Starting phenix.real_space_refine on Tue Sep 15 11:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_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 { model { file = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_0434.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nc3_0434/09_2026/6nc3_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 8.89, per 1000 atoms: 0.23 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: 4.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 9180 Ramachandran restraints generated. 4590 Oldfield, 0 Emsley, 4590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 78 sheets defined 23.7% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 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: 11.00 Time building geometry restraints manager: 5.33 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 - 17.81: 21522 17.81 - 35.62: 706 35.62 - 53.43: 194 53.43 - 71.24: 66 71.24 - 89.05: 30 Dihedral angle restraints: 22518 sinusoidal: 9030 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 22515 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: 0.12 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.670 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 39.900 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.310 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 10.702 89.051 13614 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 are 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/Z covalent geometry : bond 0.01973 / 1.06 (39702) covalent geometry : angle 1.82971 / 1.16 (53898) SS BOND : bond 0.05338 / 3.27 ( 72) SS BOND : angle 2.75832 / 1.84 ( 144) hydrogen bonds : bond 0.17343 / 11.59 ( 1494) hydrogen bonds : angle 8.43771 / 5.92 ( 3924) link_ALPHA1-3 : bond 0.02938 / 1.69 ( 12) link_ALPHA1-3 : angle 2.25068 / 1.46 ( 36) link_ALPHA1-6 : bond 0.19254 / 11.76 ( 18) link_ALPHA1-6 : angle 13.97574 / 8.20 ( 54) link_BETA1-4 : bond 0.03995 / 2.54 ( 72) link_BETA1-4 : angle 3.61722 / 2.46 ( 216) link_NAG-ASN : bond 0.03028 / 1.97 ( 60) link_NAG-ASN : angle 2.54870 / 1.76 ( 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: 0.0020 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 : 0.002 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: 0.0010 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: 0.0012 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 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.111 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: 0.0499 time to fit residues: 2.3541 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 : 0.141 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 : 0.041 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: 0.0811 time to fit residues: 3.1174 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 11 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1218 time to fit residues: 1.4435 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 : 0.046 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 : 0.034 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1088 time to fit residues: 0.9413 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 : 0.035 ------------------------------------------------------------------------------- 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... A 33 GLN H 64 GLN L 45 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.048707 restraints weight = 960.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.049233 restraints weight = 400.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049514 restraints weight = 214.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049649 restraints weight = 125.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049775 restraints weight = 83.491| |-----------------------------------------------------------------------------| r_work (final): 0.2866 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.039986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.039849 restraints weight = 249.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.039874 restraints weight = 20.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.039948 restraints weight = 4.134 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.039961 restraints weight = 0.957 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.039960 restraints weight = 0.217 | |-----------------------------------------------------------------------------| r_work (final): 0.2437 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.029542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.028438 restraints weight = 719.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.028844 restraints weight = 207.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.029070 restraints weight = 104.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.029192 restraints weight = 61.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.029296 restraints weight = 41.568| |-----------------------------------------------------------------------------| r_work (final): 0.2383 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052359 restraints weight = 567.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053469 restraints weight = 253.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054109 restraints weight = 140.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054531 restraints weight = 94.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054797 restraints weight = 65.282| |-----------------------------------------------------------------------------| r_work (final): 0.3143 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.040073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033207 restraints weight = 36340.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034233 restraints weight = 22733.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034931 restraints weight = 16070.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035481 restraints weight = 12438.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035883 restraints weight = 10058.685| |-----------------------------------------------------------------------------| r_work (final): 0.3040 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.036260 restraints weight = 11578.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037141 restraints weight = 7082.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037766 restraints weight = 4810.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.038221 restraints weight = 3542.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.038509 restraints weight = 2740.415| |-----------------------------------------------------------------------------| r_work (final): 0.2948 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.042346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036212 restraints weight = 10151.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.037234 restraints weight = 6600.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.037940 restraints weight = 4766.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.038469 restraints weight = 3718.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.038850 restraints weight = 3074.029| |-----------------------------------------------------------------------------| r_work (final): 0.3265 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.045892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.038536 restraints weight = 9207.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.039622 restraints weight = 6713.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.040499 restraints weight = 5214.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.041113 restraints weight = 4220.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.041490 restraints weight = 3554.370| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 39936 Z= 0.227 Angle : 1.002 20.257 54528 Z= 0.497 Chirality : 0.057 0.595 6546 Planarity : 0.006 0.095 6600 Dihedral : 5.764 24.941 4998 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.05 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 1.76 % 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 are not related in a simple way. whole: -0.43 (0.12), residues: 4590 helix: -0.10 (0.18), residues: 690 sheet: 0.06 (0.13), residues: 1404 loop : -0.47 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 585 TYR 0.020 0.003 TYR B 643 PHE 0.015 0.002 PHE U 83 TRP 0.050 0.004 TRP B 610 HIS 0.007 0.002 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (39702) covalent geometry : angle 0.93357 / 0.48 (53898) SS BOND : bond 0.00687 / 0.44 ( 72) SS BOND : angle 0.96632 / 0.68 ( 144) hydrogen bonds : bond 0.07362 / 4.91 ( 1494) hydrogen bonds : angle 7.35242 / 5.15 ( 3924) link_ALPHA1-3 : bond 0.00682 / 0.40 ( 12) link_ALPHA1-3 : angle 4.45541 / 2.77 ( 36) link_ALPHA1-6 : bond 0.00969 / 0.59 ( 18) link_ALPHA1-6 : angle 1.57374 / 1.08 ( 54) link_BETA1-4 : bond 0.00827 / 0.52 ( 72) link_BETA1-4 : angle 3.10652 / 2.08 ( 216) link_NAG-ASN : bond 0.02319 / 1.36 ( 60) link_NAG-ASN : angle 5.10017 / 3.68 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 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 : 0.001 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: 0.0010 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: 0.0017 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 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 24 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: F 50 THR cc_start: 0.8462 (t) cc_final: 0.8190 (t) REVERT: F 95 MET cc_start: 0.9026 (ptp) cc_final: 0.8786 (ptp) REVERT: F 100 MET cc_start: 0.9090 (mmp) cc_final: 0.8797 (mmp) REVERT: F 108 ILE cc_start: 0.9674 (mm) cc_final: 0.9403 (tp) REVERT: F 338 TRP cc_start: 0.9371 (t-100) cc_final: 0.8876 (t-100) REVERT: F 475 MET cc_start: 0.7937 (ppp) cc_final: 0.7514 (pmm) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.0516 time to fit residues: 1.7407 Evaluate side-chains 18 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.146 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 : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8559 (mtp) cc_final: 0.8285 (mtm) REVERT: B 535 MET cc_start: 0.8935 (mmp) cc_final: 0.8655 (mmm) REVERT: B 574 LYS cc_start: 0.9595 (mttt) cc_final: 0.9050 (tmtt) REVERT: B 648 ASP cc_start: 0.9413 (t0) cc_final: 0.9035 (t0) REVERT: B 655 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9047 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0680 time to fit residues: 1.5065 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 : 0.040 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 : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 69 MET cc_start: 0.6472 (mtm) cc_final: 0.6108 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0565 time to fit residues: 0.5440 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 4 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0452 time to fit residues: 0.2484 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 : 0.033 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 7.9990 chunk 358 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 379 optimal weight: 9.9990 chunk 293 optimal weight: 50.0000 chunk 414 optimal weight: 0.0370 chunk 71 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 448 optimal weight: 20.0000 overall best weight: 4.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN P 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.051962 restraints weight = 571.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052209 restraints weight = 158.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052355 restraints weight = 91.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052355 restraints weight = 66.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052355 restraints weight = 66.457| |-----------------------------------------------------------------------------| r_work (final): 0.2821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.038356 restraints weight = 209.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038430 restraints weight = 9.587 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038430 restraints weight = 0.808 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038430 restraints weight = 0.806 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038430 restraints weight = 0.806 | |-----------------------------------------------------------------------------| r_work (final): 0.2437 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.028168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.026981 restraints weight = 893.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.027345 restraints weight = 246.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.027592 restraints weight = 128.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.027734 restraints weight = 80.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.027839 restraints weight = 52.015| |-----------------------------------------------------------------------------| r_work (final): 0.2351 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044995 restraints weight = 591.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.046027 restraints weight = 358.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046744 restraints weight = 265.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047078 restraints weight = 214.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047615 restraints weight = 187.467| |-----------------------------------------------------------------------------| r_work (final): 0.2874 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.038970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.032304 restraints weight = 37395.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.033265 restraints weight = 23936.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033955 restraints weight = 17133.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034444 restraints weight = 13250.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034824 restraints weight = 10847.450| |-----------------------------------------------------------------------------| r_work (final): 0.3008 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.042591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038324 restraints weight = 11943.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039181 restraints weight = 7012.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039803 restraints weight = 4647.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040212 restraints weight = 3344.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040512 restraints weight = 2574.861| |-----------------------------------------------------------------------------| r_work (final): 0.2998 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.042437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034560 restraints weight = 12373.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.035292 restraints weight = 9453.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.035904 restraints weight = 7658.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.036298 restraints weight = 6389.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.036726 restraints weight = 5609.626| |-----------------------------------------------------------------------------| r_work (final): 0.3268 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.043991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.037196 restraints weight = 10075.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.038192 restraints weight = 7447.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.039026 restraints weight = 5800.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.039746 restraints weight = 4653.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.040333 restraints weight = 3799.345| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39936 Z= 0.200 Angle : 0.831 14.212 54528 Z= 0.414 Chirality : 0.051 0.425 6546 Planarity : 0.005 0.063 6600 Dihedral : 5.688 26.697 4998 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.29 % Allowed : 2.94 % Favored : 96.77 % 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 are not related in a simple way. whole: -0.62 (0.12), residues: 4590 helix: -0.31 (0.18), residues: 690 sheet: 0.09 (0.13), residues: 1398 loop : -0.67 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 585 TYR 0.040 0.002 TYR M 643 PHE 0.059 0.003 PHE K 519 TRP 0.056 0.003 TRP N 610 HIS 0.005 0.002 HIS Q 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (39702) covalent geometry : angle 0.76658 / 0.40 (53898) SS BOND : bond 0.00406 / 0.25 ( 72) SS BOND : angle 0.68971 / 0.47 ( 144) hydrogen bonds : bond 0.06306 / 4.15 ( 1494) hydrogen bonds : angle 6.92717 / 4.86 ( 3924) link_ALPHA1-3 : bond 0.00893 / 0.52 ( 12) link_ALPHA1-3 : angle 4.40666 / 2.74 ( 36) link_ALPHA1-6 : bond 0.00882 / 0.53 ( 18) link_ALPHA1-6 : angle 1.37743 / 0.95 ( 54) link_BETA1-4 : bond 0.00599 / 0.37 ( 72) link_BETA1-4 : angle 2.58381 / 1.75 ( 216) link_NAG-ASN : bond 0.01221 / 0.67 ( 60) link_NAG-ASN : angle 4.52258 / 3.27 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 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 : 0.001 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: 0.0011 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: 0.0012 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 18 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 338 TRP cc_start: 0.9365 (t-100) cc_final: 0.8948 (t-100) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0479 time to fit residues: 1.3362 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 : 0.170 Evaluate side-chains 23 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8508 (mtp) cc_final: 0.8177 (mtm) REVERT: M 574 LYS cc_start: 0.9588 (mttt) cc_final: 0.9129 (tmtt) REVERT: M 589 ASP cc_start: 0.9167 (m-30) cc_final: 0.8916 (m-30) REVERT: M 629 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7112 (tpp) REVERT: M 648 ASP cc_start: 0.9287 (t0) cc_final: 0.9071 (t0) REVERT: M 655 LYS cc_start: 0.9608 (mmtt) cc_final: 0.9158 (tttt) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.0816 time to fit residues: 1.8628 Evaluate side-chains 16 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.041 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 : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0662 time to fit residues: 0.4777 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 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0414 time to fit residues: 0.1882 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 : 0.046 ------------------------------------------------------------------------------- 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: 10.0000 chunk 395 optimal weight: 0.3980 chunk 374 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 372 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 381 optimal weight: 0.0370 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.050525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.048608 restraints weight = 751.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.049111 restraints weight = 404.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.049399 restraints weight = 258.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049594 restraints weight = 185.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049735 restraints weight = 142.249| |-----------------------------------------------------------------------------| r_work (final): 0.2801 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.037509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.037465 restraints weight = 282.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.037504 restraints weight = 2.627 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.037504 restraints weight = 0.046 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.037504 restraints weight = 0.045 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.037504 restraints weight = 0.045 | |-----------------------------------------------------------------------------| r_work (final): 0.2445 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.027336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.026274 restraints weight = 741.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.026623 restraints weight = 228.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.026808 restraints weight = 118.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.026963 restraints weight = 71.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.027053 restraints weight = 47.352| |-----------------------------------------------------------------------------| r_work (final): 0.2309 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045695 restraints weight = 604.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046263 restraints weight = 321.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046896 restraints weight = 248.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047166 restraints weight = 198.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.047430 restraints weight = 177.531| |-----------------------------------------------------------------------------| r_work (final): 0.2892 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.038755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.032179 restraints weight = 36967.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.033167 restraints weight = 22936.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033863 restraints weight = 16031.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034348 restraints weight = 12224.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034635 restraints weight = 9893.794| |-----------------------------------------------------------------------------| r_work (final): 0.3004 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.037590 restraints weight = 12130.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038465 restraints weight = 6902.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039079 restraints weight = 4509.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.039499 restraints weight = 3216.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039835 restraints weight = 2494.626| |-----------------------------------------------------------------------------| r_work (final): 0.2977 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.041844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.035403 restraints weight = 10291.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.036320 restraints weight = 7178.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.037032 restraints weight = 5419.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.037517 restraints weight = 4343.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.037972 restraints weight = 3655.290| |-----------------------------------------------------------------------------| r_work (final): 0.3255 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.044232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.037093 restraints weight = 10032.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.038103 restraints weight = 7570.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.039013 restraints weight = 5983.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039694 restraints weight = 4812.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.040281 restraints weight = 3999.126| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39936 Z= 0.148 Angle : 0.769 12.328 54528 Z= 0.377 Chirality : 0.050 0.358 6546 Planarity : 0.004 0.041 6600 Dihedral : 5.486 27.107 4998 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.15 % Allowed : 1.47 % Favored : 98.38 % 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 are not related in a simple way. whole: -0.57 (0.12), residues: 4590 helix: 0.09 (0.19), residues: 708 sheet: 0.09 (0.14), residues: 1338 loop : -0.73 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 30 TYR 0.040 0.002 TYR J 643 PHE 0.030 0.002 PHE X 98 TRP 0.034 0.002 TRP M 610 HIS 0.016 0.002 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (39702) covalent geometry : angle 0.71049 / 0.36 (53898) SS BOND : bond 0.00315 / 0.19 ( 72) SS BOND : angle 0.92263 / 0.62 ( 144) hydrogen bonds : bond 0.05443 / 3.61 ( 1494) hydrogen bonds : angle 6.68172 / 4.69 ( 3924) link_ALPHA1-3 : bond 0.00780 / 0.45 ( 12) link_ALPHA1-3 : angle 4.43257 / 2.76 ( 36) link_ALPHA1-6 : bond 0.00882 / 0.53 ( 18) link_ALPHA1-6 : angle 1.33892 / 0.93 ( 54) link_BETA1-4 : bond 0.00678 / 0.42 ( 72) link_BETA1-4 : angle 2.38764 / 1.62 ( 216) link_NAG-ASN : bond 0.01042 / 0.57 ( 60) link_NAG-ASN : angle 3.97597 / 2.89 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 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 : 0.001 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 : 0.002 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: 0.0011 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: 0.0016 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 16 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.157 Fit side-chains REVERT: C 45 TRP cc_start: 0.8702 (p90) cc_final: 0.8406 (p90) REVERT: C 100 MET cc_start: 0.9218 (mmp) cc_final: 0.8896 (mmp) REVERT: C 104 MET cc_start: 0.9150 (mmp) cc_final: 0.8674 (mmp) REVERT: C 434 MET cc_start: 0.9087 (tmm) cc_final: 0.8575 (tmm) REVERT: C 475 MET cc_start: 0.8782 (pmm) cc_final: 0.8483 (pmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0507 time to fit residues: 1.2578 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 : 0.090 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 : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8376 (mtp) cc_final: 0.8047 (mtm) REVERT: M 535 MET cc_start: 0.8906 (mmp) cc_final: 0.8630 (mmp) REVERT: M 574 LYS cc_start: 0.9605 (mttt) cc_final: 0.9132 (tmtt) REVERT: M 647 GLU cc_start: 0.8852 (pp20) cc_final: 0.8522 (pp20) REVERT: M 648 ASP cc_start: 0.9057 (t0) cc_final: 0.8469 (p0) REVERT: M 655 LYS cc_start: 0.9609 (mmtt) cc_final: 0.9161 (tttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0595 time to fit residues: 1.2448 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 : 0.039 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 : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0610 time to fit residues: 0.5104 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 4 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.033 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.0385 time to fit residues: 0.2175 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 : 0.032 ------------------------------------------------------------------------------- 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: 0.8980 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 264 optimal weight: 6.9990 chunk 422 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 352 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 424 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 448 ASN T 37 GLN ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.046281 restraints weight = 905.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.046748 restraints weight = 483.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.047021 restraints weight = 307.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.047163 restraints weight = 218.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047303 restraints weight = 171.891| |-----------------------------------------------------------------------------| r_work (final): 0.2759 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053203 restraints weight = 241.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.053470 restraints weight = 39.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053629 restraints weight = 14.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053695 restraints weight = 6.072 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053703 restraints weight = 2.772 | |-----------------------------------------------------------------------------| r_work (final): 0.3015 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.027551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.026430 restraints weight = 817.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.026807 restraints weight = 239.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.027006 restraints weight = 121.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.027143 restraints weight = 75.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.027241 restraints weight = 50.051| |-----------------------------------------------------------------------------| r_work (final): 0.2319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047794 restraints weight = 584.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048492 restraints weight = 310.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.048945 restraints weight = 226.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049302 restraints weight = 172.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049516 restraints weight = 145.688| |-----------------------------------------------------------------------------| r_work (final): 0.2995 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.030902 restraints weight = 40297.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.031782 restraints weight = 25263.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032419 restraints weight = 17839.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032899 restraints weight = 13661.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.033162 restraints weight = 11127.427| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037764 restraints weight = 11823.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.038665 restraints weight = 6745.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.039213 restraints weight = 4370.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039708 restraints weight = 3184.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.039924 restraints weight = 2420.950| |-----------------------------------------------------------------------------| r_work (final): 0.2985 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.041858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.035714 restraints weight = 10211.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.036648 restraints weight = 6887.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.037363 restraints weight = 5100.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.037856 restraints weight = 4006.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.038189 restraints weight = 3309.445| |-----------------------------------------------------------------------------| r_work (final): 0.3256 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.045980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.038840 restraints weight = 9628.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.039913 restraints weight = 7171.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.040814 restraints weight = 5581.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.041435 restraints weight = 4513.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.041990 restraints weight = 3777.461| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39936 Z= 0.148 Angle : 0.735 11.046 54528 Z= 0.361 Chirality : 0.049 0.333 6546 Planarity : 0.004 0.040 6600 Dihedral : 5.349 26.610 4998 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 are not related in a simple way. whole: -0.61 (0.12), residues: 4590 helix: 0.15 (0.19), residues: 696 sheet: 0.08 (0.14), residues: 1332 loop : -0.80 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 38 TYR 0.040 0.002 TYR M 643 PHE 0.031 0.002 PHE B 519 TRP 0.027 0.002 TRP J 610 HIS 0.014 0.002 HIS Q 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (39702) covalent geometry : angle 0.67990 / 0.35 (53898) SS BOND : bond 0.00306 / 0.19 ( 72) SS BOND : angle 0.73872 / 0.50 ( 144) hydrogen bonds : bond 0.05214 / 3.43 ( 1494) hydrogen bonds : angle 6.40319 / 4.50 ( 3924) link_ALPHA1-3 : bond 0.00780 / 0.45 ( 12) link_ALPHA1-3 : angle 4.45559 / 2.78 ( 36) link_ALPHA1-6 : bond 0.00816 / 0.49 ( 18) link_ALPHA1-6 : angle 1.36448 / 0.95 ( 54) link_BETA1-4 : bond 0.00606 / 0.38 ( 72) link_BETA1-4 : angle 2.34939 / 1.59 ( 216) link_NAG-ASN : bond 0.01685 / 0.98 ( 60) link_NAG-ASN : angle 3.72137 / 2.70 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.001 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 : 0.002 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: 0.0016 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 : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 434 MET cc_start: 0.9039 (tmm) cc_final: 0.8367 (tmm) REVERT: E 475 MET cc_start: 0.8510 (pmm) cc_final: 0.7789 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0414 time to fit residues: 0.9421 Evaluate side-chains 10 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.090 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 : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8349 (mtp) cc_final: 0.7999 (mtm) REVERT: M 535 MET cc_start: 0.8908 (mmp) cc_final: 0.8542 (mmp) REVERT: M 574 LYS cc_start: 0.9611 (mttt) cc_final: 0.9128 (tmtt) REVERT: M 589 ASP cc_start: 0.9130 (m-30) cc_final: 0.8867 (m-30) REVERT: M 647 GLU cc_start: 0.8829 (pp20) cc_final: 0.8566 (pp20) REVERT: M 648 ASP cc_start: 0.8961 (t0) cc_final: 0.8465 (p0) REVERT: M 655 LYS cc_start: 0.9613 (mmtt) cc_final: 0.9172 (tttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0463 time to fit residues: 0.9713 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 : 0.040 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 : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0641 time to fit residues: 0.4646 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 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0448 time to fit residues: 0.1980 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 : 0.032 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 425 optimal weight: 0.0870 chunk 68 optimal weight: 20.0000 chunk 333 optimal weight: 7.9990 chunk 216 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 378 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 448 ASN ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.047864 restraints weight = 734.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048292 restraints weight = 429.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048484 restraints weight = 321.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.048666 restraints weight = 277.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.048666 restraints weight = 237.031| |-----------------------------------------------------------------------------| r_work (final): 0.2741 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056373 restraints weight = 237.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056639 restraints weight = 18.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056689 restraints weight = 3.699 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056687 restraints weight = 0.753 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056687 restraints weight = 0.179 | |-----------------------------------------------------------------------------| r_work (final): 0.3007 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.027509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.026453 restraints weight = 664.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.026805 restraints weight = 212.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.026991 restraints weight = 109.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.027136 restraints weight = 66.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.027217 restraints weight = 42.678| |-----------------------------------------------------------------------------| r_work (final): 0.2326 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046968 restraints weight = 674.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047725 restraints weight = 329.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048178 restraints weight = 231.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048539 restraints weight = 174.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048821 restraints weight = 145.254| |-----------------------------------------------------------------------------| r_work (final): 0.2968 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.037485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.031017 restraints weight = 39897.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.031958 restraints weight = 24615.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032625 restraints weight = 17223.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.033134 restraints weight = 13090.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033515 restraints weight = 10631.185| |-----------------------------------------------------------------------------| r_work (final): 0.2968 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.042862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038393 restraints weight = 11288.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.039281 restraints weight = 6704.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039872 restraints weight = 4438.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040261 restraints weight = 3183.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040580 restraints weight = 2467.957| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.041519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.035823 restraints weight = 10529.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.036742 restraints weight = 7150.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.037421 restraints weight = 5327.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.037951 restraints weight = 4221.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.038351 restraints weight = 3466.195| |-----------------------------------------------------------------------------| r_work (final): 0.3239 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.047320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.037425 restraints weight = 10806.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.038502 restraints weight = 8134.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.039402 restraints weight = 6479.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.040116 restraints weight = 5348.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.040750 restraints weight = 4547.100| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.400 39936 Z= 0.873 Angle : 1.136 62.004 54528 Z= 0.463 Chirality : 0.087 2.348 6546 Planarity : 0.004 0.041 6600 Dihedral : 5.392 27.246 4998 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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 are not related in a simple way. whole: -0.62 (0.12), residues: 4590 helix: 0.29 (0.19), residues: 702 sheet: 0.14 (0.14), residues: 1332 loop : -0.89 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 38 TYR 0.030 0.002 TYR I 643 PHE 0.032 0.002 PHE V 98 TRP 0.021 0.002 TRP M 610 HIS 0.018 0.002 HIS Q 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (39702) covalent geometry : angle 0.69954 / 0.36 (53898) SS BOND : bond 0.00352 / 0.23 ( 72) SS BOND : angle 0.93217 / 0.66 ( 144) hydrogen bonds : bond 0.05077 / 3.37 ( 1494) hydrogen bonds : angle 6.28041 / 4.41 ( 3924) link_ALPHA1-3 : bond 0.00745 / 0.43 ( 12) link_ALPHA1-3 : angle 4.43711 / 2.77 ( 36) link_ALPHA1-6 : bond 0.00764 / 0.46 ( 18) link_ALPHA1-6 : angle 1.34556 / 0.93 ( 54) link_BETA1-4 : bond 0.00568 / 0.36 ( 72) link_BETA1-4 : angle 2.25361 / 1.53 ( 216) link_NAG-ASN : bond 0.44292 / 26.14 ( 60) link_NAG-ASN : angle 15.27853 / 11.78 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 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: 0.0017 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 : 0.002 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: 0.0011 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: 0.0013 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 14 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 434 MET cc_start: 0.8835 (tmm) cc_final: 0.8312 (tmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0364 time to fit residues: 0.8194 Evaluate side-chains 10 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.142 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: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8328 (mtp) cc_final: 0.7970 (mtm) REVERT: M 535 MET cc_start: 0.8897 (mmp) cc_final: 0.8520 (mmp) REVERT: M 574 LYS cc_start: 0.9599 (mttt) cc_final: 0.9126 (tmtt) REVERT: M 589 ASP cc_start: 0.9112 (m-30) cc_final: 0.8845 (m-30) REVERT: M 647 GLU cc_start: 0.8797 (pp20) cc_final: 0.8595 (pp20) REVERT: M 648 ASP cc_start: 0.8888 (t0) cc_final: 0.8358 (p0) REVERT: M 655 LYS cc_start: 0.9607 (mmtt) cc_final: 0.9169 (tttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0713 time to fit residues: 1.4973 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 : 0.040 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 : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0676 time to fit residues: 0.4870 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 3 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.033 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0422 time to fit residues: 0.1870 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: 8.9990 chunk 321 optimal weight: 20.0000 chunk 210 optimal weight: 0.0270 chunk 18 optimal weight: 10.0000 chunk 132 optimal weight: 0.2980 chunk 282 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 126 optimal weight: 0.0170 chunk 83 optimal weight: 0.0870 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 229 ASN ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.047762 restraints weight = 664.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048186 restraints weight = 267.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.048558 restraints weight = 184.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048726 restraints weight = 121.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.048938 restraints weight = 97.324| |-----------------------------------------------------------------------------| r_work (final): 0.2780 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056562 restraints weight = 203.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056879 restraints weight = 20.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056966 restraints weight = 4.648 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056978 restraints weight = 1.104 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056975 restraints weight = 0.294 | |-----------------------------------------------------------------------------| r_work (final): 0.2922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.029403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.028268 restraints weight = 834.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.028692 restraints weight = 232.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.028935 restraints weight = 115.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.029064 restraints weight = 68.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.029188 restraints weight = 43.562| |-----------------------------------------------------------------------------| r_work (final): 0.2366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.042315 restraints weight = 635.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042982 restraints weight = 338.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.043407 restraints weight = 254.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043613 restraints weight = 201.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.043953 restraints weight = 170.450| |-----------------------------------------------------------------------------| r_work (final): 0.2832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.037625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031139 restraints weight = 39489.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032099 restraints weight = 24197.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.032674 restraints weight = 16871.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033255 restraints weight = 13204.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033631 restraints weight = 10604.092| |-----------------------------------------------------------------------------| r_work (final): 0.2977 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.042623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037826 restraints weight = 10865.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038737 restraints weight = 6540.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039420 restraints weight = 4445.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.039865 restraints weight = 3225.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040167 restraints weight = 2516.385| |-----------------------------------------------------------------------------| r_work (final): 0.2993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.041824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036370 restraints weight = 9206.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037369 restraints weight = 5981.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.038152 restraints weight = 4293.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.038642 restraints weight = 3251.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.038963 restraints weight = 2624.514| |-----------------------------------------------------------------------------| r_work (final): 0.3247 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.047485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.037576 restraints weight = 10590.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.038626 restraints weight = 8022.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.039535 restraints weight = 6422.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.040267 restraints weight = 5327.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.040784 restraints weight = 4544.833| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39936 Z= 0.133 Angle : 0.736 11.032 54528 Z= 0.349 Chirality : 0.050 0.426 6546 Planarity : 0.004 0.041 6600 Dihedral : 5.166 26.009 4998 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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 are not related in a simple way. whole: -0.64 (0.12), residues: 4590 helix: 0.50 (0.19), residues: 702 sheet: 0.03 (0.14), residues: 1404 loop : -0.94 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.023 0.002 TYR N 643 PHE 0.024 0.002 PHE K 519 TRP 0.020 0.002 TRP C 427 HIS 0.010 0.002 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (39702) covalent geometry : angle 0.66577 / 0.33 (53898) SS BOND : bond 0.00302 / 0.18 ( 72) SS BOND : angle 0.82019 / 0.57 ( 144) hydrogen bonds : bond 0.04784 / 3.16 ( 1494) hydrogen bonds : angle 6.07571 / 4.27 ( 3924) link_ALPHA1-3 : bond 0.00596 / 0.35 ( 12) link_ALPHA1-3 : angle 4.46739 / 2.79 ( 36) link_ALPHA1-6 : bond 0.00758 / 0.45 ( 18) link_ALPHA1-6 : angle 1.36992 / 0.95 ( 54) link_BETA1-4 : bond 0.00623 / 0.40 ( 72) link_BETA1-4 : angle 2.27798 / 1.54 ( 216) link_NAG-ASN : bond 0.00938 / 0.50 ( 60) link_NAG-ASN : angle 4.46935 / 3.13 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.001 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 : 0.002 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: 0.0016 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 13 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8313 (pmm) cc_final: 0.7962 (pmm) REVERT: A 434 MET cc_start: 0.8784 (tmm) cc_final: 0.8217 (tmm) REVERT: A 475 MET cc_start: 0.8292 (pmm) cc_final: 0.7921 (pmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0464 time to fit residues: 0.9807 Evaluate side-chains 10 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.166 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 : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 530 MET cc_start: 0.8290 (mtp) cc_final: 0.7940 (mtm) REVERT: I 535 MET cc_start: 0.8918 (mmp) cc_final: 0.8584 (mmm) REVERT: I 574 LYS cc_start: 0.9591 (mttt) cc_final: 0.9111 (tmtt) REVERT: I 589 ASP cc_start: 0.9130 (m-30) cc_final: 0.8883 (m-30) REVERT: I 655 LYS cc_start: 0.9583 (mmtt) cc_final: 0.9162 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0677 time to fit residues: 1.5037 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 : 0.040 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 : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0616 time to fit residues: 0.5130 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 4 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.033 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1566 time to fit residues: 0.6916 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 : 0.032 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.0030 chunk 307 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 410 optimal weight: 0.0980 chunk 187 optimal weight: 10.0000 chunk 258 optimal weight: 0.0040 chunk 210 optimal weight: 0.2980 chunk 208 optimal weight: 0.7980 chunk 387 optimal weight: 3.9990 chunk 365 optimal weight: 0.0980 overall best weight: 0.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 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 = 0.2849 r_free = 0.2849 target = 0.049597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047952 restraints weight = 846.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.048384 restraints weight = 337.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.048616 restraints weight = 204.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048730 restraints weight = 148.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048858 restraints weight = 117.835| |-----------------------------------------------------------------------------| r_work (final): 0.2850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051250 restraints weight = 139.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051270 restraints weight = 1.453 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051267 restraints weight = 0.030 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051267 restraints weight = 177.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051267 restraints weight = 175.327| |-----------------------------------------------------------------------------| r_work (final): 0.2677 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.032048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.030398 restraints weight = 764.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.030881 restraints weight = 223.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.031160 restraints weight = 132.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.031301 restraints weight = 93.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.031404 restraints weight = 73.796| |-----------------------------------------------------------------------------| r_work (final): 0.2522 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.047380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043386 restraints weight = 478.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043760 restraints weight = 336.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044300 restraints weight = 271.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044622 restraints weight = 216.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044735 restraints weight = 189.176| |-----------------------------------------------------------------------------| r_work (final): 0.2847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.031093 restraints weight = 40101.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032037 restraints weight = 24684.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032692 restraints weight = 17266.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.033189 restraints weight = 13321.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033554 restraints weight = 10772.034| |-----------------------------------------------------------------------------| r_work (final): 0.2969 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.042891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.038472 restraints weight = 11372.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039339 restraints weight = 6609.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039790 restraints weight = 4341.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040290 restraints weight = 3309.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040600 restraints weight = 2515.891| |-----------------------------------------------------------------------------| r_work (final): 0.3019 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.035424 restraints weight = 10988.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.036236 restraints weight = 7394.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.036828 restraints weight = 5451.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.037293 restraints weight = 4275.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.037586 restraints weight = 3455.857| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.048067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.040954 restraints weight = 8829.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.042037 restraints weight = 6530.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.042881 restraints weight = 5089.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.043569 restraints weight = 4082.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.044033 restraints weight = 3346.744| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39936 Z= 0.133 Angle : 0.724 10.253 54528 Z= 0.344 Chirality : 0.050 0.408 6546 Planarity : 0.004 0.042 6600 Dihedral : 5.078 25.689 4998 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 are not related in a simple way. whole: -0.64 (0.12), residues: 4590 helix: 0.59 (0.19), residues: 702 sheet: 0.12 (0.14), residues: 1380 loop : -1.03 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 94 TYR 0.011 0.002 TYR K 643 PHE 0.017 0.001 PHE J 519 TRP 0.020 0.002 TRP C 427 HIS 0.009 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (39702) covalent geometry : angle 0.65578 / 0.33 (53898) SS BOND : bond 0.00273 / 0.17 ( 72) SS BOND : angle 0.71224 / 0.50 ( 144) hydrogen bonds : bond 0.04593 / 3.03 ( 1494) hydrogen bonds : angle 6.03465 / 4.25 ( 3924) link_ALPHA1-3 : bond 0.00620 / 0.36 ( 12) link_ALPHA1-3 : angle 4.48332 / 2.80 ( 36) link_ALPHA1-6 : bond 0.00695 / 0.42 ( 18) link_ALPHA1-6 : angle 1.37343 / 0.95 ( 54) link_BETA1-4 : bond 0.00555 / 0.35 ( 72) link_BETA1-4 : angle 2.19796 / 1.50 ( 216) link_NAG-ASN : bond 0.00946 / 0.51 ( 60) link_NAG-ASN : angle 4.36599 / 3.10 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 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: 0.0020 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: 0.0010 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: 0.0012 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 13 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: E 104 MET cc_start: 0.9393 (ttm) cc_final: 0.9073 (ttt) REVERT: E 434 MET cc_start: 0.8783 (tmm) cc_final: 0.8224 (tmm) REVERT: E 475 MET cc_start: 0.8308 (pmm) cc_final: 0.7760 (pmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0494 time to fit residues: 1.0284 Evaluate side-chains 9 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.136 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 : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 530 MET cc_start: 0.8266 (mtp) cc_final: 0.7908 (mtm) REVERT: M 535 MET cc_start: 0.8936 (mmp) cc_final: 0.8582 (mmm) REVERT: M 574 LYS cc_start: 0.9612 (mttt) cc_final: 0.9169 (tmtt) REVERT: M 589 ASP cc_start: 0.9133 (m-30) cc_final: 0.8889 (m-30) REVERT: M 626 MET cc_start: 0.7917 (ttm) cc_final: 0.7573 (ttt) REVERT: M 655 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9181 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0671 time to fit residues: 1.4837 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 : 0.047 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: 0.0674 time to fit residues: 0.4910 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 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 : 0.038 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2912 time to fit residues: 0.6474 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 212 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 214 optimal weight: 0.9980 chunk 399 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 365 optimal weight: 0.0270 chunk 372 optimal weight: 0.4980 chunk 274 optimal weight: 7.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 229 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 = 0.2795 r_free = 0.2795 target = 0.048490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.047455 restraints weight = 760.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.047779 restraints weight = 249.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.047967 restraints weight = 115.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048091 restraints weight = 75.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.048199 restraints weight = 53.385| |-----------------------------------------------------------------------------| r_work (final): 0.2818 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036934 restraints weight = 187.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036934 restraints weight = 225.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036934 restraints weight = 191.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036934 restraints weight = 223.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.036934 restraints weight = 214.319| |-----------------------------------------------------------------------------| r_work (final): 0.2361 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.030307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.029113 restraints weight = 855.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.029559 restraints weight = 232.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.029754 restraints weight = 113.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.029899 restraints weight = 71.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.029914 restraints weight = 50.403| |-----------------------------------------------------------------------------| r_work (final): 0.2403 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.041954 restraints weight = 601.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042546 restraints weight = 422.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042977 restraints weight = 335.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042976 restraints weight = 288.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042976 restraints weight = 288.481| |-----------------------------------------------------------------------------| r_work (final): 0.2770 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.030966 restraints weight = 40746.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031912 restraints weight = 24985.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032593 restraints weight = 17407.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.033098 restraints weight = 13171.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033402 restraints weight = 10654.586| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038135 restraints weight = 11250.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.038975 restraints weight = 6622.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039584 restraints weight = 4448.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039939 restraints weight = 3228.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040217 restraints weight = 2547.869| |-----------------------------------------------------------------------------| r_work (final): 0.3009 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.039755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.034537 restraints weight = 12408.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.035372 restraints weight = 8448.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.035920 restraints weight = 6291.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.036417 restraints weight = 5002.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.036663 restraints weight = 4098.954| |-----------------------------------------------------------------------------| r_work (final): 0.3259 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.047396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.040176 restraints weight = 9628.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.041348 restraints weight = 6951.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.042259 restraints weight = 5274.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.042999 restraints weight = 4167.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.043543 restraints weight = 3387.398| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39936 Z= 0.120 Angle : 0.691 9.965 54528 Z= 0.329 Chirality : 0.048 0.401 6546 Planarity : 0.004 0.042 6600 Dihedral : 4.934 25.496 4998 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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 are not related in a simple way. whole: -0.68 (0.12), residues: 4590 helix: 0.71 (0.20), residues: 702 sheet: -0.01 (0.13), residues: 1458 loop : -1.07 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.013 0.001 TYR K 643 PHE 0.014 0.001 PHE J 519 TRP 0.020 0.002 TRP F 427 HIS 0.009 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (39702) covalent geometry : angle 0.62389 / 0.31 (53898) SS BOND : bond 0.00247 / 0.15 ( 72) SS BOND : angle 0.69104 / 0.48 ( 144) hydrogen bonds : bond 0.04404 / 2.90 ( 1494) hydrogen bonds : angle 5.94211 / 4.18 ( 3924) link_ALPHA1-3 : bond 0.00632 / 0.37 ( 12) link_ALPHA1-3 : angle 4.49190 / 2.80 ( 36) link_ALPHA1-6 : bond 0.00635 / 0.38 ( 18) link_ALPHA1-6 : angle 1.41162 / 0.98 ( 54) link_BETA1-4 : bond 0.00518 / 0.33 ( 72) link_BETA1-4 : angle 2.11004 / 1.43 ( 216) link_NAG-ASN : bond 0.00832 / 0.45 ( 60) link_NAG-ASN : angle 4.19920 / 3.01 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 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: 0.0021 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: 0.0011 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 : 0.002 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: 0.0017 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 13 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 434 MET cc_start: 0.8770 (tmm) cc_final: 0.8176 (tmm) REVERT: E 475 MET cc_start: 0.8376 (pmm) cc_final: 0.7926 (pmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0415 time to fit residues: 0.8527 Evaluate side-chains 10 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.146 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 : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 535 MET cc_start: 0.8972 (mmp) cc_final: 0.8634 (mmm) REVERT: M 574 LYS cc_start: 0.9601 (mttt) cc_final: 0.9144 (tmtt) REVERT: M 589 ASP cc_start: 0.9242 (m-30) cc_final: 0.8972 (m-30) REVERT: M 647 GLU cc_start: 0.8650 (pp20) cc_final: 0.8406 (mm-30) REVERT: M 655 LYS cc_start: 0.9596 (mmtt) cc_final: 0.9195 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0660 time to fit residues: 1.4652 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 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: 0.0666 time to fit residues: 0.4819 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 revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2814 time to fit residues: 0.6197 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 : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 172 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 0.0670 chunk 370 optimal weight: 0.0000 chunk 157 optimal weight: 9.9990 chunk 440 optimal weight: 0.0020 overall best weight: 1.0330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048172 restraints weight = 724.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048597 restraints weight = 293.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048880 restraints weight = 193.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049127 restraints weight = 155.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049282 restraints weight = 117.100| |-----------------------------------------------------------------------------| r_work (final): 0.2769 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.052543 restraints weight = 198.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052606 restraints weight = 4.684 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052634 restraints weight = 0.570 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 4)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052623 restraints weight = 0.087 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 4)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052616 restraints weight = 0.014 | |-----------------------------------------------------------------------------| r_work (final): 0.2493 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.030263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.028953 restraints weight = 895.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.029342 restraints weight = 243.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.029585 restraints weight = 142.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.029700 restraints weight = 87.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.029700 restraints weight = 65.792| |-----------------------------------------------------------------------------| r_work (final): 0.2404 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.047312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.041960 restraints weight = 599.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042568 restraints weight = 413.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.042994 restraints weight = 332.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.043296 restraints weight = 286.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043353 restraints weight = 257.490| |-----------------------------------------------------------------------------| r_work (final): 0.2775 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031057 restraints weight = 39936.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031999 restraints weight = 24542.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032611 restraints weight = 17180.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033147 restraints weight = 13377.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033493 restraints weight = 10751.172| |-----------------------------------------------------------------------------| r_work (final): 0.2977 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.036595 restraints weight = 11417.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037464 restraints weight = 6725.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038051 restraints weight = 4452.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.038406 restraints weight = 3222.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038596 restraints weight = 2539.966| |-----------------------------------------------------------------------------| r_work (final): 0.2952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.041835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.036506 restraints weight = 10983.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.037670 restraints weight = 6790.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.038468 restraints weight = 4671.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.039047 restraints weight = 3387.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.039452 restraints weight = 2586.619| |-----------------------------------------------------------------------------| r_work (final): 0.3361 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.047896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.040977 restraints weight = 9130.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.042061 restraints weight = 6670.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.042914 restraints weight = 5126.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.043578 restraints weight = 4092.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.044104 restraints weight = 3369.569| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39936 Z= 0.132 Angle : 0.740 11.127 54528 Z= 0.353 Chirality : 0.050 0.392 6546 Planarity : 0.004 0.041 6600 Dihedral : 4.952 26.060 4998 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 are not related in a simple way. whole: -0.80 (0.12), residues: 4590 helix: 0.33 (0.19), residues: 714 sheet: 0.03 (0.13), residues: 1482 loop : -1.14 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 38 TYR 0.019 0.001 TYR I 643 PHE 0.012 0.001 PHE N 519 TRP 0.071 0.002 TRP J 596 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (39702) covalent geometry : angle 0.67156 / 0.34 (53898) SS BOND : bond 0.00253 / 0.16 ( 72) SS BOND : angle 0.68000 / 0.47 ( 144) hydrogen bonds : bond 0.04446 / 2.94 ( 1494) hydrogen bonds : angle 5.96520 / 4.19 ( 3924) link_ALPHA1-3 : bond 0.00654 / 0.38 ( 12) link_ALPHA1-3 : angle 4.58614 / 2.86 ( 36) link_ALPHA1-6 : bond 0.00631 / 0.38 ( 18) link_ALPHA1-6 : angle 1.39211 / 0.97 ( 54) link_BETA1-4 : bond 0.00421 / 0.27 ( 72) link_BETA1-4 : angle 2.23268 / 1.51 ( 216) link_NAG-ASN : bond 0.00849 / 0.46 ( 60) link_NAG-ASN : angle 4.41460 / 3.20 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.001 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: 0.0010 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: 0.0013 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 13 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8773 (tmm) cc_final: 0.8179 (tmm) REVERT: A 475 MET cc_start: 0.8379 (pmm) cc_final: 0.7879 (pmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0454 time to fit residues: 0.9572 Evaluate side-chains 10 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.128 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 : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 530 MET cc_start: 0.8644 (mtt) cc_final: 0.7763 (ptp) REVERT: I 535 MET cc_start: 0.8939 (mmp) cc_final: 0.8629 (mmm) REVERT: I 574 LYS cc_start: 0.9595 (mttt) cc_final: 0.9155 (tmtt) REVERT: I 589 ASP cc_start: 0.9222 (m-30) cc_final: 0.8949 (m-30) REVERT: I 655 LYS cc_start: 0.9601 (mmtt) cc_final: 0.9200 (tttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0634 time to fit residues: 1.4107 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 : 0.038 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 : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0583 time to fit residues: 0.4310 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 : 0.022 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 : 0.020 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2621 time to fit residues: 0.5716 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 : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 65 optimal weight: 0.0370 chunk 443 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 229 optimal weight: 0.1980 chunk 151 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 176 optimal weight: 5.9990 chunk 348 optimal weight: 8.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.048229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046801 restraints weight = 829.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047214 restraints weight = 325.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047378 restraints weight = 189.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.047558 restraints weight = 132.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.047656 restraints weight = 98.777| |-----------------------------------------------------------------------------| r_work (final): 0.2840 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.049535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.049039 restraints weight = 157.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049052 restraints weight = 5.419 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049072 restraints weight = 0.748 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049073 restraints weight = 0.059 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 4)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049073 restraints weight = 0.007 | |-----------------------------------------------------------------------------| r_work (final): 0.2475 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.027974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.026809 restraints weight = 771.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.027200 restraints weight = 232.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.027398 restraints weight = 115.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.027570 restraints weight = 69.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.027657 restraints weight = 44.615| |-----------------------------------------------------------------------------| r_work (final): 0.2355 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.049346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.044648 restraints weight = 506.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045151 restraints weight = 345.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045682 restraints weight = 278.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046020 restraints weight = 234.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046022 restraints weight = 200.857| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.038251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.031497 restraints weight = 37777.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032433 restraints weight = 23608.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033139 restraints weight = 16745.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033624 restraints weight = 12780.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034045 restraints weight = 10484.233| |-----------------------------------------------------------------------------| r_work (final): 0.2982 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.040813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036227 restraints weight = 11444.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037083 restraints weight = 6623.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037719 restraints weight = 4455.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038128 restraints weight = 3216.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038406 restraints weight = 2499.049| |-----------------------------------------------------------------------------| r_work (final): 0.2960 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.041976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.035943 restraints weight = 10660.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.036847 restraints weight = 7401.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.037506 restraints weight = 5565.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.038049 restraints weight = 4422.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.038442 restraints weight = 3634.850| |-----------------------------------------------------------------------------| r_work (final): 0.3265 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.047322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.040377 restraints weight = 9483.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.041519 restraints weight = 6871.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.042462 restraints weight = 5211.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.043156 restraints weight = 4096.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.043698 restraints weight = 3326.317| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4912 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= 0.119 Angle : 0.718 10.747 54528 Z= 0.343 Chirality : 0.049 0.386 6546 Planarity : 0.004 0.041 6600 Dihedral : 4.895 25.213 4998 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 are not related in a simple way. whole: -0.69 (0.13), residues: 4590 helix: 0.48 (0.20), residues: 720 sheet: 0.12 (0.14), residues: 1446 loop : -1.10 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 38 TYR 0.013 0.001 TYR G 217 PHE 0.011 0.001 PHE N 519 TRP 0.060 0.002 TRP B 596 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (39702) covalent geometry : angle 0.64965 / 0.33 (53898) SS BOND : bond 0.00270 / 0.17 ( 72) SS BOND : angle 0.68628 / 0.47 ( 144) hydrogen bonds : bond 0.04241 / 2.80 ( 1494) hydrogen bonds : angle 5.85981 / 4.12 ( 3924) link_ALPHA1-3 : bond 0.00600 / 0.35 ( 12) link_ALPHA1-3 : angle 4.50841 / 2.81 ( 36) link_ALPHA1-6 : bond 0.00605 / 0.36 ( 18) link_ALPHA1-6 : angle 1.41988 / 0.98 ( 54) link_BETA1-4 : bond 0.00540 / 0.34 ( 72) link_BETA1-4 : angle 2.19958 / 1.49 ( 216) link_NAG-ASN : bond 0.00808 / 0.44 ( 60) link_NAG-ASN : angle 4.33902 / 3.16 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.35 seconds wall clock time: 63 minutes 19.40 seconds (3799.40 seconds total)