Starting phenix.real_space_refine on Mon Sep 14 17:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ot1_20191/09_2026/6ot1_20191.cif" } resolution = 3.5 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= 0.001 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 20226 2.51 5 N 5331 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.03s 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: 32247 Number of models: 1 Model: "" Number of chains: 75 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "A" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "J" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "M" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "Q" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "R" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "S" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen 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: 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: "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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.95, per 1000 atoms: 0.22 Number of scatterers: 32247 At special positions: 0 Unit cell: (160.988, 153.475, 155.621, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 6525 8.00 N 5331 7.00 C 20226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 100A" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.02 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.03 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 98 " - pdb=" SG CYS S 100A" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " " MAN w 4 " - " MAN w 5 " " MANBA 4 " - " MANBA 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 8 3 " - " MAN 8 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " BMADA 3 " - " MANDA 4 " " BMAGA 3 " - " MANGA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 3 3 " - " MAN 3 5 " " BMA V 3 " - " MAN V 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 5 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMABA 3 " - " MANBA 6 " " BMADA 3 " - " MANDA 5 " " BMAGA 3 " - " MANGA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN E 276 " " NAG 2 1 " - " ASN P 88 " " NAG 3 1 " - " ASN P 137 " " NAG 4 1 " - " ASN P 156 " " NAG 5 1 " - " ASN P 160 " " NAG 6 1 " - " ASN P 197 " " NAG 7 1 " - " ASN P 234 " " NAG 8 1 " - " ASN P 262 " " NAG 9 1 " - " ASN P 295 " " NAG B 701 " - " ASN B 637 " " NAG D 701 " - " ASN D 637 " " NAG E 625 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG E 633 " - " ASN E 355 " " NAG G 625 " - " ASN G 133 " " NAG G 632 " - " ASN G 339 " " NAG G 633 " - " ASN G 355 " " NAG O 701 " - " ASN O 637 " " NAG P 625 " - " ASN P 133 " " NAG P 632 " - " ASN P 339 " " NAG P 633 " - " ASN P 355 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 137 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 276 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 137 " " NAG l 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 160 " " NAG p 1 " - " ASN E 197 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 262 " " NAG u 1 " - " ASN E 295 " " NAG v 1 " - " ASN E 301 " " NAG w 1 " - " ASN E 332 " " NAG x 1 " - " ASN E 363 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 392 " " NAGAA 1 " - " ASN P 301 " " NAGBA 1 " - " ASN P 332 " " NAGCA 1 " - " ASN P 363 " " NAGDA 1 " - " ASN P 386 " " NAGEA 1 " - " ASN P 392 " " NAGFA 1 " - " ASN P 448 " " NAGGA 1 " - " ASN P 276 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 93 sheets defined 11.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.894A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.588A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 354 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.406A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.089A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.671A pdb=" N ASP m 31 " --> pdb=" O LEU m 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'n' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU n 83 " --> pdb=" O ALA n 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.892A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.607A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 634 " --> pdb=" O GLN O 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER O 636 " --> pdb=" O ASP O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.827A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.408A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.893A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.741A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE P 109 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.881A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 349 removed outlier: 3.690A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.407A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.019A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.518A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.991A pdb=" N THR S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.509A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.563A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AB3, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER H 70 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 89 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS m 92 " --> pdb=" O TRP m 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP m 101 " --> pdb=" O CYS m 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR m 94 " --> pdb=" O ASP m 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'n' and resid 9 through 13 removed outlier: 3.761A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'n' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'n' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS q 35 " --> pdb=" O VAL q 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS q 92 " --> pdb=" O TRP q 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP q 103 " --> pdb=" O CYS q 92 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 94 " --> pdb=" O GLN q 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 17 through 19 Processing sheet with id=AD1, first strand: chain 'q' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER q 58 " --> pdb=" O TRP q 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR r 48 " --> pdb=" O ARG r 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'O' and resid 603 through 609 removed outlier: 7.992A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.507A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AE5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE6, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AE7, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AE8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.559A pdb=" N SER A 70 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 32 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 52 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 89 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR F 33 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS F 92 " --> pdb=" O TRP F 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP F 101 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR F 94 " --> pdb=" O ASP F 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 98 " --> pdb=" O TYR F 100M" (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AF9, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.664A pdb=" N ALA I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 35 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG J 94 " --> pdb=" O GLN J 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.502A pdb=" N SER J 58 " --> pdb=" O TRP J 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR K 48 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG9, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'P' and resid 158 through 162 Processing sheet with id=AH5, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AH6, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AH9, first strand: chain 'P' and resid 304 through 308 Processing sheet with id=AI1, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AI2, first strand: chain 'P' and resid 375 through 378 Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER M 70 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE M 32 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR M 52 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG M 94 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU N 89 " --> pdb=" O HIS N 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR Q 33 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP Q 101 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR Q 94 " --> pdb=" O ASP Q 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY Q 98 " --> pdb=" O TYR Q 100M" (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 18 through 22 Processing sheet with id=AJ2, first strand: chain 'R' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA R 84 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ4, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AJ6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS S 35 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG S 94 " --> pdb=" O GLN S 101 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 17 through 19 Processing sheet with id=AJ9, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER S 58 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AK2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP T 34 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR T 48 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 10 through 13 924 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9970 1.34 - 1.46: 8484 1.46 - 1.58: 14276 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 32946 Sorted by residual: bond pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.89e+01 bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.63e+01 bond pdb=" C1 NAG 2 1 " pdb=" O5 NAG 2 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 BMA z 3 " pdb=" C2 BMA z 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 42345 1.96 - 3.92: 1975 3.92 - 5.88: 310 5.88 - 7.84: 116 7.84 - 9.80: 44 Bond angle restraints: 44790 Sorted by residual: angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLY N 68 " pdb=" N THR N 69 " pdb=" CA THR N 69 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C CYS J 98 " pdb=" N ASP J 99 " pdb=" CA ASP J 99 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C CYS q 98 " pdb=" N ASP q 99 " pdb=" CA ASP q 99 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 ... (remaining 44785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 15985 16.52 - 33.04: 1882 33.04 - 49.57: 400 49.57 - 66.09: 66 66.09 - 82.61: 30 Dihedral angle restraints: 18363 sinusoidal: 7299 harmonic: 11064 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.91 65.91 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.90 65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 18360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4669 0.087 - 0.175: 688 0.175 - 0.262: 52 0.262 - 0.350: 30 0.350 - 0.437: 6 Chirality restraints: 5445 Sorted by residual: chirality pdb=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" N2 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.05 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C2 NAG 3 1 " pdb=" C1 NAG 3 1 " pdb=" C3 NAG 3 1 " pdb=" N2 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C2 NAG k 1 " pdb=" C1 NAG k 1 " pdb=" C3 NAG k 1 " pdb=" N2 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5442 not shown) Planarity restraints: 5547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 275 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C GLU G 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU G 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 275 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU P 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU P 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN P 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 275 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLU E 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU E 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 276 " -0.016 2.00e-02 2.50e+03 ... (remaining 5544 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 393 2.59 - 3.17: 25306 3.17 - 3.75: 47473 3.75 - 4.32: 64453 4.32 - 4.90: 107153 Nonbonded interactions: 244778 Sorted by model distance: nonbonded pdb=" OE1 GLU O 647 " pdb=" NH2 ARG D 542 " model vdw 2.015 3.120 nonbonded pdb=" NH2 ARG B 542 " pdb=" OE1 GLU D 647 " model vdw 2.021 3.120 nonbonded pdb=" CB ASP q 76B" pdb=" OH TYR E 318 " model vdw 2.032 3.440 nonbonded pdb=" OH TYR G 318 " pdb=" CB ASP S 76B" model vdw 2.048 3.440 nonbonded pdb=" OE1 GLU B 647 " pdb=" NH2 ARG O 542 " model vdw 2.048 3.120 ... (remaining 244773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'AA' selection = chain 'FA' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'j' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'DA' selection = chain 'GA' selection = chain 'V' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'CA' selection = chain 'EA' selection = chain 'W' selection = chain 'e' selection = chain 'g' selection = chain 'l' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '8' selection = chain 'a' selection = chain 't' } ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'BA' selection = chain 'd' selection = chain 'w' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'R' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'q' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.100 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 33159 Z= 0.353 Angle : 1.066 16.616 45372 Z= 0.525 Chirality : 0.063 0.437 5445 Planarity : 0.007 0.064 5490 Dihedral : 14.632 82.609 11106 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.72 % Allowed : 9.69 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z 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: -4.15 (0.11), residues: 3801 helix: -4.64 (0.10), residues: 387 sheet: -2.13 (0.14), residues: 1230 loop : -2.84 (0.10), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 327 TYR 0.013 0.002 TYR Q 100M PHE 0.031 0.002 PHE S 100D TRP 0.019 0.002 TRP E 112 HIS 0.006 0.001 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.35 (32946) covalent geometry : angle 1.01029 / 0.51 (44790) SS BOND : bond 0.00548 / 0.38 ( 57) SS BOND : angle 2.22938 / 1.57 ( 114) hydrogen bonds : bond 0.26641 / 17.52 ( 870) hydrogen bonds : angle 9.84750 / 6.84 ( 2214) link_ALPHA1-2 : bond 0.00041 / 0.02 ( 3) link_ALPHA1-2 : angle 1.75686 / 1.13 ( 9) link_ALPHA1-3 : bond 0.00521 / 0.33 ( 15) link_ALPHA1-3 : angle 2.52274 / 1.81 ( 45) link_ALPHA1-6 : bond 0.00393 / 0.27 ( 12) link_ALPHA1-6 : angle 1.60195 / 1.05 ( 36) link_BETA1-4 : bond 0.01035 / 0.72 ( 69) link_BETA1-4 : angle 2.68981 / 1.88 ( 207) link_NAG-ASN : bond 0.00966 / 0.62 ( 57) link_NAG-ASN : angle 4.46696 / 3.32 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 434 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8400 (m-80) cc_final: 0.8016 (m-10) REVERT: B 654 GLU cc_start: 0.8443 (tp30) cc_final: 0.8176 (tp30) REVERT: B 657 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 272 ILE cc_start: 0.8932 (pt) cc_final: 0.8458 (mt) REVERT: G 426 MET cc_start: 0.7357 (mmm) cc_final: 0.7137 (mmt) REVERT: H 36 TRP cc_start: 0.2994 (m100) cc_final: 0.2702 (m100) REVERT: L 50 GLU cc_start: 0.4860 (mt-10) cc_final: 0.4481 (mm-30) REVERT: m 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8096 (mppt) REVERT: r 17 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 32 PHE cc_start: 0.7258 (m-80) cc_final: 0.6722 (m-10) REVERT: C 50 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4727 (mm-30) REVERT: F 13 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7757 (mmmt) REVERT: F 103 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8165 (mppt) REVERT: I 49 TYR cc_start: 0.8377 (p90) cc_final: 0.8108 (p90) REVERT: D 519 PHE cc_start: 0.8575 (m-80) cc_final: 0.8237 (m-10) REVERT: P 439 ILE cc_start: 0.8856 (pt) cc_final: 0.8563 (pt) REVERT: N 50 GLU cc_start: 0.4691 (mt-10) cc_final: 0.4323 (mm-30) REVERT: Q 103 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7945 (mppt) REVERT: T 11 LEU cc_start: 0.9046 (tp) cc_final: 0.8792 (tt) REVERT: T 78 ASP cc_start: 0.8748 (t70) cc_final: 0.8489 (t70) outliers start: 24 outliers final: 8 residues processed: 458 average time/residue: 0.2192 time to fit residues: 156.4214 Evaluate side-chains 303 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 GLN G 67 ASN G 103 GLN G 183 GLN G 203 GLN L 93 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN n 38 GLN O 575 GLN E 67 ASN E 103 GLN E 183 GLN E 203 GLN A 77 GLN C 93 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 38 GLN D 575 GLN P 67 ASN P 103 GLN P 183 GLN P 203 GLN M 3 GLN M 77 GLN N 93 GLN ** Q 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 38 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066662 restraints weight = 80191.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068713 restraints weight = 45859.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069981 restraints weight = 33577.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070787 restraints weight = 28406.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071203 restraints weight = 25647.085| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33159 Z= 0.144 Angle : 0.728 11.760 45372 Z= 0.355 Chirality : 0.045 0.289 5445 Planarity : 0.005 0.057 5490 Dihedral : 5.977 44.332 4175 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.00 % Allowed : 14.47 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.44 (0.12), residues: 3801 helix: -3.43 (0.17), residues: 414 sheet: -1.66 (0.14), residues: 1230 loop : -2.47 (0.11), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 38 TYR 0.017 0.001 TYR H 59 PHE 0.019 0.002 PHE M 78 TRP 0.014 0.001 TRP D 571 HIS 0.003 0.001 HIS H 31B Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (32946) covalent geometry : angle 0.68737 / 0.35 (44790) SS BOND : bond 0.00302 / 0.22 ( 57) SS BOND : angle 1.85473 / 1.23 ( 114) hydrogen bonds : bond 0.04636 / 3.02 ( 870) hydrogen bonds : angle 6.58957 / 4.58 ( 2214) link_ALPHA1-2 : bond 0.00546 / 0.25 ( 3) link_ALPHA1-2 : angle 1.96304 / 1.26 ( 9) link_ALPHA1-3 : bond 0.00914 / 0.56 ( 15) link_ALPHA1-3 : angle 1.94117 / 1.34 ( 45) link_ALPHA1-6 : bond 0.00554 / 0.36 ( 12) link_ALPHA1-6 : angle 1.54678 / 1.00 ( 36) link_BETA1-4 : bond 0.00553 / 0.40 ( 69) link_BETA1-4 : angle 1.73333 / 1.22 ( 207) link_NAG-ASN : bond 0.00374 / 0.23 ( 57) link_NAG-ASN : angle 3.02955 / 2.24 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 342 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8213 (m-80) cc_final: 0.7977 (m-10) REVERT: G 33 ASN cc_start: 0.8021 (p0) cc_final: 0.7812 (p0) REVERT: G 125 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8442 (tt) REVERT: G 203 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: G 272 ILE cc_start: 0.8880 (pt) cc_final: 0.8509 (mt) REVERT: L 50 GLU cc_start: 0.4968 (mt-10) cc_final: 0.4698 (mm-30) REVERT: m 32 ASN cc_start: 0.8610 (m-40) cc_final: 0.8342 (m110) REVERT: m 43 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9095 (mmmm) REVERT: m 103 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8186 (mppt) REVERT: n 49 TYR cc_start: 0.8386 (p90) cc_final: 0.8113 (p90) REVERT: n 87 TYR cc_start: 0.8359 (m-80) cc_final: 0.7854 (m-80) REVERT: q 76 ASP cc_start: 0.8005 (t0) cc_final: 0.7768 (t0) REVERT: q 100 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7706 (t80) REVERT: E 33 ASN cc_start: 0.8001 (p0) cc_final: 0.7552 (p0) REVERT: A 4 LEU cc_start: 0.5799 (mt) cc_final: 0.5498 (mt) REVERT: C 50 GLU cc_start: 0.5069 (mt-10) cc_final: 0.4832 (mm-30) REVERT: F 43 LYS cc_start: 0.9378 (mmmm) cc_final: 0.9139 (mttt) REVERT: F 103 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8215 (mppt) REVERT: J 99 ASP cc_start: 0.8928 (p0) cc_final: 0.8728 (p0) REVERT: K 1 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: K 98 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7504 (tm-30) REVERT: P 33 ASN cc_start: 0.8093 (p0) cc_final: 0.7830 (p0) REVERT: P 255 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (m) REVERT: N 50 GLU cc_start: 0.4970 (mt-10) cc_final: 0.4634 (mm-30) REVERT: Q 32 ASN cc_start: 0.8465 (m-40) cc_final: 0.8197 (m-40) REVERT: Q 103 LYS cc_start: 0.8322 (mmmm) cc_final: 0.8098 (mppt) REVERT: S 100 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7649 (t80) outliers start: 67 outliers final: 27 residues processed: 394 average time/residue: 0.2175 time to fit residues: 135.7698 Evaluate side-chains 325 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 20 optimal weight: 2.9990 chunk 315 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 285 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 77 GLN L 93 GLN D 543 ASN M 5 GLN N 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.105262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.063739 restraints weight = 82487.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.065821 restraints weight = 47162.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067114 restraints weight = 34472.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067898 restraints weight = 29149.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068263 restraints weight = 26516.059| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33159 Z= 0.231 Angle : 0.753 11.302 45372 Z= 0.364 Chirality : 0.046 0.297 5445 Planarity : 0.004 0.057 5490 Dihedral : 5.770 41.273 4174 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.93 % Allowed : 16.50 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.03 (0.12), residues: 3801 helix: -2.61 (0.21), residues: 396 sheet: -1.52 (0.14), residues: 1248 loop : -2.22 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 30 TYR 0.014 0.001 TYR A 59 PHE 0.042 0.002 PHE L 98 TRP 0.014 0.001 TRP G 112 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (32946) covalent geometry : angle 0.71686 / 0.36 (44790) SS BOND : bond 0.00687 / 0.55 ( 57) SS BOND : angle 1.52572 / 0.98 ( 114) hydrogen bonds : bond 0.04104 / 2.68 ( 870) hydrogen bonds : angle 6.04772 / 4.20 ( 2214) link_ALPHA1-2 : bond 0.00528 / 0.25 ( 3) link_ALPHA1-2 : angle 2.07683 / 1.35 ( 9) link_ALPHA1-3 : bond 0.00622 / 0.38 ( 15) link_ALPHA1-3 : angle 1.83244 / 1.30 ( 45) link_ALPHA1-6 : bond 0.00461 / 0.32 ( 12) link_ALPHA1-6 : angle 1.58466 / 1.03 ( 36) link_BETA1-4 : bond 0.00488 / 0.36 ( 69) link_BETA1-4 : angle 1.74286 / 1.20 ( 207) link_NAG-ASN : bond 0.00588 / 0.38 ( 57) link_NAG-ASN : angle 2.98607 / 2.22 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 306 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8214 (m-80) cc_final: 0.7982 (m-10) REVERT: B 530 MET cc_start: 0.8315 (mtt) cc_final: 0.8098 (mtt) REVERT: G 161 MET cc_start: 0.7634 (tpp) cc_final: 0.7417 (ttm) REVERT: G 272 ILE cc_start: 0.8902 (pt) cc_final: 0.8533 (mt) REVERT: L 50 GLU cc_start: 0.5050 (mt-10) cc_final: 0.4845 (mm-30) REVERT: m 32 ASN cc_start: 0.8440 (m-40) cc_final: 0.8210 (m110) REVERT: m 103 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8205 (mppt) REVERT: n 87 TYR cc_start: 0.8335 (m-80) cc_final: 0.7712 (m-80) REVERT: q 76 ASP cc_start: 0.7987 (t0) cc_final: 0.7717 (t0) REVERT: O 663 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8777 (pp) REVERT: E 33 ASN cc_start: 0.7997 (p0) cc_final: 0.7591 (p0) REVERT: C 50 GLU cc_start: 0.5100 (mt-10) cc_final: 0.4816 (mm-30) REVERT: F 103 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8227 (mppt) REVERT: I 54 ARG cc_start: 0.8593 (ptt-90) cc_final: 0.8225 (ptt180) REVERT: K 1 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: D 519 PHE cc_start: 0.8350 (m-10) cc_final: 0.8148 (m-10) REVERT: P 33 ASN cc_start: 0.8071 (p0) cc_final: 0.7846 (p0) REVERT: P 255 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8769 (m) REVERT: P 302 ASN cc_start: 0.8668 (t0) cc_final: 0.8360 (t0) REVERT: N 50 GLU cc_start: 0.4804 (mt-10) cc_final: 0.4564 (mm-30) REVERT: Q 32 ASN cc_start: 0.8320 (m-40) cc_final: 0.7982 (m-40) REVERT: Q 103 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8133 (mppt) REVERT: S 100 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7706 (t80) REVERT: T 32 MET cc_start: 0.8321 (tpt) cc_final: 0.7906 (tpp) outliers start: 98 outliers final: 55 residues processed: 388 average time/residue: 0.2059 time to fit residues: 127.5715 Evaluate side-chains 347 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 98 CYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 357 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 317 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 181 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 314 optimal weight: 50.0000 overall best weight: 2.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN H 76 ASN L 38 GLN C 38 GLN N 38 GLN S 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.105430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063978 restraints weight = 82083.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066062 restraints weight = 46840.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067317 restraints weight = 34453.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068149 restraints weight = 29072.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068664 restraints weight = 26264.659| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33159 Z= 0.210 Angle : 0.734 10.811 45372 Z= 0.354 Chirality : 0.046 0.297 5445 Planarity : 0.004 0.055 5490 Dihedral : 5.644 39.972 4173 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.23 % Allowed : 17.97 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.82 (0.13), residues: 3801 helix: -2.15 (0.23), residues: 393 sheet: -1.52 (0.14), residues: 1302 loop : -2.05 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 30 TYR 0.017 0.001 TYR N 87 PHE 0.038 0.002 PHE L 98 TRP 0.014 0.001 TRP P 112 HIS 0.005 0.001 HIS m 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (32946) covalent geometry : angle 0.69845 / 0.35 (44790) SS BOND : bond 0.00342 / 0.23 ( 57) SS BOND : angle 1.86436 / 1.19 ( 114) hydrogen bonds : bond 0.03674 / 2.41 ( 870) hydrogen bonds : angle 5.74608 / 3.98 ( 2214) link_ALPHA1-2 : bond 0.00453 / 0.21 ( 3) link_ALPHA1-2 : angle 1.89505 / 1.22 ( 9) link_ALPHA1-3 : bond 0.00572 / 0.34 ( 15) link_ALPHA1-3 : angle 1.81996 / 1.29 ( 45) link_ALPHA1-6 : bond 0.00448 / 0.31 ( 12) link_ALPHA1-6 : angle 1.55327 / 1.01 ( 36) link_BETA1-4 : bond 0.00468 / 0.34 ( 69) link_BETA1-4 : angle 1.63502 / 1.13 ( 207) link_NAG-ASN : bond 0.00543 / 0.35 ( 57) link_NAG-ASN : angle 2.85823 / 2.13 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8301 (m-80) cc_final: 0.8055 (m-10) REVERT: B 657 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8178 (tm-30) REVERT: G 161 MET cc_start: 0.7680 (tpp) cc_final: 0.7399 (ttm) REVERT: G 272 ILE cc_start: 0.8911 (pt) cc_final: 0.8553 (mt) REVERT: m 103 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8219 (mppt) REVERT: n 87 TYR cc_start: 0.8317 (m-80) cc_final: 0.7689 (m-80) REVERT: q 100 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7768 (t80) REVERT: O 663 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8769 (pp) REVERT: E 33 ASN cc_start: 0.8007 (p0) cc_final: 0.7720 (p0) REVERT: E 95 MET cc_start: 0.8429 (ptm) cc_final: 0.7792 (ttp) REVERT: C 50 GLU cc_start: 0.4941 (mt-10) cc_final: 0.4716 (mm-30) REVERT: F 43 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9054 (mtmt) REVERT: F 103 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8259 (mppt) REVERT: I 54 ARG cc_start: 0.8640 (ptt-90) cc_final: 0.8257 (ptt180) REVERT: J 100 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8035 (t80) REVERT: K 1 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: K 32 MET cc_start: 0.8432 (tpt) cc_final: 0.7187 (tpp) REVERT: K 98 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7553 (tm-30) REVERT: P 33 ASN cc_start: 0.8025 (p0) cc_final: 0.7822 (p0) REVERT: P 255 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8789 (m) REVERT: P 302 ASN cc_start: 0.8664 (t0) cc_final: 0.8318 (t0) REVERT: Q 32 ASN cc_start: 0.8250 (m-40) cc_final: 0.7884 (m-40) REVERT: Q 103 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8171 (mppt) REVERT: S 100 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7796 (t80) outliers start: 108 outliers final: 63 residues processed: 393 average time/residue: 0.2075 time to fit residues: 131.2050 Evaluate side-chains 348 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 434 MET Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 280 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 345 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN P 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065582 restraints weight = 81980.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067671 restraints weight = 46345.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068984 restraints weight = 33839.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069635 restraints weight = 28433.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070152 restraints weight = 25940.264| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33159 Z= 0.142 Angle : 0.694 11.281 45372 Z= 0.334 Chirality : 0.044 0.287 5445 Planarity : 0.004 0.057 5490 Dihedral : 5.447 43.117 4173 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.90 % Allowed : 19.16 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.60 (0.13), residues: 3801 helix: -1.81 (0.25), residues: 396 sheet: -1.33 (0.14), residues: 1236 loop : -1.98 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.019 0.001 TYR L 87 PHE 0.024 0.001 PHE C 98 TRP 0.031 0.001 TRP H 36 HIS 0.005 0.001 HIS Q 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32946) covalent geometry : angle 0.66241 / 0.33 (44790) SS BOND : bond 0.00462 / 0.36 ( 57) SS BOND : angle 1.68075 / 1.14 ( 114) hydrogen bonds : bond 0.03285 / 2.15 ( 870) hydrogen bonds : angle 5.43747 / 3.74 ( 2214) link_ALPHA1-2 : bond 0.00560 / 0.25 ( 3) link_ALPHA1-2 : angle 1.61204 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00573 / 0.37 ( 15) link_ALPHA1-3 : angle 1.74256 / 1.23 ( 45) link_ALPHA1-6 : bond 0.00468 / 0.32 ( 12) link_ALPHA1-6 : angle 1.48752 / 0.97 ( 36) link_BETA1-4 : bond 0.00458 / 0.33 ( 69) link_BETA1-4 : angle 1.51432 / 1.05 ( 207) link_NAG-ASN : bond 0.00387 / 0.24 ( 57) link_NAG-ASN : angle 2.63793 / 1.98 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 308 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8279 (m-80) cc_final: 0.8036 (m-10) REVERT: B 657 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 161 MET cc_start: 0.7606 (tpp) cc_final: 0.7284 (ttm) REVERT: G 272 ILE cc_start: 0.8900 (pt) cc_final: 0.8581 (mt) REVERT: m 43 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8987 (mtpt) REVERT: m 103 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8263 (mppt) REVERT: n 49 TYR cc_start: 0.8463 (p90) cc_final: 0.8201 (p90) REVERT: n 87 TYR cc_start: 0.8332 (m-80) cc_final: 0.6606 (m-80) REVERT: q 100 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7729 (t80) REVERT: O 626 MET cc_start: 0.8052 (mtp) cc_final: 0.7837 (mtp) REVERT: O 663 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8805 (pp) REVERT: E 33 ASN cc_start: 0.7963 (p0) cc_final: 0.7678 (p0) REVERT: E 95 MET cc_start: 0.8431 (ptm) cc_final: 0.7767 (ttp) REVERT: C 50 GLU cc_start: 0.4966 (mt-10) cc_final: 0.4718 (mm-30) REVERT: F 43 LYS cc_start: 0.9344 (mmmm) cc_final: 0.9065 (mtmt) REVERT: F 103 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8227 (mppt) REVERT: I 49 TYR cc_start: 0.8423 (p90) cc_final: 0.8050 (p90) REVERT: I 54 ARG cc_start: 0.8639 (ptt-90) cc_final: 0.8235 (ptt180) REVERT: J 100 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7436 (t80) REVERT: K 1 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: K 32 MET cc_start: 0.8374 (tpt) cc_final: 0.7120 (tpp) REVERT: K 98 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7644 (tm-30) REVERT: P 33 ASN cc_start: 0.8003 (p0) cc_final: 0.7802 (p0) REVERT: P 255 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8758 (m) REVERT: P 302 ASN cc_start: 0.8671 (t0) cc_final: 0.8329 (t0) REVERT: Q 13 LYS cc_start: 0.8298 (mmmt) cc_final: 0.8036 (mmmt) REVERT: Q 16 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7046 (tm-30) REVERT: Q 32 ASN cc_start: 0.8182 (m-40) cc_final: 0.7770 (m-40) REVERT: Q 43 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8924 (mtpt) REVERT: S 100 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7931 (t80) outliers start: 97 outliers final: 58 residues processed: 393 average time/residue: 0.2023 time to fit residues: 128.5662 Evaluate side-chains 340 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 191 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 304 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 216 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30EHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.106992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066091 restraints weight = 80240.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068148 restraints weight = 45561.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069497 restraints weight = 33163.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070163 restraints weight = 27737.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070680 restraints weight = 25164.505| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33159 Z= 0.136 Angle : 0.674 10.226 45372 Z= 0.324 Chirality : 0.044 0.287 5445 Planarity : 0.004 0.056 5490 Dihedral : 5.239 40.475 4173 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.23 % Allowed : 19.67 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.43 (0.13), residues: 3801 helix: -1.53 (0.25), residues: 396 sheet: -1.16 (0.15), residues: 1218 loop : -1.93 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 30 TYR 0.021 0.001 TYR Q 100O PHE 0.023 0.001 PHE A 32 TRP 0.042 0.001 TRP M 36 HIS 0.006 0.001 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (32946) covalent geometry : angle 0.64449 / 0.32 (44790) SS BOND : bond 0.00278 / 0.19 ( 57) SS BOND : angle 1.35726 / 0.91 ( 114) hydrogen bonds : bond 0.03133 / 2.04 ( 870) hydrogen bonds : angle 5.14006 / 3.54 ( 2214) link_ALPHA1-2 : bond 0.00530 / 0.24 ( 3) link_ALPHA1-2 : angle 1.60817 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00554 / 0.35 ( 15) link_ALPHA1-3 : angle 1.70259 / 1.20 ( 45) link_ALPHA1-6 : bond 0.00454 / 0.31 ( 12) link_ALPHA1-6 : angle 1.47244 / 0.96 ( 36) link_BETA1-4 : bond 0.00446 / 0.32 ( 69) link_BETA1-4 : angle 1.47415 / 1.02 ( 207) link_NAG-ASN : bond 0.00372 / 0.23 ( 57) link_NAG-ASN : angle 2.53885 / 1.90 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 299 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8290 (m-80) cc_final: 0.8006 (m-10) REVERT: B 571 TRP cc_start: 0.6466 (m-90) cc_final: 0.6261 (m-90) REVERT: G 161 MET cc_start: 0.7758 (tpp) cc_final: 0.7404 (ttm) REVERT: G 272 ILE cc_start: 0.8899 (pt) cc_final: 0.8615 (mt) REVERT: G 482 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: H 32 PHE cc_start: 0.6928 (m-80) cc_final: 0.6421 (m-10) REVERT: n 49 TYR cc_start: 0.8459 (p90) cc_final: 0.8203 (p90) REVERT: q 100 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7580 (t80) REVERT: O 626 MET cc_start: 0.8015 (mtp) cc_final: 0.7750 (mtp) REVERT: E 33 ASN cc_start: 0.7945 (p0) cc_final: 0.7661 (p0) REVERT: E 95 MET cc_start: 0.8445 (ptm) cc_final: 0.7788 (ttp) REVERT: C 90 GLN cc_start: 0.4609 (OUTLIER) cc_final: 0.4181 (pm20) REVERT: F 43 LYS cc_start: 0.9311 (mmmm) cc_final: 0.9048 (mtmt) REVERT: F 103 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8209 (mppt) REVERT: I 49 TYR cc_start: 0.8412 (p90) cc_final: 0.8022 (p90) REVERT: I 54 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.8271 (ptt180) REVERT: J 100 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7502 (t80) REVERT: K 1 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: K 98 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7650 (tm-30) REVERT: P 95 MET cc_start: 0.8426 (ptm) cc_final: 0.7871 (ttp) REVERT: P 255 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8753 (m) REVERT: P 302 ASN cc_start: 0.8672 (t0) cc_final: 0.8298 (t0) REVERT: M 4 LEU cc_start: 0.7209 (mp) cc_final: 0.6967 (tp) REVERT: Q 13 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7966 (mmmt) REVERT: Q 16 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6977 (tm-30) REVERT: Q 32 ASN cc_start: 0.8144 (m-40) cc_final: 0.7702 (m-40) REVERT: S 100 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7909 (t80) REVERT: T 32 MET cc_start: 0.8358 (tpt) cc_final: 0.7562 (tpp) outliers start: 108 outliers final: 72 residues processed: 391 average time/residue: 0.2001 time to fit residues: 126.9374 Evaluate side-chains 357 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 140 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 199 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN E 203 GLN A 3 GLN C 34 HIS ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066485 restraints weight = 81138.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068608 restraints weight = 45666.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069955 restraints weight = 33085.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070596 restraints weight = 27691.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071100 restraints weight = 25314.032| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33159 Z= 0.127 Angle : 0.666 10.191 45372 Z= 0.320 Chirality : 0.044 0.284 5445 Planarity : 0.004 0.059 5490 Dihedral : 5.109 38.342 4172 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.14 % Allowed : 20.51 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.31 (0.13), residues: 3801 helix: -1.44 (0.25), residues: 402 sheet: -1.05 (0.15), residues: 1218 loop : -1.86 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 30 TYR 0.023 0.001 TYR Q 100O PHE 0.031 0.001 PHE C 98 TRP 0.030 0.001 TRP H 34 HIS 0.005 0.001 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32946) covalent geometry : angle 0.63830 / 0.31 (44790) SS BOND : bond 0.00257 / 0.17 ( 57) SS BOND : angle 1.23955 / 0.84 ( 114) hydrogen bonds : bond 0.03002 / 1.95 ( 870) hydrogen bonds : angle 4.96886 / 3.42 ( 2214) link_ALPHA1-2 : bond 0.00533 / 0.24 ( 3) link_ALPHA1-2 : angle 1.55564 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00561 / 0.35 ( 15) link_ALPHA1-3 : angle 1.68536 / 1.18 ( 45) link_ALPHA1-6 : bond 0.00457 / 0.31 ( 12) link_ALPHA1-6 : angle 1.46100 / 0.95 ( 36) link_BETA1-4 : bond 0.00441 / 0.32 ( 69) link_BETA1-4 : angle 1.43992 / 1.00 ( 207) link_NAG-ASN : bond 0.00340 / 0.20 ( 57) link_NAG-ASN : angle 2.44803 / 1.84 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 294 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8279 (m-80) cc_final: 0.7998 (m-10) REVERT: G 161 MET cc_start: 0.7772 (tpp) cc_final: 0.7400 (ttm) REVERT: G 272 ILE cc_start: 0.8919 (pt) cc_final: 0.8663 (mt) REVERT: G 482 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: H 32 PHE cc_start: 0.6917 (m-80) cc_final: 0.6513 (m-10) REVERT: m 30 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8581 (mtp-110) REVERT: m 43 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8888 (mtpt) REVERT: n 49 TYR cc_start: 0.8431 (p90) cc_final: 0.8177 (p90) REVERT: E 33 ASN cc_start: 0.7940 (p0) cc_final: 0.7664 (p0) REVERT: E 95 MET cc_start: 0.8434 (ptm) cc_final: 0.7794 (ttp) REVERT: F 30 ARG cc_start: 0.8776 (ttp-110) cc_final: 0.8209 (tpp80) REVERT: F 43 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9023 (mtmt) REVERT: F 103 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8171 (mppt) REVERT: I 49 TYR cc_start: 0.8396 (p90) cc_final: 0.8134 (p90) REVERT: I 54 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8312 (ptt180) REVERT: J 100 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7430 (t80) REVERT: K 1 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: K 78 ASP cc_start: 0.8266 (t70) cc_final: 0.7893 (t0) REVERT: K 98 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7646 (tm-30) REVERT: D 657 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8285 (pp20) REVERT: P 95 MET cc_start: 0.8388 (ptm) cc_final: 0.7701 (ttp) REVERT: P 255 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (m) REVERT: P 302 ASN cc_start: 0.8663 (t0) cc_final: 0.8284 (t0) REVERT: M 4 LEU cc_start: 0.7248 (mp) cc_final: 0.6989 (tp) REVERT: Q 16 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6885 (tm-30) REVERT: Q 32 ASN cc_start: 0.8139 (m-40) cc_final: 0.7718 (m-40) REVERT: Q 43 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8898 (mtpt) REVERT: Q 96 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8584 (mmmt) REVERT: S 100 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7880 (t80) outliers start: 105 outliers final: 78 residues processed: 382 average time/residue: 0.2009 time to fit residues: 124.1096 Evaluate side-chains 361 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 222 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 262 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 275 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 27 GLN ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN N 34 HIS Q 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.105127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063670 restraints weight = 80929.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.065702 restraints weight = 46144.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066850 restraints weight = 33937.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067689 restraints weight = 28850.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068064 restraints weight = 26114.459| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 33159 Z= 0.260 Angle : 0.757 11.553 45372 Z= 0.363 Chirality : 0.046 0.300 5445 Planarity : 0.004 0.057 5490 Dihedral : 5.337 38.994 4172 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.41 % Allowed : 20.99 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.35 (0.13), residues: 3801 helix: -1.44 (0.26), residues: 384 sheet: -1.20 (0.14), residues: 1302 loop : -1.82 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 30 TYR 0.021 0.002 TYR Q 100O PHE 0.024 0.002 PHE J 100D TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (32946) covalent geometry : angle 0.72706 / 0.36 (44790) SS BOND : bond 0.00393 / 0.28 ( 57) SS BOND : angle 1.37871 / 0.94 ( 114) hydrogen bonds : bond 0.03387 / 2.20 ( 870) hydrogen bonds : angle 5.14260 / 3.55 ( 2214) link_ALPHA1-2 : bond 0.00279 / 0.12 ( 3) link_ALPHA1-2 : angle 1.92800 / 1.22 ( 9) link_ALPHA1-3 : bond 0.00510 / 0.33 ( 15) link_ALPHA1-3 : angle 1.80786 / 1.29 ( 45) link_ALPHA1-6 : bond 0.00408 / 0.27 ( 12) link_ALPHA1-6 : angle 1.53570 / 0.99 ( 36) link_BETA1-4 : bond 0.00451 / 0.32 ( 69) link_BETA1-4 : angle 1.60985 / 1.10 ( 207) link_NAG-ASN : bond 0.00645 / 0.42 ( 57) link_NAG-ASN : angle 2.73483 / 2.04 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 281 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8318 (m-80) cc_final: 0.8023 (m-10) REVERT: G 161 MET cc_start: 0.7847 (tpp) cc_final: 0.7443 (ttm) REVERT: G 272 ILE cc_start: 0.8980 (pt) cc_final: 0.8658 (mt) REVERT: G 482 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: H 32 PHE cc_start: 0.7044 (m-80) cc_final: 0.6709 (m-10) REVERT: m 43 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8898 (mtpt) REVERT: n 49 TYR cc_start: 0.8526 (p90) cc_final: 0.8264 (p90) REVERT: E 33 ASN cc_start: 0.7980 (p0) cc_final: 0.7713 (p0) REVERT: A 4 LEU cc_start: 0.6734 (pt) cc_final: 0.6510 (pp) REVERT: F 30 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8277 (tpp80) REVERT: F 103 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8211 (mppt) REVERT: I 49 TYR cc_start: 0.8531 (p90) cc_final: 0.8312 (p90) REVERT: I 54 ARG cc_start: 0.8651 (ptt-90) cc_final: 0.8299 (ptt90) REVERT: J 100 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7504 (t80) REVERT: K 1 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: K 32 MET cc_start: 0.7966 (tpp) cc_final: 0.7625 (ttt) REVERT: K 98 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7641 (tm-30) REVERT: P 95 MET cc_start: 0.8551 (ptm) cc_final: 0.8053 (ttp) REVERT: P 302 ASN cc_start: 0.8747 (t0) cc_final: 0.8311 (t0) REVERT: M 4 LEU cc_start: 0.7149 (mp) cc_final: 0.6797 (mt) REVERT: M 94 ARG cc_start: 0.6700 (ttp-110) cc_final: 0.6126 (ttp-170) REVERT: Q 13 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8063 (mmmt) REVERT: Q 16 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6887 (tm-30) REVERT: Q 32 ASN cc_start: 0.8243 (m-40) cc_final: 0.7784 (m-40) REVERT: Q 43 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8896 (mtpt) REVERT: S 100 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7867 (t80) REVERT: T 32 MET cc_start: 0.8319 (tpt) cc_final: 0.7223 (tpp) outliers start: 114 outliers final: 89 residues processed: 380 average time/residue: 0.2051 time to fit residues: 126.1386 Evaluate side-chains 364 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 271 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 8.9990 chunk 349 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 330 optimal weight: 50.0000 chunk 253 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 HIS ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN F 97 HIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.105539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064183 restraints weight = 80339.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066228 restraints weight = 45929.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067355 restraints weight = 33641.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068192 restraints weight = 28587.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068706 restraints weight = 25963.786| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33159 Z= 0.225 Angle : 0.743 10.318 45372 Z= 0.357 Chirality : 0.045 0.301 5445 Planarity : 0.004 0.056 5490 Dihedral : 5.342 37.642 4172 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.23 % Allowed : 21.64 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.25 (0.13), residues: 3801 helix: -1.41 (0.25), residues: 384 sheet: -1.02 (0.15), residues: 1218 loop : -1.81 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 30 TYR 0.023 0.001 TYR L 87 PHE 0.025 0.002 PHE J 100D TRP 0.028 0.001 TRP M 34 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (32946) covalent geometry : angle 0.71317 / 0.35 (44790) SS BOND : bond 0.00350 / 0.23 ( 57) SS BOND : angle 1.52467 / 1.06 ( 114) hydrogen bonds : bond 0.03311 / 2.17 ( 870) hydrogen bonds : angle 5.08648 / 3.51 ( 2214) link_ALPHA1-2 : bond 0.00444 / 0.20 ( 3) link_ALPHA1-2 : angle 1.84593 / 1.18 ( 9) link_ALPHA1-3 : bond 0.00515 / 0.32 ( 15) link_ALPHA1-3 : angle 1.79339 / 1.27 ( 45) link_ALPHA1-6 : bond 0.00401 / 0.27 ( 12) link_ALPHA1-6 : angle 1.52378 / 0.99 ( 36) link_BETA1-4 : bond 0.00448 / 0.32 ( 69) link_BETA1-4 : angle 1.53435 / 1.04 ( 207) link_NAG-ASN : bond 0.00556 / 0.36 ( 57) link_NAG-ASN : angle 2.68771 / 2.01 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 280 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 PHE cc_start: 0.8260 (m-80) cc_final: 0.8021 (m-10) REVERT: G 161 MET cc_start: 0.7832 (tpp) cc_final: 0.7468 (ttm) REVERT: G 272 ILE cc_start: 0.8941 (pt) cc_final: 0.8667 (mt) REVERT: G 482 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: H 32 PHE cc_start: 0.6973 (m-80) cc_final: 0.6625 (m-10) REVERT: n 49 TYR cc_start: 0.8516 (p90) cc_final: 0.8261 (p90) REVERT: E 33 ASN cc_start: 0.7977 (p0) cc_final: 0.7688 (p0) REVERT: F 30 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8234 (tpp80) REVERT: F 43 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8967 (mtmt) REVERT: F 103 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8197 (mppt) REVERT: I 49 TYR cc_start: 0.8485 (p90) cc_final: 0.8274 (p90) REVERT: K 1 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: K 98 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7624 (tm-30) REVERT: P 33 ASN cc_start: 0.7888 (p0) cc_final: 0.7584 (p0) REVERT: P 95 MET cc_start: 0.8531 (ptm) cc_final: 0.8027 (ttp) REVERT: P 302 ASN cc_start: 0.8715 (t0) cc_final: 0.8269 (t0) REVERT: M 4 LEU cc_start: 0.7075 (mp) cc_final: 0.6873 (mt) REVERT: Q 13 LYS cc_start: 0.8298 (mmmt) cc_final: 0.8045 (mmmt) REVERT: Q 16 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6765 (tm-30) REVERT: Q 32 ASN cc_start: 0.8208 (m-40) cc_final: 0.7724 (m-40) REVERT: Q 43 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8890 (mtpt) REVERT: S 100 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7880 (t80) REVERT: T 32 MET cc_start: 0.8267 (tpt) cc_final: 0.7235 (tpp) outliers start: 108 outliers final: 91 residues processed: 373 average time/residue: 0.2029 time to fit residues: 122.3554 Evaluate side-chains 357 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 263 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 78 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 358 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 292 optimal weight: 0.0000 chunk 85 optimal weight: 0.0570 chunk 334 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 chunk 247 optimal weight: 0.0170 chunk 124 optimal weight: 10.0000 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 51 ASN q 101 GLN ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN I 51 ASN M 5 GLN R 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.107998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073955 restraints weight = 80752.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071509 restraints weight = 61908.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072492 restraints weight = 48771.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073508 restraints weight = 38115.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073523 restraints weight = 33358.282| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33159 Z= 0.111 Angle : 0.683 12.737 45372 Z= 0.330 Chirality : 0.044 0.281 5445 Planarity : 0.004 0.071 5490 Dihedral : 5.073 38.478 4172 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.30 % Allowed : 22.42 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.12 (0.13), residues: 3801 helix: -1.44 (0.25), residues: 420 sheet: -0.94 (0.15), residues: 1224 loop : -1.69 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 30 TYR 0.024 0.001 TYR Q 100O PHE 0.017 0.001 PHE J 100D TRP 0.029 0.001 TRP M 34 HIS 0.004 0.001 HIS m 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (32946) covalent geometry : angle 0.65823 / 0.32 (44790) SS BOND : bond 0.00275 / 0.19 ( 57) SS BOND : angle 1.45101 / 1.02 ( 114) hydrogen bonds : bond 0.02914 / 1.91 ( 870) hydrogen bonds : angle 4.76230 / 3.28 ( 2214) link_ALPHA1-2 : bond 0.00686 / 0.30 ( 3) link_ALPHA1-2 : angle 1.33297 / 0.83 ( 9) link_ALPHA1-3 : bond 0.00547 / 0.36 ( 15) link_ALPHA1-3 : angle 1.65606 / 1.16 ( 45) link_ALPHA1-6 : bond 0.00455 / 0.31 ( 12) link_ALPHA1-6 : angle 1.43817 / 0.94 ( 36) link_BETA1-4 : bond 0.00445 / 0.32 ( 69) link_BETA1-4 : angle 1.37691 / 0.95 ( 207) link_NAG-ASN : bond 0.00267 / 0.15 ( 57) link_NAG-ASN : angle 2.32052 / 1.75 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.7750 (tpp) cc_final: 0.7373 (ttm) REVERT: G 272 ILE cc_start: 0.8882 (pt) cc_final: 0.8636 (mt) REVERT: H 32 PHE cc_start: 0.6172 (m-80) cc_final: 0.5431 (m-10) REVERT: L 6 GLN cc_start: 0.0560 (OUTLIER) cc_final: -0.0787 (mm110) REVERT: m 30 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8649 (mtp-110) REVERT: m 43 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8875 (mtpt) REVERT: E 33 ASN cc_start: 0.7982 (p0) cc_final: 0.7706 (p0) REVERT: C 30 HIS cc_start: 0.3320 (OUTLIER) cc_final: 0.2399 (t70) REVERT: F 13 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7922 (mmmt) REVERT: F 30 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8196 (tpp80) REVERT: F 32 ASN cc_start: 0.8409 (m-40) cc_final: 0.8197 (m-40) REVERT: F 43 LYS cc_start: 0.9289 (mmmm) cc_final: 0.9004 (mtmt) REVERT: F 103 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8224 (mppt) REVERT: K 98 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 657 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8360 (pp20) REVERT: P 33 ASN cc_start: 0.8018 (p0) cc_final: 0.7746 (p0) REVERT: P 95 MET cc_start: 0.8347 (ptm) cc_final: 0.7776 (ttp) REVERT: P 255 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (m) REVERT: P 302 ASN cc_start: 0.8642 (t0) cc_final: 0.8213 (t0) REVERT: M 59 TYR cc_start: 0.5592 (m-80) cc_final: 0.4948 (m-10) REVERT: Q 16 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6931 (tm-30) REVERT: Q 32 ASN cc_start: 0.8220 (m-40) cc_final: 0.7783 (m-40) REVERT: Q 43 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8932 (mtpt) REVERT: S 99 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8461 (p0) REVERT: S 100 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7854 (t80) outliers start: 77 outliers final: 63 residues processed: 371 average time/residue: 0.1968 time to fit residues: 118.5408 Evaluate side-chains 344 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 314 optimal weight: 40.0000 chunk 241 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 377 optimal weight: 0.6980 chunk 187 optimal weight: 50.0000 chunk 172 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.107042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.064984 restraints weight = 80843.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067022 restraints weight = 46743.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068280 restraints weight = 34530.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068928 restraints weight = 29257.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069471 restraints weight = 26785.569| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33159 Z= 0.213 Angle : 0.742 10.890 45372 Z= 0.355 Chirality : 0.045 0.294 5445 Planarity : 0.004 0.059 5490 Dihedral : 5.182 36.305 4172 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.63 % Allowed : 22.57 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.06 (0.13), residues: 3801 helix: -1.25 (0.26), residues: 384 sheet: -0.83 (0.15), residues: 1206 loop : -1.73 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 30 TYR 0.029 0.001 TYR Q 100O PHE 0.024 0.002 PHE C 98 TRP 0.025 0.001 TRP M 34 HIS 0.004 0.001 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (32946) covalent geometry : angle 0.71412 / 0.35 (44790) SS BOND : bond 0.00314 / 0.21 ( 57) SS BOND : angle 1.45846 / 1.02 ( 114) hydrogen bonds : bond 0.03218 / 2.10 ( 870) hydrogen bonds : angle 4.91695 / 3.38 ( 2214) link_ALPHA1-2 : bond 0.00352 / 0.16 ( 3) link_ALPHA1-2 : angle 1.89855 / 1.21 ( 9) link_ALPHA1-3 : bond 0.00529 / 0.32 ( 15) link_ALPHA1-3 : angle 1.73908 / 1.23 ( 45) link_ALPHA1-6 : bond 0.00423 / 0.28 ( 12) link_ALPHA1-6 : angle 1.52525 / 0.99 ( 36) link_BETA1-4 : bond 0.00474 / 0.34 ( 69) link_BETA1-4 : angle 1.50214 / 1.02 ( 207) link_NAG-ASN : bond 0.00539 / 0.35 ( 57) link_NAG-ASN : angle 2.59426 / 1.93 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6284.36 seconds wall clock time: 109 minutes 18.63 seconds (6558.63 seconds total)