" O ILE g 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AI2, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP h 34 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AI5, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP i 34 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.46 Time building geometry restraints manager: 9.27 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: 9634 1.34 - 1.46: 7150 1.46 - 1.57: 15811 1.57 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 32812 Sorted by residual: bond pdb=" C1 NAG B 646 " pdb=" O5 NAG B 646 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG C 647 " pdb=" O5 NAG C 647 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 MAN t 4 " pdb=" C2 MAN t 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 MAN v 4 " pdb=" O5 MAN v 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 32807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 43908 3.04 - 6.08: 584 6.08 - 9.11: 121 9.11 - 12.15: 3 12.15 - 15.19: 3 Bond angle restraints: 44619 Sorted by residual: angle pdb=" C ASN A 332 " pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 122.11 128.03 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 131.49 -15.19 3.50e+00 8.16e-02 1.88e+01 angle pdb=" N PHE f 115 " pdb=" CA PHE f 115 " pdb=" C PHE f 115 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N PHE Q 115 " pdb=" CA PHE Q 115 " pdb=" C PHE Q 115 " ideal model delta sigma weight residual 109.81 119.27 -9.46 2.21e+00 2.05e-01 1.83e+01 angle pdb=" CA LEU B 494 " pdb=" CB LEU B 494 " pdb=" CG LEU B 494 " ideal model delta sigma weight residual 116.30 131.27 -14.97 3.50e+00 8.16e-02 1.83e+01 ... (remaining 44614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 19957 23.16 - 46.33: 942 46.33 - 69.49: 197 69.49 - 92.65: 209 92.65 - 115.81: 117 Dihedral angle restraints: 21422 sinusoidal: 10430 harmonic: 10992 Sorted by residual: dihedral pdb=" CA GLN L 50 " pdb=" C GLN L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -137.35 -42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN 4 50 " pdb=" C GLN 4 50 " pdb=" N VAL 4 51 " pdb=" CA VAL 4 51 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA GLN 2 50 " pdb=" C GLN 2 50 " pdb=" N VAL 2 51 " pdb=" CA VAL 2 51 " ideal model delta harmonic sigma weight residual -180.00 -137.76 -42.24 0 5.00e+00 4.00e-02 7.14e+01 ... (remaining 21419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5033 0.110 - 0.220: 295 0.220 - 0.330: 40 0.330 - 0.441: 0 0.441 - 0.551: 3 Chirality restraints: 5371 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.08e+01 chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN A 392 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 ... (remaining 5368 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 115 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO Q 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Q 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 116 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE g 115 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO g 116 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO g 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO g 116 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE f 115 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO f 116 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO f 116 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO f 116 " -0.041 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9327 2.81 - 3.33: 26640 3.33 - 3.85: 54080 3.85 - 4.38: 59156 4.38 - 4.90: 102943 Nonbonded interactions: 252146 Sorted by model distance: nonbonded pdb=" OG1 THR B 373 " pdb=" N HIS B 374 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR C 373 " pdb=" N HIS C 374 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR A 373 " pdb=" N HIS A 374 " model vdw 2.294 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP g 79 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP Q 79 " model vdw 2.314 3.040 ... (remaining 252141 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: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'n' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'd' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '8' selection = chain 'AA' selection = chain 'K' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'q' selection = chain 's' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '9' selection = chain 'F' selection = chain 'J' selection = chain 'W' selection = chain 'j' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'I' selection = chain 'c' selection = chain 'e' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } 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: 3.230 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: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 68.960 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.360 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 0.067 32997 Z= 0.320 Angle : 0.979 15.191 45120 Z= 0.466 Chirality : 0.059 0.551 5371 Planarity : 0.006 0.076 5463 Dihedral : 18.405 115.815 14222 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 6.01 % Allowed : 7.18 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.46 (0.11), residues: 3777 helix: -2.59 (0.18), residues: 429 sheet: -1.79 (0.13), residues: 1239 loop : -2.59 (0.11), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 96 HIS 0.008 0.001 HIS A 374 PHE 0.025 0.002 PHE C 288 TYR 0.016 0.002 TYR f 87 ARG 0.003 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 27) link_NAG-ASN : angle 4.21957 ( 81) link_ALPHA1-6 : bond 0.00293 ( 11) link_ALPHA1-6 : angle 1.76889 ( 33) link_BETA1-4 : bond 0.00822 ( 72) link_BETA1-4 : angle 3.78145 ( 216) link_ALPHA1-2 : bond 0.00316 ( 3) link_ALPHA1-2 : angle 1.64334 ( 9) link_ALPHA1-3 : bond 0.00508 ( 18) link_ALPHA1-3 : angle 1.64684 ( 54) hydrogen bonds : bond 0.12858 ( 1064) hydrogen bonds : angle 7.70509 ( 2817) SS BOND : bond 0.00398 ( 54) SS BOND : angle 1.23976 ( 108) covalent geometry : bond 0.00664 (32812) covalent geometry : angle 0.92611 (44619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 615 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 1 70 LEU cc_start: 0.9177 (mt) cc_final: 0.8877 (mp) REVERT: 1 94 ARG cc_start: 0.8316 (tmm160) cc_final: 0.7868 (ttp80) REVERT: 2 3 VAL cc_start: 0.9238 (t) cc_final: 0.9021 (p) REVERT: 3 94 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7496 (ttp80) REVERT: 4 3 VAL cc_start: 0.9281 (t) cc_final: 0.9040 (p) REVERT: 4 5 THR cc_start: 0.8265 (m) cc_final: 0.8022 (p) REVERT: 6 535 MET cc_start: 0.8557 (mmt) cc_final: 0.8334 (tpp) REVERT: 6 584 GLU cc_start: 0.8558 (tt0) cc_final: 0.8355 (tt0) REVERT: 6 601 LYS cc_start: 0.8698 (mttt) cc_final: 0.8393 (ttpp) REVERT: 6 657 GLU cc_start: 0.9312 (tt0) cc_final: 0.9027 (tm-30) REVERT: 6 659 ASP cc_start: 0.9201 (t0) cc_final: 0.8893 (m-30) REVERT: A 37 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 138 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 475 MET cc_start: 0.8890 (mmm) cc_final: 0.8668 (mmm) REVERT: A 494 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8837 (pt) REVERT: B 138 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 475 MET cc_start: 0.8937 (mmm) cc_final: 0.8706 (mmm) REVERT: C 138 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8236 (tp) REVERT: C 494 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8892 (pt) REVERT: D 543 ASN cc_start: 0.8952 (m-40) cc_final: 0.8721 (t0) REVERT: D 595 ILE cc_start: 0.9298 (pt) cc_final: 0.8796 (pt) REVERT: D 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9197 (mp) REVERT: D 633 LYS cc_start: 0.9579 (mttt) cc_final: 0.9372 (mtmm) REVERT: D 651 ASN cc_start: 0.9245 (t0) cc_final: 0.8917 (p0) REVERT: D 657 GLU cc_start: 0.9224 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 659 ASP cc_start: 0.9182 (t0) cc_final: 0.8954 (m-30) REVERT: E 601 LYS cc_start: 0.8743 (mttt) cc_final: 0.8413 (ttpp) REVERT: E 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.8942 (mt) REVERT: E 633 LYS cc_start: 0.9554 (mttt) cc_final: 0.9354 (mtmm) REVERT: E 638 TYR cc_start: 0.8507 (m-80) cc_final: 0.7995 (m-10) REVERT: E 659 ASP cc_start: 0.9245 (t0) cc_final: 0.8935 (m-30) REVERT: H 94 ARG cc_start: 0.8402 (tmm160) cc_final: 0.7727 (ttp80) REVERT: L 3 VAL cc_start: 0.9215 (t) cc_final: 0.8976 (p) REVERT: N 54 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8349 (ptt90) REVERT: N 62 PHE cc_start: 0.8457 (m-80) cc_final: 0.8241 (m-10) REVERT: N 67 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9042 (p) REVERT: R 10 ILE cc_start: 0.9511 (mt) cc_final: 0.9291 (mm) REVERT: X 82 VAL cc_start: 0.8783 (t) cc_final: 0.8366 (t) REVERT: Y 100 LYS cc_start: 0.9500 (mptt) cc_final: 0.9274 (mmmm) REVERT: Z 54 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8353 (ptm160) REVERT: Z 67 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9030 (p) REVERT: a 28 LEU cc_start: 0.9182 (mp) cc_final: 0.8903 (mp) REVERT: a 54 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.8253 (ptt90) REVERT: a 67 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8897 (p) REVERT: f 32 TYR cc_start: 0.9004 (m-80) cc_final: 0.8779 (m-10) REVERT: h 10 ILE cc_start: 0.9523 (mt) cc_final: 0.9299 (mm) REVERT: h 32 MET cc_start: 0.8551 (tpp) cc_final: 0.8053 (tpp) REVERT: h 50 ASP cc_start: 0.8858 (t0) cc_final: 0.8331 (t0) REVERT: h 51 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9344 (p) REVERT: h 70 ASP cc_start: 0.8929 (m-30) cc_final: 0.8418 (m-30) REVERT: h 104 LEU cc_start: 0.8666 (tp) cc_final: 0.8449 (mt) REVERT: i 32 MET cc_start: 0.8364 (tpp) cc_final: 0.7109 (tpp) REVERT: i 104 LEU cc_start: 0.8482 (tp) cc_final: 0.8149 (mt) outliers start: 200 outliers final: 45 residues processed: 797 average time/residue: 0.4998 time to fit residues: 597.7144 Evaluate side-chains 377 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 293 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 58 ASN 1 65 ASN 2 38 GLN ** 3 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 58 ASN 3 65 ASN 4 38 GLN 6 577 GLN 6 611 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 203 GLN A 287 GLN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 156 ASN B 203 GLN B 287 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 156 ASN C 203 GLN C 287 GLN D 575 GLN D 577 GLN D 611 ASN E 577 GLN E 611 ASN H 58 ASN H 65 ASN L 38 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN f 118 GLN g 6 GLN g 118 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.044160 restraints weight = 146987.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045729 restraints weight = 72263.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046726 restraints weight = 47885.153| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32997 Z= 0.185 Angle : 0.786 14.675 45120 Z= 0.373 Chirality : 0.048 0.404 5371 Planarity : 0.005 0.060 5463 Dihedral : 16.037 82.154 7364 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.49 % Allowed : 13.07 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.57 (0.12), residues: 3777 helix: -0.71 (0.24), residues: 399 sheet: -1.46 (0.14), residues: 1251 loop : -2.08 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 427 HIS 0.008 0.001 HIS M 3 PHE 0.019 0.002 PHE 6 519 TYR 0.019 0.002 TYR Z 49 ARG 0.010 0.001 ARG B 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 27) link_NAG-ASN : angle 3.38115 ( 81) link_ALPHA1-6 : bond 0.00319 ( 11) link_ALPHA1-6 : angle 1.81501 ( 33) link_BETA1-4 : bond 0.00543 ( 72) link_BETA1-4 : angle 2.85666 ( 216) link_ALPHA1-2 : bond 0.00428 ( 3) link_ALPHA1-2 : angle 1.57416 ( 9) link_ALPHA1-3 : bond 0.00992 ( 18) link_ALPHA1-3 : angle 2.40757 ( 54) hydrogen bonds : bond 0.03683 ( 1064) hydrogen bonds : angle 6.62321 ( 2817) SS BOND : bond 0.00433 ( 54) SS BOND : angle 0.93553 ( 108) covalent geometry : bond 0.00394 (32812) covalent geometry : angle 0.74315 (44619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 391 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 76 ASN cc_start: 0.9060 (t0) cc_final: 0.8786 (t0) REVERT: 1 94 ARG cc_start: 0.7974 (tmm160) cc_final: 0.7581 (ttp80) REVERT: 2 45 ARG cc_start: 0.8933 (tpm170) cc_final: 0.8555 (tpm170) REVERT: 3 76 ASN cc_start: 0.8952 (t0) cc_final: 0.8741 (t0) REVERT: 3 94 ARG cc_start: 0.7860 (tmm160) cc_final: 0.7650 (ttp80) REVERT: 4 24 ARG cc_start: 0.9077 (mtt90) cc_final: 0.8844 (mmt90) REVERT: 6 535 MET cc_start: 0.8705 (mmt) cc_final: 0.8469 (tpp) REVERT: 6 638 TYR cc_start: 0.8502 (m-10) cc_final: 0.8288 (m-10) REVERT: 6 659 ASP cc_start: 0.9230 (t0) cc_final: 0.8859 (m-30) REVERT: A 114 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8549 (tm-30) REVERT: B 125 LEU cc_start: 0.9660 (tp) cc_final: 0.9318 (tp) REVERT: B 475 MET cc_start: 0.8917 (mmm) cc_final: 0.8673 (mmm) REVERT: C 114 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8725 (tm-30) REVERT: C 195 ASN cc_start: 0.8845 (p0) cc_final: 0.8492 (p0) REVERT: D 601 LYS cc_start: 0.8805 (mttt) cc_final: 0.8506 (ttpp) REVERT: D 629 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9345 (mp) REVERT: D 651 ASN cc_start: 0.9396 (t0) cc_final: 0.8988 (p0) REVERT: D 659 ASP cc_start: 0.9189 (t0) cc_final: 0.8898 (m-30) REVERT: E 601 LYS cc_start: 0.8808 (mttt) cc_final: 0.8370 (ttpp) REVERT: E 629 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9097 (mt) REVERT: E 638 TYR cc_start: 0.8617 (m-80) cc_final: 0.8155 (m-10) REVERT: E 659 ASP cc_start: 0.9177 (t0) cc_final: 0.8892 (m-30) REVERT: H 94 ARG cc_start: 0.8046 (tmm160) cc_final: 0.7496 (ttp80) REVERT: M 23 ASN cc_start: 0.8899 (t0) cc_final: 0.8643 (t0) REVERT: M 100 MET cc_start: 0.8991 (mpp) cc_final: 0.8657 (mpp) REVERT: N 47 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8900 (mt) REVERT: N 54 ARG cc_start: 0.8640 (ptt-90) cc_final: 0.8290 (ptt90) REVERT: N 67 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9029 (p) REVERT: N 96 TRP cc_start: 0.8061 (m100) cc_final: 0.7583 (m100) REVERT: Q 3 GLN cc_start: 0.8219 (mm110) cc_final: 0.7983 (mp10) REVERT: Q 118 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8602 (tm-30) REVERT: R 70 ASP cc_start: 0.9025 (m-30) cc_final: 0.8800 (p0) REVERT: X 23 ASN cc_start: 0.8800 (t0) cc_final: 0.8528 (t0) REVERT: X 64 LYS cc_start: 0.9078 (tppt) cc_final: 0.8456 (tppt) REVERT: X 100 MET cc_start: 0.8959 (mpp) cc_final: 0.8296 (mmm) REVERT: Y 23 ASN cc_start: 0.8999 (t0) cc_final: 0.8695 (t0) REVERT: Y 53 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7358 (p0) REVERT: Z 67 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9028 (p) REVERT: Z 100 GLU cc_start: 0.8494 (pm20) cc_final: 0.8199 (pm20) REVERT: a 28 LEU cc_start: 0.9151 (mp) cc_final: 0.8882 (mp) REVERT: a 67 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9009 (p) REVERT: a 96 TRP cc_start: 0.7971 (m100) cc_final: 0.7600 (m100) REVERT: f 3 GLN cc_start: 0.8289 (mm110) cc_final: 0.8073 (mp10) REVERT: g 111 TYR cc_start: 0.8818 (m-80) cc_final: 0.8240 (m-80) REVERT: h 1 GLU cc_start: 0.7542 (pt0) cc_final: 0.7046 (mp0) REVERT: h 32 MET cc_start: 0.8432 (tpp) cc_final: 0.7929 (tpp) REVERT: h 70 ASP cc_start: 0.9144 (m-30) cc_final: 0.8893 (p0) REVERT: i 32 MET cc_start: 0.7982 (tpp) cc_final: 0.7553 (tpp) outliers start: 116 outliers final: 65 residues processed: 497 average time/residue: 0.4893 time to fit residues: 374.3254 Evaluate side-chains 383 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 311 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 63.5924 > 50: distance: 30 - 189: 24.442 distance: 31 - 187: 13.114 distance: 34 - 198: 21.051 distance: 147 - 193: 19.960 distance: 150 - 190: 25.518 distance: 173 - 175: 14.924 distance: 175 - 176: 8.908 distance: 176 - 177: 18.321 distance: 176 - 179: 11.745 distance: 177 - 178: 28.035 distance: 177 - 184: 6.834 distance: 179 - 180: 24.368 distance: 180 - 181: 32.086 distance: 181 - 182: 24.555 distance: 181 - 183: 21.615 distance: 184 - 185: 23.222 distance: 185 - 186: 8.595 distance: 185 - 188: 51.410 distance: 186 - 187: 34.538 distance: 186 - 190: 44.747 distance: 188 - 189: 45.031 distance: 190 - 191: 9.983 distance: 191 - 192: 46.943 distance: 191 - 194: 34.385 distance: 192 - 193: 39.901 distance: 192 - 198: 4.519 distance: 194 - 195: 45.844 distance: 195 - 196: 22.509 distance: 196 - 197: 22.043 distance: 198 - 199: 25.584 distance: 199 - 200: 44.078 distance: 199 - 202: 47.986 distance: 200 - 201: 42.364 distance: 200 - 210: 40.589 distance: 202 - 203: 14.597 distance: 203 - 204: 18.394 distance: 203 - 205: 17.061 distance: 204 - 206: 17.348 distance: 205 - 207: 22.451 distance: 206 - 208: 12.426 distance: 207 - 208: 7.233 distance: 208 - 209: 10.765 distance: 210 - 211: 26.694 distance: 211 - 212: 40.178 distance: 211 - 214: 12.850 distance: 212 - 213: 16.293 distance: 212 - 215: 20.882 distance: 215 - 216: 37.678 distance: 215 - 221: 34.013 distance: 216 - 217: 38.653 distance: 216 - 219: 55.681 distance: 217 - 218: 42.922 distance: 217 - 222: 47.116 distance: 219 - 220: 32.434 distance: 220 - 221: 41.741 distance: 222 - 223: 47.370 distance: 222 - 228: 41.108 distance: 223 - 224: 33.559 distance: 223 - 226: 44.562 distance: 224 - 225: 17.894 distance: 224 - 229: 27.215 distance: 226 - 227: 17.122 distance: 227 - 228: 36.311 distance: 229 - 230: 22.123 distance: 230 - 231: 8.936 distance: 230 - 233: 12.344 distance: 231 - 232: 5.491 distance: 231 - 237: 10.331 distance: 233 - 234: 6.662 distance: 233 - 235: 6.836 distance: 234 - 236: 10.592 distance: 237 - 238: 17.958 distance: 238 - 239: 16.279 distance: 238 - 241: 10.009 distance: 239 - 240: 22.182 distance: 239 - 246: 18.852 distance: 241 - 242: 13.951 distance: 242 - 243: 10.172 distance: 243 - 244: 3.026 distance: 246 - 247: 33.986 distance: 247 - 248: 36.720 distance: 248 - 249: 34.549 distance: 248 - 250: 27.242