Starting phenix.real_space_refine on Sat Mar 23 23:06:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nc3_0434/03_2024/6nc3_0434.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.164 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 246 5.16 5 C 24492 2.51 5 N 6438 2.21 5 O 7728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38904 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "B" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "I" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "O" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "P" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "U" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "Q" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "V" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "R" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "W" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3387 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 3 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "S" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "X" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 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: "h" 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: 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: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 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: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: "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: 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: "1" 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: "2" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 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: "5" 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: "6" 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: "7" 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: "8" 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: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 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: "BA" 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: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 19.65, per 1000 atoms: 0.51 Number of scatterers: 38904 At special positions: 0 Unit cell: (161.71, 142.14, 231.75, 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 246 16.00 O 7728 8.00 N 6438 7.00 C 24492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.06 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.21 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.04 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 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.06 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.21 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.04 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 I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.06 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.21 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.06 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.06 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.21 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.06 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.06 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.21 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.06 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.06 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.21 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.06 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 7 3 " - " MAN 7 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " " BMA p 3 " - " MAN p 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 5 " " BMA 7 3 " - " MAN 7 5 " " BMA 9 3 " - " MAN 9 4 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 5 " " BMA f 3 " - " MAN f 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 5 " " BMA m 3 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 5 " " BMA t 3 " - " MAN t 5 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " 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 y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN F 88 " " NAG 1 1 " - " ASN F 197 " " NAG 2 1 " - " ASN F 241 " " NAG 3 1 " - " ASN F 262 " " NAG 4 1 " - " ASN F 276 " " NAG 5 1 " - " ASN F 332 " " NAG 6 1 " - " ASN F 448 " " NAG 7 1 " - " ASN G 88 " " NAG 8 1 " - " ASN G 197 " " NAG 9 1 " - " ASN G 241 " " NAG A 608 " - " ASN A 234 " " NAG A 620 " - " ASN A 295 " " NAG A 627 " - " ASN A 130 " " NAG C 608 " - " ASN C 234 " " NAG C 620 " - " ASN C 295 " " NAG C 627 " - " ASN C 130 " " NAG D 608 " - " ASN D 234 " " NAG D 620 " - " ASN D 295 " " NAG D 627 " - " ASN D 130 " " NAG E 608 " - " ASN E 234 " " NAG E 620 " - " ASN E 295 " " NAG E 627 " - " ASN E 130 " " NAG F 608 " - " ASN F 234 " " NAG F 620 " - " ASN F 295 " " NAG F 627 " - " ASN F 130 " " NAG G 608 " - " ASN G 234 " " NAG G 620 " - " ASN G 295 " " NAG G 627 " - " ASN G 130 " " NAG Y 1 " - " ASN A 88 " " NAG Z 1 " - " ASN A 197 " " NAG a 1 " - " ASN A 241 " " NAG b 1 " - " ASN A 262 " " NAG c 1 " - " ASN A 276 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN A 448 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 241 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 276 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN D 88 " " NAG n 1 " - " ASN D 197 " " NAG o 1 " - " ASN D 241 " " NAG p 1 " - " ASN D 262 " " NAG q 1 " - " ASN D 276 " " NAG r 1 " - " ASN D 332 " " NAG s 1 " - " ASN D 448 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 197 " " NAG v 1 " - " ASN E 241 " " NAG w 1 " - " ASN E 262 " " NAG x 1 " - " ASN E 276 " " NAG y 1 " - " ASN E 332 " " NAG z 1 " - " ASN E 448 " " NAGAA 1 " - " ASN G 262 " " NAGBA 1 " - " ASN G 276 " " NAGCA 1 " - " ASN G 332 " " NAGDA 1 " - " ASN G 448 " Time building additional restraints: 18.46 Conformation dependent library (CDL) restraints added in 7.1 seconds 9180 Ramachandran restraints generated. 4590 Oldfield, 0 Emsley, 4590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 78 sheets defined 23.7% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.186A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.898A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 570 through 597 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.016A pdb=" N ASN H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 97 through 100A Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.186A pdb=" N GLU C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.899A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 543 Processing helix chain 'I' and resid 570 through 597 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG I 633 " --> pdb=" O MET I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN I 637 " --> pdb=" O GLU I 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 634 through 637' Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 650 through 662 Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.015A pdb=" N ASN O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 97 through 100A Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.185A pdb=" N GLU D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.898A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 Processing helix chain 'J' and resid 570 through 597 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG J 633 " --> pdb=" O MET J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN J 637 " --> pdb=" O GLU J 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 634 through 637' Processing helix chain 'J' and resid 638 through 649 Processing helix chain 'J' and resid 650 through 662 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.016A pdb=" N ASN P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 97 through 100A Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 Processing helix chain 'E' and resid 334 through 354 removed outlier: 4.186A pdb=" N GLU E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.898A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 536 through 543 Processing helix chain 'K' and resid 570 through 597 Processing helix chain 'K' and resid 618 through 624 Processing helix chain 'K' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN K 637 " --> pdb=" O GLU K 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 634 through 637' Processing helix chain 'K' and resid 638 through 649 Processing helix chain 'K' and resid 650 through 662 Processing helix chain 'Q' and resid 28 through 32 removed outlier: 4.016A pdb=" N ASN Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'Q' and resid 97 through 100A Processing helix chain 'V' and resid 79 through 83 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 334 through 354 removed outlier: 4.186A pdb=" N GLU F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 388 through 392 Processing helix chain 'F' and resid 474 through 484 removed outlier: 3.899A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 534 Processing helix chain 'M' and resid 536 through 543 Processing helix chain 'M' and resid 570 through 597 Processing helix chain 'M' and resid 618 through 624 Processing helix chain 'M' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG M 633 " --> pdb=" O MET M 629 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN M 637 " --> pdb=" O GLU M 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 634 through 637' Processing helix chain 'M' and resid 638 through 649 Processing helix chain 'M' and resid 650 through 662 Processing helix chain 'R' and resid 28 through 32 removed outlier: 4.015A pdb=" N ASN R 32 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 73 through 75 No H-bonds generated for 'chain 'R' and resid 73 through 75' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'R' and resid 97 through 100A Processing helix chain 'W' and resid 79 through 83 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.580A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 Processing helix chain 'G' and resid 334 through 354 removed outlier: 4.185A pdb=" N GLU G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.898A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 536 through 543 Processing helix chain 'N' and resid 570 through 597 Processing helix chain 'N' and resid 618 through 624 Processing helix chain 'N' and resid 627 through 633 removed outlier: 4.279A pdb=" N ARG N 633 " --> pdb=" O MET N 629 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 637 removed outlier: 5.407A pdb=" N ASN N 637 " --> pdb=" O GLU N 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 634 through 637' Processing helix chain 'N' and resid 638 through 649 Processing helix chain 'N' and resid 650 through 662 Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.016A pdb=" N ASN S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 73 through 75 No H-bonds generated for 'chain 'S' and resid 73 through 75' Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'S' and resid 97 through 100A Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.170A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.314A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 215 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.363A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.757A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.757A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.643A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.171A pdb=" N VAL C 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.313A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 215 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 217 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C 249 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.364A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AC2, first strand: chain 'C' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN C 448 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N LYS C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.644A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.171A pdb=" N VAL D 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD2, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.313A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 215 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR D 217 " --> pdb=" O HIS D 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS D 249 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.363A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AD6, first strand: chain 'D' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN D 448 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N LYS D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.644A pdb=" N LEU U 33 " --> pdb=" O TYR U 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR U 49 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.170A pdb=" N VAL E 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.314A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 215 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR E 217 " --> pdb=" O HIS E 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS E 249 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AE8, first strand: chain 'E' and resid 120 through 121 removed outlier: 6.363A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 170 through 177 Processing sheet with id=AF1, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS E 296 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN E 448 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N LYS E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.757A pdb=" N GLU Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.757A pdb=" N GLU Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.643A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.171A pdb=" N VAL F 36 " --> pdb=" O THR M 606 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AG1, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.313A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE F 215 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR F 217 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS F 249 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AG3, first strand: chain 'F' and resid 120 through 121 removed outlier: 6.364A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 170 through 177 Processing sheet with id=AG5, first strand: chain 'F' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N CYS F 296 " --> pdb=" O GLN F 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN F 448 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N LYS F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'W' and resid 10 through 13 removed outlier: 6.644A pdb=" N LEU W 33 " --> pdb=" O TYR W 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR W 49 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.171A pdb=" N VAL G 36 " --> pdb=" O THR N 606 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AH5, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.313A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 215 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR G 217 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS G 249 " --> pdb=" O TYR G 217 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AH7, first strand: chain 'G' and resid 120 through 121 removed outlier: 6.363A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 170 through 177 Processing sheet with id=AH9, first strand: chain 'G' and resid 271 through 274 removed outlier: 4.141A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.453A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N GLN G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS G 296 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN G 448 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N LYS G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AI3, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.758A pdb=" N GLU S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'X' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.644A pdb=" N LEU X 33 " --> pdb=" O TYR X 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR X 49 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) 1530 hydrogen bonds defined for protein. 3924 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: 16.81 Time building geometry restraints manager: 19.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8440 1.32 - 1.46: 12702 1.46 - 1.59: 18194 1.59 - 1.73: 42 1.73 - 1.86: 324 Bond restraints: 39702 Sorted by residual: bond pdb=" NE1 TRP H 50 " pdb=" CE2 TRP H 50 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.62e+01 bond pdb=" NE1 TRP Q 50 " pdb=" CE2 TRP Q 50 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.62e+01 bond pdb=" NE1 TRP S 50 " pdb=" CE2 TRP S 50 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP P 50 " pdb=" CE2 TRP P 50 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP O 50 " pdb=" CE2 TRP O 50 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.60e+01 ... (remaining 39697 not shown) Histogram of bond angle deviations from ideal: 95.05 - 102.86: 384 102.86 - 110.67: 13824 110.67 - 118.48: 18352 118.48 - 126.29: 20714 126.29 - 134.10: 624 Bond angle restraints: 53898 Sorted by residual: angle pdb=" N PHE E 361 " pdb=" CA PHE E 361 " pdb=" C PHE E 361 " ideal model delta sigma weight residual 110.91 120.50 -9.59 1.17e+00 7.31e-01 6.71e+01 angle pdb=" N PHE A 361 " pdb=" CA PHE A 361 " pdb=" C PHE A 361 " ideal model delta sigma weight residual 110.91 120.50 -9.59 1.17e+00 7.31e-01 6.71e+01 angle pdb=" N PHE D 361 " pdb=" CA PHE D 361 " pdb=" C PHE D 361 " ideal model delta sigma weight residual 110.91 120.48 -9.57 1.17e+00 7.31e-01 6.69e+01 angle pdb=" N PHE G 361 " pdb=" CA PHE G 361 " pdb=" C PHE G 361 " ideal model delta sigma weight residual 110.91 120.48 -9.57 1.17e+00 7.31e-01 6.69e+01 angle pdb=" N PHE F 361 " pdb=" CA PHE F 361 " pdb=" C PHE F 361 " ideal model delta sigma weight residual 110.91 120.47 -9.56 1.17e+00 7.31e-01 6.68e+01 ... (remaining 53893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 24430 21.71 - 43.42: 802 43.42 - 65.13: 256 65.13 - 86.84: 168 86.84 - 108.55: 144 Dihedral angle restraints: 25800 sinusoidal: 12312 harmonic: 13488 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual 93.00 147.48 -54.48 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 74 " pdb=" CB CYS D 74 " ideal model delta sinusoidal sigma weight residual 93.00 147.48 -54.48 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual 93.00 147.48 -54.48 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 25797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 5952 0.179 - 0.358: 534 0.358 - 0.536: 42 0.536 - 0.715: 12 0.715 - 0.894: 6 Chirality restraints: 6546 Sorted by residual: chirality pdb=" C1 MAN t 5 " pdb=" O6 BMA t 3 " pdb=" C2 MAN t 5 " pdb=" O5 MAN t 5 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 2.00e+03 chirality pdb=" C1 MAN Y 5 " pdb=" O6 BMA Y 3 " pdb=" C2 MAN Y 5 " pdb=" O5 MAN Y 5 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 2.00e+03 chirality pdb=" C1 MAN 7 5 " pdb=" O6 BMA 7 3 " pdb=" C2 MAN 7 5 " pdb=" O5 MAN 7 5 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.99e+03 ... (remaining 6543 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 1 " 0.071 2.00e-02 2.50e+03 5.81e-02 4.22e+01 pdb=" C7 NAG q 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG q 1 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG q 1 " -0.091 2.00e-02 2.50e+03 pdb=" O7 NAG q 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAGBA 1 " -0.071 2.00e-02 2.50e+03 5.81e-02 4.22e+01 pdb=" C7 NAGBA 1 " 0.018 2.00e-02 2.50e+03 pdb=" C8 NAGBA 1 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAGBA 1 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAGBA 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 4 1 " -0.071 2.00e-02 2.50e+03 5.81e-02 4.21e+01 pdb=" C7 NAG 4 1 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG 4 1 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG 4 1 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG 4 1 " 0.015 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 15818 2.88 - 3.39: 35784 3.39 - 3.89: 68000 3.89 - 4.40: 79232 4.40 - 4.90: 125757 Nonbonded interactions: 324591 Sorted by model distance: nonbonded pdb=" N ASN A 197 " pdb=" OD1 ASN A 197 " model vdw 2.381 2.520 nonbonded pdb=" N ASN E 197 " pdb=" OD1 ASN E 197 " model vdw 2.381 2.520 nonbonded pdb=" N ASN G 197 " pdb=" OD1 ASN G 197 " model vdw 2.381 2.520 nonbonded pdb=" N ASN D 197 " pdb=" OD1 ASN D 197 " model vdw 2.381 2.520 nonbonded pdb=" N ASN F 197 " pdb=" OD1 ASN F 197 " model vdw 2.382 2.520 ... (remaining 324586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '7' selection = chain 'AA' selection = chain 'Y' selection = chain 'b' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'p' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '8' selection = chain 'BA' selection = chain 'Z' selection = chain 'c' selection = chain 'g' selection = chain 'j' selection = chain 'n' selection = chain 'q' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '9' selection = chain 'a' selection = chain 'h' selection = chain 'o' selection = chain 'v' } ncs_group { reference = chain '5' selection = chain '6' selection = chain 'CA' selection = chain 'DA' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'l' selection = chain 'r' selection = chain 's' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain '0' selection = chain '3' selection = chain '7' selection = chain 'AA' selection = chain 'Y' selection = chain 'b' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'p' selection = chain 't' selection = chain 'w' } pdb_interpretation.ncs_group { reference = chain '1' selection = chain '4' selection = chain '8' selection = chain 'BA' selection = chain 'Z' selection = chain 'c' selection = chain 'g' selection = chain 'j' selection = chain 'n' selection = chain 'q' selection = chain 'u' selection = chain 'x' } pdb_interpretation.ncs_group { reference = chain '2' selection = chain '9' selection = chain 'a' selection = chain 'h' selection = chain 'o' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain '5' selection = chain '6' selection = chain 'CA' selection = chain 'DA' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'l' selection = chain 'r' selection = chain 's' selection = chain 'y' selection = chain 'z' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. 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: 0.010 Normalize map: mean=0, sd=1: 2.260 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: 11.530 Check model and map are aligned: 0.550 Set scattering table: 0.370 Process input model: 102.190 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.880 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.020 0.131 39702 Z= 1.273 Angle : 1.830 16.736 53898 Z= 1.164 Chirality : 0.114 0.894 6546 Planarity : 0.009 0.058 6600 Dihedral : 16.387 108.547 16896 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % Rotamer: Outliers : 0.15 % Allowed : 1.62 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4590 helix: -0.55 (0.17), residues: 714 sheet: 0.50 (0.14), residues: 1296 loop : 0.12 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.012 TRP H 47 HIS 0.012 0.003 HIS G 363 PHE 0.049 0.006 PHE W 98 TYR 0.048 0.009 TYR A 384 ARG 0.006 0.001 ARG P 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9180 Ramachandran restraints generated. 4590 Oldfield, 0 Emsley, 4590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9180 Ramachandran restraints generated. 4590 Oldfield, 0 Emsley, 4590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0041 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0039 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 35 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 50 THR cc_start: 0.8837 (t) cc_final: 0.8546 (t) REVERT: A 104 MET cc_start: 0.9380 (mmm) cc_final: 0.8843 (mmp) REVERT: A 338 TRP cc_start: 0.9395 (t-100) cc_final: 0.8765 (t-100) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1390 time to fit residues: 6.5201 Evaluate side-chains 15 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.334 Evaluate side-chains 36 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9070 (mtp) cc_final: 0.8867 (mtm) REVERT: B 574 LYS cc_start: 0.9670 (mttt) cc_final: 0.9112 (tmtt) REVERT: B 589 ASP cc_start: 0.9150 (m-30) cc_final: 0.8704 (p0) REVERT: B 655 LYS cc_start: 0.9552 (mmtt) cc_final: 0.9080 (tttt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1704 time to fit residues: 6.5813 Evaluate side-chains 16 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.126 Evaluate side-chains 11 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.2656 time to fit residues: 3.1840 Evaluate side-chains 5 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.113 Evaluate side-chains 8 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.100 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.2460 time to fit residues: 2.1801 Evaluate side-chains 3 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 30.0000 chunk 341 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 116 optimal weight: 0.0270 chunk 230 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 overall best weight: 2.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 64 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 39702 Z= 0.297 Angle : 0.924 16.908 53898 Z= 0.486 Chirality : 0.057 0.576 6546 Planarity : 0.006 0.096 6600 Dihedral : 14.185 75.907 8280 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.18 % Favored : 95.42 % Rotamer: Outliers : 0.29 % Allowed : 1.62 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4590 helix: -0.11 (0.18), residues: 690 sheet: 0.17 (0.13), residues: 1380 loop : -0.49 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 610 HIS 0.008 0.002 HIS S 35 PHE 0.013 0.002 PHE V 98 TYR 0.019 0.002 TYR S 91 ARG 0.011 0.001 ARG P 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 23 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: F 100 MET cc_start: 0.9015 (mmp) cc_final: 0.8793 (mmp) REVERT: F 338 TRP cc_start: 0.9346 (t-100) cc_final: 0.8865 (t-100) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1306 time to fit residues: 4.4450 Evaluate side-chains 17 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.440 Evaluate side-chains 20 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.133 Fit side-chains REVERT: B 530 MET cc_start: 0.8759 (mtp) cc_final: 0.8525 (mtm) REVERT: B 535 MET cc_start: 0.9075 (mmp) cc_final: 0.8869 (mmm) REVERT: B 574 LYS cc_start: 0.9624 (mttt) cc_final: 0.9075 (tmtt) REVERT: B 589 ASP cc_start: 0.9058 (m-30) cc_final: 0.8461 (p0) REVERT: B 626 MET cc_start: 0.8257 (ttm) cc_final: 0.8053 (ttt) REVERT: B 648 ASP cc_start: 0.9056 (t0) cc_final: 0.8679 (t0) REVERT: B 655 LYS cc_start: 0.9520 (mmtt) cc_final: 0.8969 (tttt) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1307 time to fit residues: 2.9941 Evaluate side-chains 13 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.115 Evaluate side-chains 8 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 69 MET cc_start: 0.7280 (mtm) cc_final: 0.7003 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1311 time to fit residues: 1.2763 Evaluate side-chains 5 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.104 Evaluate side-chains 4 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1069 time to fit residues: 0.5916 Evaluate side-chains 3 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 328 optimal weight: 0.0770 overall best weight: 4.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39702 Z= 0.278 Angle : 0.813 17.074 53898 Z= 0.421 Chirality : 0.053 0.388 6546 Planarity : 0.005 0.080 6600 Dihedral : 11.441 64.783 8280 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.15 % Allowed : 3.52 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4590 helix: -0.72 (0.17), residues: 726 sheet: 0.09 (0.13), residues: 1398 loop : -0.70 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP I 610 HIS 0.014 0.003 HIS H 53 PHE 0.022 0.003 PHE K 519 TYR 0.025 0.002 TYR F 39 ARG 0.013 0.001 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0039 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 20 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: F 50 THR cc_start: 0.8752 (t) cc_final: 0.8520 (t) REVERT: F 95 MET cc_start: 0.8982 (ptp) cc_final: 0.8768 (ptp) REVERT: F 100 MET cc_start: 0.9052 (mmp) cc_final: 0.8593 (mmp) REVERT: F 112 TRP cc_start: 0.8867 (t60) cc_final: 0.7971 (t60) REVERT: F 434 MET cc_start: 0.8894 (tmm) cc_final: 0.8629 (tmm) REVERT: F 475 MET cc_start: 0.8514 (pmm) cc_final: 0.8124 (pmm) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1114 time to fit residues: 3.2215 Evaluate side-chains 16 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.441 Evaluate side-chains 18 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: I 530 MET cc_start: 0.8690 (mtp) cc_final: 0.8387 (mtm) REVERT: I 574 LYS cc_start: 0.9623 (mttt) cc_final: 0.9128 (tmtt) REVERT: I 589 ASP cc_start: 0.9115 (m-30) cc_final: 0.8890 (m-30) REVERT: I 648 ASP cc_start: 0.8941 (t0) cc_final: 0.8734 (t0) REVERT: I 655 LYS cc_start: 0.9535 (mmtt) cc_final: 0.9092 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1819 time to fit residues: 3.6528 Evaluate side-chains 13 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.118 Evaluate side-chains 6 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 69 MET cc_start: 0.7280 (mtm) cc_final: 0.6978 (mtt) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1623 time to fit residues: 1.1733 Evaluate side-chains 5 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.099 Evaluate side-chains 3 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1070 time to fit residues: 0.4785 Evaluate side-chains 2 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 212 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 434 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 389 optimal weight: 0.0030 chunk 117 optimal weight: 10.0000 overall best weight: 2.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39702 Z= 0.221 Angle : 0.706 6.623 53898 Z= 0.369 Chirality : 0.051 0.489 6546 Planarity : 0.005 0.054 6600 Dihedral : 8.717 55.537 8280 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.15 % Allowed : 1.91 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4590 helix: -0.49 (0.18), residues: 732 sheet: 0.11 (0.13), residues: 1362 loop : -0.94 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 610 HIS 0.006 0.002 HIS G 249 PHE 0.028 0.002 PHE T 98 TYR 0.036 0.003 TYR B 643 ARG 0.013 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0043 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0035 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 19 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.433 Fit side-chains REVERT: C 50 THR cc_start: 0.8677 (t) cc_final: 0.8414 (t) REVERT: C 100 MET cc_start: 0.9057 (mmp) cc_final: 0.8694 (mmp) REVERT: C 112 TRP cc_start: 0.8825 (t60) cc_final: 0.8394 (t60) REVERT: C 434 MET cc_start: 0.8932 (tmm) cc_final: 0.8595 (tmm) REVERT: C 475 MET cc_start: 0.8388 (pmm) cc_final: 0.8065 (pmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1195 time to fit residues: 3.4496 Evaluate side-chains 14 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.426 Evaluate side-chains 17 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: M 530 MET cc_start: 0.8658 (mtp) cc_final: 0.8311 (mtm) REVERT: M 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8686 (mmp) REVERT: M 574 LYS cc_start: 0.9618 (mttt) cc_final: 0.9134 (tmtt) REVERT: M 589 ASP cc_start: 0.9088 (m-30) cc_final: 0.8858 (m-30) REVERT: M 655 LYS cc_start: 0.9551 (mmtt) cc_final: 0.9119 (tttt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1818 time to fit residues: 3.4428 Evaluate side-chains 14 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.130 Evaluate side-chains 7 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 69 MET cc_start: 0.7425 (mtm) cc_final: 0.7004 (mtt) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1527 time to fit residues: 1.3038 Evaluate side-chains 5 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.146 Evaluate side-chains 4 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.099 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.1108 time to fit residues: 0.6207 Evaluate side-chains 2 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 371 optimal weight: 30.0000 chunk 300 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 222 optimal weight: 0.4980 chunk 390 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 overall best weight: 5.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 82 GLN G 448 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 39 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39702 Z= 0.256 Angle : 0.724 12.305 53898 Z= 0.373 Chirality : 0.080 2.097 6546 Planarity : 0.005 0.043 6600 Dihedral : 7.892 57.623 8280 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4590 helix: -0.73 (0.18), residues: 732 sheet: 0.05 (0.13), residues: 1326 loop : -1.14 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 610 HIS 0.020 0.003 HIS Q 35 PHE 0.024 0.003 PHE T 87 TYR 0.031 0.003 TYR N 643 ARG 0.012 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0037 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 17 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 50 THR cc_start: 0.8825 (t) cc_final: 0.8575 (t) REVERT: G 434 MET cc_start: 0.9119 (tmm) cc_final: 0.8208 (tmm) REVERT: G 475 MET cc_start: 0.8497 (pmm) cc_final: 0.8169 (pmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1219 time to fit residues: 3.1076 Evaluate side-chains 11 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.427 Evaluate side-chains 15 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 530 MET cc_start: 0.8637 (mtp) cc_final: 0.8325 (mtm) REVERT: I 535 MET cc_start: 0.9104 (mmp) cc_final: 0.8862 (mmm) REVERT: I 574 LYS cc_start: 0.9645 (mttt) cc_final: 0.9160 (tmtt) REVERT: I 589 ASP cc_start: 0.9104 (m-30) cc_final: 0.8883 (m-30) REVERT: I 655 LYS cc_start: 0.9531 (mmtt) cc_final: 0.9114 (tttt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1807 time to fit residues: 3.0296 Evaluate side-chains 13 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.108 Evaluate side-chains 6 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 69 MET cc_start: 0.7324 (mtm) cc_final: 0.6925 (mtt) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1375 time to fit residues: 0.9988 Evaluate side-chains 5 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.115 Evaluate side-chains 2 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.1083 time to fit residues: 0.3900 Evaluate side-chains 2 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2666 > 50: distance: 0 - 1: 25.805 distance: 0 - 67: 19.307 distance: 1 - 2: 31.206 distance: 1 - 4: 26.317 distance: 2 - 3: 17.745 distance: 2 - 7: 10.904 distance: 3 - 64: 16.408 distance: 4 - 5: 11.530 distance: 4 - 6: 55.772 distance: 7 - 8: 15.713 distance: 8 - 9: 9.574 distance: 8 - 11: 9.629 distance: 9 - 15: 5.800 distance: 11 - 12: 20.669 distance: 12 - 13: 29.883 distance: 12 - 14: 30.292 distance: 15 - 16: 5.312 distance: 16 - 19: 4.540 distance: 17 - 18: 6.642 distance: 17 - 23: 8.621 distance: 19 - 20: 5.330 distance: 20 - 21: 14.752 distance: 20 - 22: 8.816 distance: 23 - 24: 4.124 distance: 24 - 25: 8.567 distance: 24 - 27: 12.787 distance: 25 - 26: 10.035 distance: 27 - 28: 14.246 distance: 28 - 29: 14.790 distance: 29 - 30: 10.487 distance: 30 - 31: 9.038 distance: 31 - 32: 7.688 distance: 31 - 33: 16.471 distance: 34 - 35: 45.001 distance: 35 - 36: 15.984 distance: 36 - 37: 28.790 distance: 36 - 38: 19.943 distance: 38 - 39: 15.850 distance: 39 - 40: 19.898 distance: 39 - 42: 14.947 distance: 40 - 41: 9.745 distance: 40 - 47: 14.692 distance: 42 - 43: 9.779 distance: 43 - 44: 7.864 distance: 44 - 45: 6.354 distance: 44 - 46: 10.501 distance: 47 - 48: 22.055 distance: 48 - 49: 24.772 distance: 48 - 51: 21.426 distance: 49 - 50: 29.899 distance: 49 - 55: 29.736 distance: 51 - 52: 58.267 distance: 51 - 53: 37.450 distance: 52 - 54: 33.795 distance: 55 - 56: 20.160 distance: 56 - 57: 19.085 distance: 56 - 59: 17.279 distance: 57 - 58: 19.616 distance: 57 - 64: 11.221 distance: 59 - 60: 12.142 distance: 60 - 61: 10.679 distance: 61 - 62: 22.621 distance: 62 - 63: 18.280 distance: 64 - 65: 8.808 distance: 65 - 66: 5.428 distance: 65 - 68: 3.231 distance: 66 - 67: 11.657 distance: 66 - 72: 10.666 distance: 68 - 69: 4.086 distance: 69 - 70: 3.276 distance: 72 - 73: 6.768 distance: 73 - 74: 4.351 distance: 73 - 76: 4.903 distance: 74 - 75: 5.655 distance: 76 - 77: 4.803