Starting phenix.real_space_refine on Tue Aug 26 17:01:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_0434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_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/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_0434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_0434.map" model { file = "/net/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_0434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nc3_0434/08_2025/6nc3_0434.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 10.66, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " 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: 3.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.04 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: 12.05 Time building geometry restraints manager: 4.93 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: 0.00 - 3.35: 49970 3.35 - 6.69: 3670 6.69 - 10.04: 242 10.04 - 13.39: 4 13.39 - 16.74: 12 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 3.120 nonbonded pdb=" N ASN E 197 " pdb=" OD1 ASN E 197 " model vdw 2.381 3.120 nonbonded pdb=" N ASN G 197 " pdb=" OD1 ASN G 197 " model vdw 2.381 3.120 nonbonded pdb=" N ASN D 197 " pdb=" OD1 ASN D 197 " model vdw 2.381 3.120 nonbonded pdb=" N ASN F 197 " pdb=" OD1 ASN F 197 " model vdw 2.382 3.120 ... (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 Time spend for trying shortcut: 0.13 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: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.220 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- 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 0.331 39936 Z= 1.084 Angle : 1.897 37.537 54528 Z= 1.172 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG P 38 TYR 0.048 0.009 TYR A 384 PHE 0.049 0.006 PHE W 98 TRP 0.071 0.012 TRP H 47 HIS 0.012 0.003 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.01973 (39702) covalent geometry : angle 1.82971 (53898) SS BOND : bond 0.05338 ( 72) SS BOND : angle 2.75832 ( 144) hydrogen bonds : bond 0.17343 ( 1494) hydrogen bonds : angle 8.43771 ( 3924) link_ALPHA1-3 : bond 0.02938 ( 12) link_ALPHA1-3 : angle 2.25068 ( 36) link_ALPHA1-6 : bond 0.19254 ( 18) link_ALPHA1-6 : angle 13.97574 ( 54) link_BETA1-4 : bond 0.03995 ( 72) link_BETA1-4 : angle 3.61722 ( 216) link_NAG-ASN : bond 0.03028 ( 60) link_NAG-ASN : angle 2.54870 ( 180) *********************** 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 to be fit. 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: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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 to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 THR cc_start: 0.8837 (t) cc_final: 0.8560 (t) REVERT: A 104 MET cc_start: 0.9380 (mmm) cc_final: 0.8839 (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: 0.0571 time to fit residues: 2.7015 Evaluate side-chains 16 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.140 Evaluate side-chains 36 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.040 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: 0.0887 time to fit residues: 3.4087 Evaluate side-chains 16 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.041 Evaluate side-chains 11 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1304 time to fit residues: 1.5365 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.038 Evaluate side-chains 8 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.036 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1202 time to fit residues: 1.0397 Evaluate side-chains 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.0570 overall best weight: 0.1478 ------------------------------------------------------------------------------- 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... 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050482 restraints weight = 664.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050787 restraints weight = 208.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050941 restraints weight = 108.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050944 restraints weight = 71.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050956 restraints weight = 70.903| |-----------------------------------------------------------------------------| r_work (final): 0.2832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.038598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.038409 restraints weight = 255.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.038586 restraints weight = 32.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.038592 restraints weight = 2.848 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.038594 restraints weight = 0.787 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.038588 restraints weight = 0.209 | |-----------------------------------------------------------------------------| r_work (final): 0.2339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.028997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.028007 restraints weight = 785.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.028326 restraints weight = 220.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.028539 restraints weight = 110.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.028670 restraints weight = 65.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.028670 restraints weight = 41.318| |-----------------------------------------------------------------------------| r_work (final): 0.2388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054729 restraints weight = 501.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055981 restraints weight = 285.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056904 restraints weight = 177.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057487 restraints weight = 128.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.057939 restraints weight = 96.517| |-----------------------------------------------------------------------------| r_work (final): 0.3251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.040110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033227 restraints weight = 36243.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034254 restraints weight = 22666.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034979 restraints weight = 16011.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035516 restraints weight = 12323.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035917 restraints weight = 9999.883| |-----------------------------------------------------------------------------| r_work (final): 0.3042 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036518 restraints weight = 11670.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.037380 restraints weight = 7107.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.037946 restraints weight = 4809.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038424 restraints weight = 3566.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038747 restraints weight = 2756.939| |-----------------------------------------------------------------------------| r_work (final): 0.2953 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.042377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036249 restraints weight = 10143.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.037266 restraints weight = 6582.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.037966 restraints weight = 4753.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.038510 restraints weight = 3709.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.038767 restraints weight = 3060.599| |-----------------------------------------------------------------------------| r_work (final): 0.3262 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.045977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.038611 restraints weight = 9204.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.039691 restraints weight = 6698.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.040550 restraints weight = 5203.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.041139 restraints weight = 4244.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.041635 restraints weight = 3595.037| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 39936 Z= 0.230 Angle : 1.030 20.427 54528 Z= 0.506 Chirality : 0.058 0.633 6546 Planarity : 0.006 0.091 6600 Dihedral : 13.814 74.506 8280 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.05 % Favored : 95.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.12), residues: 4590 helix: -0.14 (0.18), residues: 690 sheet: 0.01 (0.13), residues: 1416 loop : -0.51 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 585 TYR 0.019 0.003 TYR N 643 PHE 0.014 0.002 PHE T 83 TRP 0.051 0.004 TRP K 610 HIS 0.008 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00500 (39702) covalent geometry : angle 0.95292 (53898) SS BOND : bond 0.00505 ( 72) SS BOND : angle 0.99341 ( 144) hydrogen bonds : bond 0.07361 ( 1494) hydrogen bonds : angle 7.36936 ( 3924) link_ALPHA1-3 : bond 0.00261 ( 12) link_ALPHA1-3 : angle 5.62424 ( 36) link_ALPHA1-6 : bond 0.01301 ( 18) link_ALPHA1-6 : angle 1.46029 ( 54) link_BETA1-4 : bond 0.01011 ( 72) link_BETA1-4 : angle 3.50310 ( 216) link_NAG-ASN : bond 0.01830 ( 60) link_NAG-ASN : angle 5.18615 ( 180) *********************** 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 to be fit. 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: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 25 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: F 45 TRP cc_start: 0.8868 (p90) cc_final: 0.8615 (p90) REVERT: F 50 THR cc_start: 0.8442 (t) cc_final: 0.8161 (t) REVERT: F 95 MET cc_start: 0.9024 (ptp) cc_final: 0.8766 (ptp) REVERT: F 100 MET cc_start: 0.9086 (mmp) cc_final: 0.8776 (mmp) REVERT: F 108 ILE cc_start: 0.9676 (mm) cc_final: 0.9403 (tp) REVERT: F 338 TRP cc_start: 0.9368 (t-100) cc_final: 0.8876 (t-100) REVERT: F 475 MET cc_start: 0.7931 (ppp) cc_final: 0.7516 (pmm) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0572 time to fit residues: 1.9994 Evaluate side-chains 19 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.139 Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8559 (mtp) cc_final: 0.8300 (mtm) REVERT: B 535 MET cc_start: 0.8933 (mmp) cc_final: 0.8679 (mmm) REVERT: B 574 LYS cc_start: 0.9589 (mttt) cc_final: 0.9048 (tmtt) REVERT: B 589 ASP cc_start: 0.9113 (m-30) cc_final: 0.8475 (p0) REVERT: B 648 ASP cc_start: 0.9382 (t0) cc_final: 0.9006 (t0) REVERT: B 655 LYS cc_start: 0.9557 (mmtt) cc_final: 0.9034 (tttt) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0726 time to fit residues: 1.6819 Evaluate side-chains 14 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.041 Evaluate side-chains 8 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 69 MET cc_start: 0.6480 (mtm) cc_final: 0.6125 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0582 time to fit residues: 0.5568 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.038 Evaluate side-chains 4 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.034 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0484 time to fit residues: 0.2610 Evaluate side-chains 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 340 optimal weight: 8.9990 chunk 199 optimal weight: 0.0170 chunk 79 optimal weight: 30.0000 chunk 358 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 414 optimal weight: 0.0060 chunk 71 optimal weight: 0.0010 chunk 24 optimal weight: 7.9990 chunk 448 optimal weight: 20.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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: ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: W 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.048754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.046821 restraints weight = 678.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.047322 restraints weight = 407.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047605 restraints weight = 278.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047781 restraints weight = 206.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047889 restraints weight = 166.873| |-----------------------------------------------------------------------------| r_work (final): 0.2771 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.055305 restraints weight = 166.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055908 restraints weight = 30.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.056088 restraints weight = 9.949 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056140 restraints weight = 3.342 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056177 restraints weight = 1.394 | |-----------------------------------------------------------------------------| r_work (final): 0.2905 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.027828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.026953 restraints weight = 921.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.027332 restraints weight = 234.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.027496 restraints weight = 108.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.027602 restraints weight = 58.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.027685 restraints weight = 33.564| |-----------------------------------------------------------------------------| r_work (final): 0.2301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054960 restraints weight = 431.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055796 restraints weight = 208.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056476 restraints weight = 129.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056824 restraints weight = 87.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.057092 restraints weight = 65.557| |-----------------------------------------------------------------------------| r_work (final): 0.3141 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.033027 restraints weight = 36934.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.033981 restraints weight = 23548.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034682 restraints weight = 16922.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035193 restraints weight = 13091.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.035583 restraints weight = 10692.256| |-----------------------------------------------------------------------------| r_work (final): 0.3036 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.043851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039310 restraints weight = 11689.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.040166 restraints weight = 6947.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040817 restraints weight = 4705.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041243 restraints weight = 3433.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041480 restraints weight = 2664.321| |-----------------------------------------------------------------------------| r_work (final): 0.3019 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.042918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.034841 restraints weight = 12048.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.035580 restraints weight = 9097.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.036219 restraints weight = 7351.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036616 restraints weight = 6147.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.037065 restraints weight = 5334.278| |-----------------------------------------------------------------------------| r_work (final): 0.3200 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.044359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.037546 restraints weight = 9996.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.038509 restraints weight = 7425.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.039358 restraints weight = 5798.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.039858 restraints weight = 4673.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.040505 restraints weight = 3977.934| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39936 Z= 0.184 Angle : 0.896 20.003 54528 Z= 0.436 Chirality : 0.053 0.424 6546 Planarity : 0.005 0.075 6600 Dihedral : 10.885 60.067 8280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.29 % Allowed : 3.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.12), residues: 4590 helix: -0.56 (0.18), residues: 726 sheet: 0.09 (0.13), residues: 1392 loop : -0.75 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 135 TYR 0.039 0.003 TYR B 643 PHE 0.046 0.003 PHE N 519 TRP 0.046 0.004 TRP B 610 HIS 0.006 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00383 (39702) covalent geometry : angle 0.82625 (53898) SS BOND : bond 0.00422 ( 72) SS BOND : angle 0.69026 ( 144) hydrogen bonds : bond 0.06412 ( 1494) hydrogen bonds : angle 6.97253 ( 3924) link_ALPHA1-3 : bond 0.00277 ( 12) link_ALPHA1-3 : angle 5.32591 ( 36) link_ALPHA1-6 : bond 0.01112 ( 18) link_ALPHA1-6 : angle 1.40793 ( 54) link_BETA1-4 : bond 0.00820 ( 72) link_BETA1-4 : angle 3.03735 ( 216) link_NAG-ASN : bond 0.01255 ( 60) link_NAG-ASN : angle 4.61084 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 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 to be fit. 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: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 23 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 50 THR cc_start: 0.8307 (t) cc_final: 0.8022 (t) REVERT: F 112 TRP cc_start: 0.8794 (t60) cc_final: 0.7861 (t60) REVERT: F 338 TRP cc_start: 0.9351 (t-100) cc_final: 0.8926 (t-100) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0488 time to fit residues: 1.5991 Evaluate side-chains 17 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.158 Evaluate side-chains 20 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8486 (mtp) cc_final: 0.8167 (mtm) REVERT: M 574 LYS cc_start: 0.9597 (mttt) cc_final: 0.9110 (tmtt) REVERT: M 629 MET cc_start: 0.7481 (mmt) cc_final: 0.7246 (tpp) REVERT: M 648 ASP cc_start: 0.9266 (t0) cc_final: 0.9038 (t0) REVERT: M 655 LYS cc_start: 0.9606 (mmtt) cc_final: 0.9150 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0971 time to fit residues: 2.0894 Evaluate side-chains 14 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.042 Evaluate side-chains 6 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0707 time to fit residues: 0.5090 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.034 Evaluate side-chains 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0415 time to fit residues: 0.1838 Evaluate side-chains 2 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 247 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 374 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 283 optimal weight: 0.0470 chunk 372 optimal weight: 0.0470 chunk 130 optimal weight: 30.0000 chunk 381 optimal weight: 0.9990 chunk 98 optimal weight: 0.0770 chunk 97 optimal weight: 7.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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: ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.049180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047484 restraints weight = 734.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047945 restraints weight = 330.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048227 restraints weight = 203.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048406 restraints weight = 136.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048527 restraints weight = 100.961| |-----------------------------------------------------------------------------| r_work (final): 0.2759 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.051930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.051614 restraints weight = 255.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051812 restraints weight = 25.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051879 restraints weight = 6.681 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051878 restraints weight = 1.830 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051878 restraints weight = 0.572 | |-----------------------------------------------------------------------------| r_work (final): 0.2928 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.031702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.031172 restraints weight = 769.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.031334 restraints weight = 147.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.031519 restraints weight = 70.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.031594 restraints weight = 31.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.031631 restraints weight = 18.849| |-----------------------------------------------------------------------------| r_work (final): 0.2359 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.051695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046587 restraints weight = 547.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046983 restraints weight = 345.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047399 restraints weight = 274.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047399 restraints weight = 232.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047399 restraints weight = 232.927| |-----------------------------------------------------------------------------| r_work (final): 0.2874 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.033003 restraints weight = 37067.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033945 restraints weight = 23507.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034609 restraints weight = 16741.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035127 restraints weight = 12995.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035495 restraints weight = 10592.194| |-----------------------------------------------------------------------------| r_work (final): 0.3025 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.042723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038103 restraints weight = 12115.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038980 restraints weight = 7081.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.039596 restraints weight = 4718.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.040027 restraints weight = 3394.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040347 restraints weight = 2633.925| |-----------------------------------------------------------------------------| r_work (final): 0.2990 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.042256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.035664 restraints weight = 10120.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036602 restraints weight = 7123.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.037333 restraints weight = 5408.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.037876 restraints weight = 4313.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.038329 restraints weight = 3585.646| |-----------------------------------------------------------------------------| r_work (final): 0.3276 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.044391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.037335 restraints weight = 10018.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.038360 restraints weight = 7552.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.039212 restraints weight = 5954.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.039901 restraints weight = 4830.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.040502 restraints weight = 4023.908| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39936 Z= 0.164 Angle : 0.826 12.251 54528 Z= 0.400 Chirality : 0.052 0.371 6546 Planarity : 0.005 0.049 6600 Dihedral : 8.516 52.146 8280 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.12), residues: 4590 helix: -0.39 (0.18), residues: 744 sheet: 0.06 (0.14), residues: 1332 loop : -0.86 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 135 TYR 0.034 0.003 TYR F 61 PHE 0.029 0.002 PHE X 98 TRP 0.030 0.003 TRP K 610 HIS 0.010 0.002 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00347 (39702) covalent geometry : angle 0.76130 (53898) SS BOND : bond 0.01308 ( 72) SS BOND : angle 1.19049 ( 144) hydrogen bonds : bond 0.05674 ( 1494) hydrogen bonds : angle 6.76106 ( 3924) link_ALPHA1-3 : bond 0.00358 ( 12) link_ALPHA1-3 : angle 4.83379 ( 36) link_ALPHA1-6 : bond 0.01001 ( 18) link_ALPHA1-6 : angle 1.46908 ( 54) link_BETA1-4 : bond 0.00767 ( 72) link_BETA1-4 : angle 2.87976 ( 216) link_NAG-ASN : bond 0.01044 ( 60) link_NAG-ASN : angle 4.06970 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 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 to be fit. 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: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 22 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8417 (t) cc_final: 0.8047 (t) REVERT: C 104 MET cc_start: 0.9116 (mmp) cc_final: 0.8827 (mmp) REVERT: C 112 TRP cc_start: 0.8741 (t60) cc_final: 0.8148 (t60) REVERT: C 338 TRP cc_start: 0.9368 (t-100) cc_final: 0.8973 (t-100) REVERT: C 434 MET cc_start: 0.9076 (tmm) cc_final: 0.8606 (tmm) REVERT: C 475 MET cc_start: 0.8718 (pmm) cc_final: 0.8377 (pmm) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.0507 time to fit residues: 1.6464 Evaluate side-chains 16 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.149 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 530 MET cc_start: 0.8384 (mtp) cc_final: 0.8044 (mtm) REVERT: I 535 MET cc_start: 0.8892 (mmp) cc_final: 0.8610 (mmp) REVERT: I 574 LYS cc_start: 0.9604 (mttt) cc_final: 0.9128 (tmtt) REVERT: I 647 GLU cc_start: 0.8867 (pp20) cc_final: 0.8566 (pp20) REVERT: I 648 ASP cc_start: 0.9066 (t0) cc_final: 0.8476 (p0) REVERT: I 655 LYS cc_start: 0.9606 (mmtt) cc_final: 0.9166 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0757 time to fit residues: 1.5018 Evaluate side-chains 15 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.049 Evaluate side-chains 7 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0669 time to fit residues: 0.5622 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.041 Evaluate side-chains 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0486 time to fit residues: 0.2170 Evaluate side-chains 2 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 435 optimal weight: 0.0570 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 264 optimal weight: 0.2980 chunk 422 optimal weight: 7.9990 chunk 30 optimal weight: 0.0370 chunk 280 optimal weight: 40.0000 chunk 352 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.0780 ------------------------------------------------------------------------------- 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: E 448 ASN 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: ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: W 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049444 restraints weight = 760.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049983 restraints weight = 342.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.050293 restraints weight = 210.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.050499 restraints weight = 152.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.050630 restraints weight = 116.184| |-----------------------------------------------------------------------------| r_work (final): 0.2824 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053747 restraints weight = 193.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053873 restraints weight = 8.398 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 5)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053875 restraints weight = 0.790 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 4)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053877 restraints weight = 0.086 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 4)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053875 restraints weight = 0.009 | |-----------------------------------------------------------------------------| r_work (final): 0.2948 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.027091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2215 r_free = 0.2215 target = 0.026459 restraints weight = 969.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.026747 restraints weight = 239.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2215 r_free = 0.2215 target = 0.026877 restraints weight = 103.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.026966 restraints weight = 51.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.027015 restraints weight = 27.566| |-----------------------------------------------------------------------------| r_work (final): 0.2220 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046142 restraints weight = 620.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.046613 restraints weight = 340.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047053 restraints weight = 258.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047052 restraints weight = 226.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047052 restraints weight = 226.031| |-----------------------------------------------------------------------------| r_work (final): 0.2831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.037555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031167 restraints weight = 39715.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.032090 restraints weight = 24648.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032741 restraints weight = 17333.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033226 restraints weight = 13237.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033584 restraints weight = 10789.808| |-----------------------------------------------------------------------------| r_work (final): 0.2981 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.042023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037655 restraints weight = 12096.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038507 restraints weight = 6960.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.039109 restraints weight = 4577.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039543 restraints weight = 3295.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039760 restraints weight = 2539.311| |-----------------------------------------------------------------------------| r_work (final): 0.2975 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.042919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.034764 restraints weight = 11862.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035551 restraints weight = 8977.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.036167 restraints weight = 7230.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036560 restraints weight = 6077.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.036915 restraints weight = 5348.935| |-----------------------------------------------------------------------------| r_work (final): 0.3469 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.044728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.037685 restraints weight = 9735.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.038686 restraints weight = 7369.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.039609 restraints weight = 5840.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.040292 restraints weight = 4634.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.040812 restraints weight = 3835.218| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.379 39936 Z= 0.859 Angle : 1.157 60.032 54528 Z= 0.476 Chirality : 0.084 2.280 6546 Planarity : 0.004 0.041 6600 Dihedral : 7.561 53.839 8280 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.12), residues: 4590 helix: -0.52 (0.18), residues: 732 sheet: 0.07 (0.14), residues: 1272 loop : -1.10 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 135 TYR 0.036 0.002 TYR N 643 PHE 0.028 0.002 PHE L 98 TRP 0.026 0.003 TRP M 610 HIS 0.008 0.002 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00327 (39702) covalent geometry : angle 0.71406 (53898) SS BOND : bond 0.00378 ( 72) SS BOND : angle 0.71165 ( 144) hydrogen bonds : bond 0.05265 ( 1494) hydrogen bonds : angle 6.60433 ( 3924) link_ALPHA1-3 : bond 0.00396 ( 12) link_ALPHA1-3 : angle 4.12585 ( 36) link_ALPHA1-6 : bond 0.00801 ( 18) link_ALPHA1-6 : angle 1.43560 ( 54) link_BETA1-4 : bond 0.00754 ( 72) link_BETA1-4 : angle 2.83407 ( 216) link_NAG-ASN : bond 0.43609 ( 60) link_NAG-ASN : angle 15.45475 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 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 to be fit. 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: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 18 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 50 THR cc_start: 0.8584 (t) cc_final: 0.8278 (t) REVERT: E 338 TRP cc_start: 0.9379 (t-100) cc_final: 0.9070 (t-100) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0456 time to fit residues: 1.2207 Evaluate side-chains 13 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.113 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8358 (mtp) cc_final: 0.8004 (mtm) REVERT: M 535 MET cc_start: 0.8910 (mmp) cc_final: 0.8532 (mmp) REVERT: M 574 LYS cc_start: 0.9609 (mttt) cc_final: 0.9135 (tmtt) REVERT: M 589 ASP cc_start: 0.9226 (m-30) cc_final: 0.9004 (m-30) REVERT: M 647 GLU cc_start: 0.8814 (pp20) cc_final: 0.8563 (pp20) REVERT: M 648 ASP cc_start: 0.8922 (t0) cc_final: 0.8413 (p0) REVERT: M 655 LYS cc_start: 0.9611 (mmtt) cc_final: 0.9168 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0751 time to fit residues: 1.4949 Evaluate side-chains 16 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.042 Evaluate side-chains 6 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0693 time to fit residues: 0.4981 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.032 Evaluate side-chains 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0342 time to fit residues: 0.1422 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 139 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 346 optimal weight: 0.9990 chunk 76 optimal weight: 40.0000 chunk 425 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 227 optimal weight: 30.0000 chunk 378 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: E 229 ASN 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: ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.049243 restraints weight = 738.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049815 restraints weight = 368.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050135 restraints weight = 232.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050369 restraints weight = 166.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050535 restraints weight = 126.813| |-----------------------------------------------------------------------------| r_work (final): 0.2850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053979 restraints weight = 197.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054487 restraints weight = 33.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054904 restraints weight = 12.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055033 restraints weight = 4.705 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055090 restraints weight = 2.166 | |-----------------------------------------------------------------------------| r_work (final): 0.2970 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.033035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.032510 restraints weight = 763.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.032783 restraints weight = 146.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.032921 restraints weight = 58.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.032972 restraints weight = 27.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.033008 restraints weight = 13.964| |-----------------------------------------------------------------------------| r_work (final): 0.2524 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045577 restraints weight = 295.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047156 restraints weight = 125.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047840 restraints weight = 58.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048281 restraints weight = 37.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.048488 restraints weight = 24.943| |-----------------------------------------------------------------------------| r_work (final): 0.2919 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030471 restraints weight = 41771.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031345 restraints weight = 26167.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.031976 restraints weight = 18488.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032448 restraints weight = 14147.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032701 restraints weight = 11535.095| |-----------------------------------------------------------------------------| r_work (final): 0.2933 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.037411 restraints weight = 11445.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.038242 restraints weight = 6695.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038843 restraints weight = 4496.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039250 restraints weight = 3253.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.039547 restraints weight = 2512.990| |-----------------------------------------------------------------------------| r_work (final): 0.2961 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.042393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.034413 restraints weight = 12152.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.035161 restraints weight = 9247.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.035728 restraints weight = 7461.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.036121 restraints weight = 6277.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.036552 restraints weight = 5524.549| |-----------------------------------------------------------------------------| r_work (final): 0.3435 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.046614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.039204 restraints weight = 9858.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.040209 restraints weight = 7639.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.041003 restraints weight = 6072.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.041636 restraints weight = 5008.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.042141 restraints weight = 4237.674| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39936 Z= 0.203 Angle : 0.835 12.037 54528 Z= 0.400 Chirality : 0.052 0.503 6546 Planarity : 0.005 0.037 6600 Dihedral : 7.313 54.592 8280 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.12), residues: 4590 helix: -0.71 (0.18), residues: 708 sheet: -0.10 (0.14), residues: 1332 loop : -1.09 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 135 TYR 0.028 0.002 TYR B 643 PHE 0.032 0.003 PHE V 98 TRP 0.034 0.004 TRP D 112 HIS 0.014 0.003 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00441 (39702) covalent geometry : angle 0.75697 (53898) SS BOND : bond 0.00406 ( 72) SS BOND : angle 0.97300 ( 144) hydrogen bonds : bond 0.05391 ( 1494) hydrogen bonds : angle 6.62815 ( 3924) link_ALPHA1-3 : bond 0.00459 ( 12) link_ALPHA1-3 : angle 3.84953 ( 36) link_ALPHA1-6 : bond 0.00663 ( 18) link_ALPHA1-6 : angle 1.54431 ( 54) link_BETA1-4 : bond 0.00554 ( 72) link_BETA1-4 : angle 2.77512 ( 216) link_NAG-ASN : bond 0.01131 ( 60) link_NAG-ASN : angle 5.07318 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 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 to be fit. 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: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 15 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: E 50 THR cc_start: 0.8697 (t) cc_final: 0.8405 (t) REVERT: E 95 MET cc_start: 0.8700 (pmm) cc_final: 0.8330 (pmm) REVERT: E 475 MET cc_start: 0.8605 (pmm) cc_final: 0.7965 (ppp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0503 time to fit residues: 1.1781 Evaluate side-chains 12 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.139 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8464 (mtp) cc_final: 0.8118 (mtm) REVERT: M 535 MET cc_start: 0.8928 (mmp) cc_final: 0.8615 (mmm) REVERT: M 574 LYS cc_start: 0.9626 (mttt) cc_final: 0.9160 (tmtt) REVERT: M 589 ASP cc_start: 0.9240 (m-30) cc_final: 0.9034 (m-30) REVERT: M 655 LYS cc_start: 0.9618 (mmtt) cc_final: 0.9195 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0796 time to fit residues: 1.5733 Evaluate side-chains 15 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.040 Evaluate side-chains 6 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0706 time to fit residues: 0.5038 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.041 Evaluate side-chains 2 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0399 time to fit residues: 0.1398 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 99 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 282 optimal weight: 30.0000 chunk 227 optimal weight: 30.0000 chunk 155 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 overall best weight: 5.0786 ------------------------------------------------------------------------------- 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: E 160 ASN 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: ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.042009 restraints weight = 846.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.042343 restraints weight = 289.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.042582 restraints weight = 137.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.042713 restraints weight = 68.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.042811 restraints weight = 35.910| |-----------------------------------------------------------------------------| r_work (final): 0.2664 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053699 restraints weight = 170.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054139 restraints weight = 25.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 9)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054485 restraints weight = 9.972 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054577 restraints weight = 4.432 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054654 restraints weight = 1.986 | |-----------------------------------------------------------------------------| r_work (final): 0.2938 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.027884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.027124 restraints weight = 991.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.027498 restraints weight = 253.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.027677 restraints weight = 108.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.027787 restraints weight = 54.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.027843 restraints weight = 30.872| |-----------------------------------------------------------------------------| r_work (final): 0.2257 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054873 restraints weight = 459.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055395 restraints weight = 184.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056039 restraints weight = 116.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056334 restraints weight = 72.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056567 restraints weight = 51.938| |-----------------------------------------------------------------------------| r_work (final): 0.3079 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.036482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.030416 restraints weight = 42403.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031314 restraints weight = 26267.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.031929 restraints weight = 18477.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.032280 restraints weight = 14165.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.032673 restraints weight = 11848.662| |-----------------------------------------------------------------------------| r_work (final): 0.2934 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.036720 restraints weight = 11792.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037547 restraints weight = 7037.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.038095 restraints weight = 4760.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038516 restraints weight = 3497.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038764 restraints weight = 2715.817| |-----------------------------------------------------------------------------| r_work (final): 0.2941 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.039548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.034528 restraints weight = 10426.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.035505 restraints weight = 6987.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.036230 restraints weight = 5057.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.036704 restraints weight = 3832.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.037195 restraints weight = 3070.087| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.047237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.039896 restraints weight = 9813.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.040847 restraints weight = 7710.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.041674 restraints weight = 6262.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.042349 restraints weight = 5189.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.042982 restraints weight = 4383.276| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39936 Z= 0.181 Angle : 0.780 10.660 54528 Z= 0.379 Chirality : 0.050 0.437 6546 Planarity : 0.005 0.058 6600 Dihedral : 6.973 55.989 8280 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.12), residues: 4590 helix: -0.81 (0.18), residues: 708 sheet: -0.03 (0.14), residues: 1308 loop : -1.31 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 135 TYR 0.033 0.003 TYR T 94 PHE 0.021 0.002 PHE C 159 TRP 0.038 0.004 TRP H 47 HIS 0.008 0.002 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00389 (39702) covalent geometry : angle 0.71069 (53898) SS BOND : bond 0.00343 ( 72) SS BOND : angle 0.82292 ( 144) hydrogen bonds : bond 0.05042 ( 1494) hydrogen bonds : angle 6.59051 ( 3924) link_ALPHA1-3 : bond 0.00617 ( 12) link_ALPHA1-3 : angle 3.23344 ( 36) link_ALPHA1-6 : bond 0.00546 ( 18) link_ALPHA1-6 : angle 1.49970 ( 54) link_BETA1-4 : bond 0.00532 ( 72) link_BETA1-4 : angle 2.65849 ( 216) link_NAG-ASN : bond 0.00882 ( 60) link_NAG-ASN : angle 4.62656 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 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 to be fit. 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: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 15 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8676 (pmm) cc_final: 0.8359 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0590 time to fit residues: 1.3816 Evaluate side-chains 12 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.141 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 535 MET cc_start: 0.8944 (mmp) cc_final: 0.8632 (mmm) REVERT: I 574 LYS cc_start: 0.9604 (mttt) cc_final: 0.9152 (tmtt) REVERT: I 589 ASP cc_start: 0.9239 (m-30) cc_final: 0.9027 (m-30) REVERT: I 655 LYS cc_start: 0.9616 (mmtt) cc_final: 0.9195 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0746 time to fit residues: 1.4811 Evaluate side-chains 14 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.041 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0756 time to fit residues: 0.4565 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.037 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0585 time to fit residues: 0.1239 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 131 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 410 optimal weight: 1.9990 chunk 187 optimal weight: 0.0010 chunk 258 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 387 optimal weight: 0.0870 chunk 365 optimal weight: 8.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- 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: ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.045995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.044750 restraints weight = 778.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.045228 restraints weight = 203.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.045435 restraints weight = 92.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.045651 restraints weight = 63.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.045674 restraints weight = 39.283| |-----------------------------------------------------------------------------| r_work (final): 0.2811 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.034696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.033786 restraints weight = 301.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.034176 restraints weight = 88.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.034411 restraints weight = 39.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.034528 restraints weight = 19.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.034598 restraints weight = 9.948 | |-----------------------------------------------------------------------------| r_work (final): 0.2431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.032732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.032192 restraints weight = 1029.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.032515 restraints weight = 179.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.032642 restraints weight = 61.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.032675 restraints weight = 25.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.032699 restraints weight = 12.668| |-----------------------------------------------------------------------------| r_work (final): 0.2549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051742 restraints weight = 562.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052521 restraints weight = 177.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052952 restraints weight = 85.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053233 restraints weight = 46.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053378 restraints weight = 24.262| |-----------------------------------------------------------------------------| r_work (final): 0.3091 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.038012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.031628 restraints weight = 38359.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.032513 restraints weight = 24229.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033176 restraints weight = 17239.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033650 restraints weight = 13337.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033980 restraints weight = 10959.880| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.037046 restraints weight = 11597.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.037904 restraints weight = 6872.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.038484 restraints weight = 4618.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038896 restraints weight = 3381.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.039138 restraints weight = 2635.690| |-----------------------------------------------------------------------------| r_work (final): 0.2963 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.041722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.036097 restraints weight = 10562.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.037224 restraints weight = 7048.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.038030 restraints weight = 5045.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.038550 restraints weight = 3811.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.039113 restraints weight = 3052.453| |-----------------------------------------------------------------------------| r_work (final): 0.3339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.047451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.040248 restraints weight = 9139.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.041078 restraints weight = 7357.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.041868 restraints weight = 6144.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.042469 restraints weight = 5170.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.042836 restraints weight = 4456.496| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39936 Z= 0.138 Angle : 0.749 10.202 54528 Z= 0.362 Chirality : 0.050 0.408 6546 Planarity : 0.005 0.038 6600 Dihedral : 6.539 53.876 8280 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.12), residues: 4590 helix: -0.73 (0.18), residues: 702 sheet: -0.10 (0.14), residues: 1392 loop : -1.37 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 135 TYR 0.024 0.002 TYR F 39 PHE 0.028 0.002 PHE T 98 TRP 0.030 0.003 TRP A 45 HIS 0.008 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00295 (39702) covalent geometry : angle 0.68624 (53898) SS BOND : bond 0.00290 ( 72) SS BOND : angle 0.76938 ( 144) hydrogen bonds : bond 0.04793 ( 1494) hydrogen bonds : angle 6.42179 ( 3924) link_ALPHA1-3 : bond 0.00776 ( 12) link_ALPHA1-3 : angle 2.46455 ( 36) link_ALPHA1-6 : bond 0.00723 ( 18) link_ALPHA1-6 : angle 1.41964 ( 54) link_BETA1-4 : bond 0.00607 ( 72) link_BETA1-4 : angle 2.53282 ( 216) link_NAG-ASN : bond 0.00839 ( 60) link_NAG-ASN : angle 4.34149 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 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 to be fit. 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: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 15 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8447 (pmm) cc_final: 0.8120 (pmm) REVERT: C 475 MET cc_start: 0.8559 (pmm) cc_final: 0.8317 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0499 time to fit residues: 1.1778 Evaluate side-chains 11 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.144 Evaluate side-chains 19 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 530 MET cc_start: 0.8627 (mtt) cc_final: 0.7813 (mtt) REVERT: I 535 MET cc_start: 0.8932 (mmp) cc_final: 0.8683 (mmm) REVERT: I 574 LYS cc_start: 0.9600 (mttt) cc_final: 0.9125 (tmtt) REVERT: I 589 ASP cc_start: 0.9214 (m-30) cc_final: 0.8984 (m-30) REVERT: I 626 MET cc_start: 0.8247 (ttm) cc_final: 0.7921 (ttt) REVERT: I 655 LYS cc_start: 0.9616 (mmtt) cc_final: 0.9207 (tttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0724 time to fit residues: 1.5172 Evaluate side-chains 14 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.044 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0729 time to fit residues: 0.4456 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Evaluate side-chains 2 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0320 time to fit residues: 0.1230 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 79 optimal weight: 50.0000 chunk 112 optimal weight: 0.0170 chunk 317 optimal weight: 0.0030 chunk 358 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 378 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.2034 ------------------------------------------------------------------------------- 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: ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.039588 restraints weight = 1071.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.039882 restraints weight = 423.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040049 restraints weight = 216.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040154 restraints weight = 128.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040218 restraints weight = 77.866| |-----------------------------------------------------------------------------| r_work (final): 0.2589 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.035191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.034294 restraints weight = 297.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.034689 restraints weight = 85.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.034931 restraints weight = 37.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.035029 restraints weight = 18.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.035101 restraints weight = 9.566 | |-----------------------------------------------------------------------------| r_work (final): 0.2510 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.028563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.028037 restraints weight = 811.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2287 r_free = 0.2287 target = 0.028294 restraints weight = 185.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.028406 restraints weight = 74.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.028467 restraints weight = 33.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.028512 restraints weight = 16.840| |-----------------------------------------------------------------------------| r_work (final): 0.2295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.044079 restraints weight = 579.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.044409 restraints weight = 436.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.044731 restraints weight = 380.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044964 restraints weight = 344.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045129 restraints weight = 321.181| |-----------------------------------------------------------------------------| r_work (final): 0.2778 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.030761 restraints weight = 41812.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.031615 restraints weight = 25884.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032256 restraints weight = 18386.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032713 restraints weight = 14103.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033069 restraints weight = 11543.187| |-----------------------------------------------------------------------------| r_work (final): 0.2958 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.041320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037247 restraints weight = 11607.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038047 restraints weight = 6681.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038609 restraints weight = 4387.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038902 restraints weight = 3118.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039200 restraints weight = 2447.734| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.041515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035293 restraints weight = 10396.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036117 restraints weight = 7431.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.036774 restraints weight = 5767.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.037312 restraints weight = 4681.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.037743 restraints weight = 3934.620| |-----------------------------------------------------------------------------| r_work (final): 0.3251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.047503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.039684 restraints weight = 9776.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.040631 restraints weight = 7850.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.041429 restraints weight = 6491.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.042092 restraints weight = 5463.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.042448 restraints weight = 4692.451| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39936 Z= 0.135 Angle : 0.705 9.918 54528 Z= 0.343 Chirality : 0.048 0.400 6546 Planarity : 0.004 0.042 6600 Dihedral : 6.216 53.452 8280 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.12), residues: 4590 helix: -0.46 (0.19), residues: 702 sheet: -0.17 (0.14), residues: 1368 loop : -1.51 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 135 TYR 0.025 0.002 TYR C 39 PHE 0.021 0.002 PHE F 159 TRP 0.029 0.003 TRP A 45 HIS 0.008 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00294 (39702) covalent geometry : angle 0.64103 (53898) SS BOND : bond 0.00310 ( 72) SS BOND : angle 0.73414 ( 144) hydrogen bonds : bond 0.04479 ( 1494) hydrogen bonds : angle 6.37308 ( 3924) link_ALPHA1-3 : bond 0.00943 ( 12) link_ALPHA1-3 : angle 1.98073 ( 36) link_ALPHA1-6 : bond 0.00523 ( 18) link_ALPHA1-6 : angle 1.45278 ( 54) link_BETA1-4 : bond 0.00578 ( 72) link_BETA1-4 : angle 2.49013 ( 216) link_NAG-ASN : bond 0.00816 ( 60) link_NAG-ASN : angle 4.28646 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 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 to be fit. 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 to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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 to be fit. 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: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 14 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8540 (pmm) cc_final: 0.8312 (pmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0428 time to fit residues: 0.9719 Evaluate side-chains 11 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.089 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8770 (mtt) cc_final: 0.7911 (mtt) REVERT: M 535 MET cc_start: 0.8986 (mmp) cc_final: 0.8723 (mmm) REVERT: M 574 LYS cc_start: 0.9615 (mttt) cc_final: 0.9157 (tmtt) REVERT: M 589 ASP cc_start: 0.9239 (m-30) cc_final: 0.9008 (m-30) REVERT: M 626 MET cc_start: 0.8227 (ttm) cc_final: 0.7989 (ttt) REVERT: M 655 LYS cc_start: 0.9609 (mmtt) cc_final: 0.9197 (tttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0614 time to fit residues: 1.2084 Evaluate side-chains 14 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.050 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1035 time to fit residues: 0.6146 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.039 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0474 time to fit residues: 0.1048 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 293 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 378 optimal weight: 0.4980 chunk 323 optimal weight: 0.9990 chunk 405 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 410 optimal weight: 0.0020 chunk 446 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: ** N 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.046091 restraints weight = 885.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046457 restraints weight = 272.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046668 restraints weight = 137.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046665 restraints weight = 93.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046665 restraints weight = 93.505| |-----------------------------------------------------------------------------| r_work (final): 0.2849 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.035495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.034475 restraints weight = 317.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.034942 restraints weight = 88.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.035194 restraints weight = 39.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.035323 restraints weight = 19.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.035378 restraints weight = 10.184| |-----------------------------------------------------------------------------| r_work (final): 0.2477 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.028122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.027345 restraints weight = 801.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.027703 restraints weight = 235.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.027914 restraints weight = 104.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.028011 restraints weight = 53.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.028074 restraints weight = 27.612| |-----------------------------------------------------------------------------| r_work (final): 0.2271 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.043096 restraints weight = 269.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.044345 restraints weight = 138.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045129 restraints weight = 77.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.045672 restraints weight = 46.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046024 restraints weight = 27.771| |-----------------------------------------------------------------------------| r_work (final): 0.2907 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.031396 restraints weight = 38556.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.032290 restraints weight = 24327.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032941 restraints weight = 17396.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.033374 restraints weight = 13493.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033602 restraints weight = 11244.735| |-----------------------------------------------------------------------------| r_work (final): 0.2960 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035298 restraints weight = 12926.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.036098 restraints weight = 7003.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036615 restraints weight = 4441.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037012 restraints weight = 3125.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037290 restraints weight = 2335.273| |-----------------------------------------------------------------------------| r_work (final): 0.2916 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.040490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.035004 restraints weight = 10854.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.035795 restraints weight = 7654.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.036405 restraints weight = 5809.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.036868 restraints weight = 4651.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.037237 restraints weight = 3883.116| |-----------------------------------------------------------------------------| r_work (final): 0.3272 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.047873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.039986 restraints weight = 9446.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.040911 restraints weight = 7589.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.041676 restraints weight = 6268.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.042355 restraints weight = 5306.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.042872 restraints weight = 4549.116| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39936 Z= 0.134 Angle : 0.735 9.904 54528 Z= 0.363 Chirality : 0.049 0.386 6546 Planarity : 0.004 0.039 6600 Dihedral : 6.155 53.468 8280 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.12), residues: 4590 helix: -0.48 (0.20), residues: 702 sheet: -0.14 (0.14), residues: 1314 loop : -1.64 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 135 TYR 0.025 0.002 TYR F 39 PHE 0.020 0.002 PHE C 159 TRP 0.030 0.003 TRP E 45 HIS 0.008 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00281 (39702) covalent geometry : angle 0.67662 (53898) SS BOND : bond 0.00271 ( 72) SS BOND : angle 0.71624 ( 144) hydrogen bonds : bond 0.04525 ( 1494) hydrogen bonds : angle 6.45689 ( 3924) link_ALPHA1-3 : bond 0.00935 ( 12) link_ALPHA1-3 : angle 1.77171 ( 36) link_ALPHA1-6 : bond 0.00607 ( 18) link_ALPHA1-6 : angle 1.40881 ( 54) link_BETA1-4 : bond 0.00607 ( 72) link_BETA1-4 : angle 2.46037 ( 216) link_NAG-ASN : bond 0.00781 ( 60) link_NAG-ASN : angle 4.19890 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 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 to be fit. 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: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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 to be fit. 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: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 15 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 MET cc_start: 0.8481 (pmm) cc_final: 0.8215 (pmm) REVERT: F 475 MET cc_start: 0.8551 (pmm) cc_final: 0.8283 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0525 time to fit residues: 1.2228 Evaluate side-chains 11 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.145 Evaluate side-chains 17 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 530 MET cc_start: 0.8698 (mtt) cc_final: 0.7623 (mtt) REVERT: N 535 MET cc_start: 0.8931 (mmp) cc_final: 0.8629 (mmm) REVERT: N 574 LYS cc_start: 0.9629 (mttt) cc_final: 0.9113 (tmtt) REVERT: N 626 MET cc_start: 0.8249 (ttm) cc_final: 0.7835 (ttt) REVERT: N 648 ASP cc_start: 0.8989 (t0) cc_final: 0.8776 (p0) REVERT: N 655 LYS cc_start: 0.9619 (mmtt) cc_final: 0.9229 (tttt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0792 time to fit residues: 1.4817 Evaluate side-chains 13 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.050 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0795 time to fit residues: 0.4801 Evaluate side-chains 5 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0455 time to fit residues: 0.1003 Evaluate side-chains 1 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1957 > 50: distance: 0 - 1: 21.215 distance: 1 - 2: 13.762 distance: 1 - 4: 10.824 distance: 2 - 3: 19.539 distance: 2 - 8: 24.420 distance: 4 - 5: 22.984 distance: 5 - 6: 11.256 distance: 5 - 7: 6.105 distance: 8 - 9: 15.615 distance: 9 - 10: 50.314 distance: 9 - 12: 11.836 distance: 10 - 11: 8.477 distance: 10 - 19: 39.129 distance: 12 - 13: 22.660 distance: 13 - 14: 24.736 distance: 13 - 15: 23.057 distance: 14 - 16: 20.325 distance: 15 - 17: 39.061 distance: 16 - 18: 33.506 distance: 17 - 18: 32.815 distance: 19 - 20: 19.424 distance: 20 - 21: 8.195 distance: 20 - 23: 38.189 distance: 21 - 22: 13.920 distance: 21 - 27: 14.126 distance: 23 - 24: 20.932 distance: 24 - 25: 23.538 distance: 24 - 26: 34.821 distance: 27 - 28: 42.525 distance: 28 - 29: 13.586 distance: 28 - 31: 12.510 distance: 29 - 30: 35.220 distance: 29 - 35: 18.172 distance: 31 - 32: 10.957 distance: 32 - 33: 16.928 distance: 33 - 34: 34.977 distance: 35 - 36: 17.438 distance: 36 - 37: 10.067 distance: 36 - 39: 11.697 distance: 37 - 38: 10.948 distance: 37 - 49: 24.710 distance: 39 - 40: 23.233 distance: 40 - 41: 9.686 distance: 40 - 42: 7.915 distance: 41 - 43: 10.581 distance: 42 - 44: 6.067 distance: 42 - 45: 5.531 distance: 43 - 44: 12.032 distance: 44 - 46: 9.779 distance: 45 - 47: 9.153 distance: 46 - 48: 9.936 distance: 47 - 48: 8.036 distance: 49 - 50: 26.085 distance: 50 - 51: 10.031 distance: 50 - 53: 30.644 distance: 51 - 52: 34.916 distance: 51 - 58: 24.208 distance: 53 - 54: 32.813 distance: 54 - 55: 47.997 distance: 55 - 56: 24.569 distance: 56 - 57: 35.443 distance: 58 - 59: 21.343 distance: 59 - 60: 33.734 distance: 59 - 62: 25.668 distance: 60 - 61: 45.475 distance: 60 - 66: 42.017 distance: 62 - 63: 17.988 distance: 63 - 64: 6.463 distance: 63 - 65: 20.728 distance: 66 - 67: 7.016 distance: 67 - 68: 12.326 distance: 67 - 70: 11.851 distance: 68 - 69: 32.835 distance: 68 - 74: 23.232 distance: 70 - 71: 22.326 distance: 71 - 72: 23.051 distance: 71 - 73: 34.756 distance: 74 - 75: 4.566 distance: 75 - 76: 8.221 distance: 75 - 78: 17.060 distance: 76 - 77: 3.560 distance: 76 - 82: 17.441 distance: 78 - 79: 8.710 distance: 79 - 80: 29.566 distance: 80 - 81: 16.628 distance: 82 - 83: 6.775 distance: 83 - 84: 5.036 distance: 83 - 86: 3.953 distance: 84 - 85: 4.968 distance: 86 - 87: 8.058