Starting phenix.real_space_refine on Thu Oct 29 12:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nf2_9359/10_2026/6nf2_9359.cif" } resolution = 3.7 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= -0.002 sd= 0.074 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 171 5.16 5 C 20430 2.51 5 N 5331 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32604 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 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: "C" 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: "D" 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: "E" 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: "F" 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: "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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" 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: "N" 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: "O" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "P" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "X" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 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: "d" 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: "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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: 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: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "k" 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: "l" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" 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: "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: "q" 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: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: "v" 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: "w" 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: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "2" 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: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 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: 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: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "8" Number of atoms: 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: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 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: "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: 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: "DA" 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: "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: 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: "GA" 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: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "IA" 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: "JA" 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: "A" 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: "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: "G" 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: "I" 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: "Q" 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: "R" 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 Time building chain proxies: 7.81, per 1000 atoms: 0.24 Number of scatterers: 32604 At special positions: 0 Unit cell: (160.988, 152.402, 156.695, 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 171 16.00 O 6672 8.00 N 5331 7.00 C 20430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 100A" distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 98 " - pdb=" SG CYS N 100A" distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 54 " - pdb=" SG CYS Q 74 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 126 " - pdb=" SG CYS Q 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 201 " - pdb=" SG CYS Q 433 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 218 " - pdb=" SG CYS Q 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 228 " - pdb=" SG CYS Q 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 296 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 378 " - pdb=" SG CYS Q 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 385 " - pdb=" SG CYS Q 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 98 " - pdb=" SG CYS V 100A" distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " 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 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN f 4 " - " MAN f 5 " " MAN l 4 " - " MAN l 5 " " MAN l 5 " - " MAN l 6 " " MAN v 4 " - " MAN v 5 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA 3 3 " - " MAN 3 4 " " BMA 6 3 " - " MAN 6 4 " " BMA 7 3 " - " MAN 7 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " MAN l 7 " - " MAN l 8 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA v 3 " - " MAN v 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA 7 3 " - " MAN 7 5 " " BMA 9 3 " - " MAN 9 4 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 5 " " BMA l 3 " - " MAN l 7 " " MAN l 7 " - " MAN l 9 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 6 " " BMA z 3 " - " MAN z 5 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " 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 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN G 392 " " NAG 1 1 " - " ASN G 332 " " NAG 2 1 " - " ASN G 448 " " NAG 3 1 " - " ASN G 276 " " NAG 4 1 " - " ASN Q 88 " " NAG 5 1 " - " ASN Q 133 " " NAG 6 1 " - " ASN Q 137 " " NAG 7 1 " - " ASN Q 156 " " NAG 8 1 " - " ASN Q 160 " " NAG 9 1 " - " ASN Q 197 " " NAG A 634 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG G 634 " - " ASN G 355 " " NAG I 701 " - " ASN I 637 " " NAG I 702 " - " ASN I 611 " " NAG Q 634 " - " ASN Q 355 " " NAG R 701 " - " ASN R 637 " " NAG R 702 " - " ASN R 611 " " NAG Y 1 " - " ASN A 88 " " NAG Z 1 " - " ASN A 133 " " NAG a 1 " - " ASN A 137 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN A 160 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 234 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 295 " " NAG h 1 " - " ASN A 301 " " NAG i 1 " - " ASN A 363 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 392 " " NAG l 1 " - " ASN A 332 " " NAG m 1 " - " ASN A 448 " " NAG n 1 " - " ASN A 276 " " NAG o 1 " - " ASN G 88 " " NAG p 1 " - " ASN G 133 " " NAG q 1 " - " ASN G 137 " " NAG r 1 " - " ASN G 156 " " NAG s 1 " - " ASN G 160 " " NAG t 1 " - " ASN G 197 " " NAG u 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 262 " " NAG w 1 " - " ASN G 295 " " NAG x 1 " - " ASN G 301 " " NAG y 1 " - " ASN G 363 " " NAG z 1 " - " ASN G 386 " " NAGAA 1 " - " ASN Q 234 " " NAGBA 1 " - " ASN Q 262 " " NAGCA 1 " - " ASN Q 295 " " NAGDA 1 " - " ASN Q 301 " " NAGEA 1 " - " ASN Q 363 " " NAGFA 1 " - " ASN Q 386 " " NAGGA 1 " - " ASN Q 392 " " NAGHA 1 " - " ASN Q 332 " " NAGIA 1 " - " ASN Q 448 " " NAGJA 1 " - " ASN Q 276 " Time building additional restraints: 3.47 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: 7080 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 78 sheets defined 13.7% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.960A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.187A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 removed outlier: 3.549A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.904A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 100D through 100H Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.827A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.959A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 570 through 596 removed outlier: 4.186A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER I 615 " --> pdb=" O ASN I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.579A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 663 removed outlier: 3.550A pdb=" N LEU I 663 " --> pdb=" O ASP I 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN N 64 " --> pdb=" O ARG N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.547A pdb=" N TYR Q 61 " --> pdb=" O ASP Q 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 Processing helix chain 'Q' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS Q 126 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 350 Processing helix chain 'Q' and resid 351 through 353 No H-bonds generated for 'chain 'Q' and resid 351 through 353' Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.828A pdb=" N THR Q 373 " --> pdb=" O LEU Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 475 through 480 removed outlier: 3.958A pdb=" N TRP Q 479 " --> pdb=" O MET Q 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 537 through 543 Processing helix chain 'R' and resid 570 through 596 removed outlier: 4.185A pdb=" N LEU R 581 " --> pdb=" O GLN R 577 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER R 615 " --> pdb=" O ASN R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 623 Processing helix chain 'R' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS R 633 " --> pdb=" O LEU R 629 " (cutoff:3.500A) Processing helix chain 'R' and resid 641 through 663 removed outlier: 3.548A pdb=" N LEU R 663 " --> pdb=" O ASP R 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 100D through 100H Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'V' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN V 64 " --> pdb=" O ARG V 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 61 through 64' Processing helix chain 'V' and resid 83 through 87 removed outlier: 4.113A pdb=" N THR V 87 " --> pdb=" O PRO V 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.610A pdb=" N VAL I 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL A 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR I 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL A 44 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.382A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 31 through 31B Processing sheet with id=AB3, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.871A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.521A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 40 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE C 45 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR D 5 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU D 11 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER E 70 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR E 33 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.753A pdb=" N TYR E 100O" --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100A Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL F 11 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AC6, first strand: chain 'G' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC9, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.946A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 301 through 308 removed outlier: 7.369A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP O 34 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 30 through 31B Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.623A pdb=" N SER J 70 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.833A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR J 100O" --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 99 through 100A Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL K 11 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.536A pdb=" N THR M 5 " --> pdb=" O LYS M 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU M 11 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN M 36 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU M 45 " --> pdb=" O GLN M 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.522A pdb=" N THR N 70 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE N 40 " --> pdb=" O PHE N 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE N 45 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 495 through 499 removed outlier: 5.614A pdb=" N VAL R 608 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL Q 38 " --> pdb=" O THR R 606 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR R 606 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE Q 225 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 91 through 94 removed outlier: 3.511A pdb=" N GLU Q 91 " --> pdb=" O CYS Q 239 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 130 through 133 Processing sheet with id=AG3, first strand: chain 'Q' and resid 181 through 183 Processing sheet with id=AG4, first strand: chain 'Q' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN Q 293 " --> pdb=" O SER Q 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER Q 334 " --> pdb=" O GLN Q 293 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 271 through 273 removed outlier: 11.067A pdb=" N VAL Q 286 " --> pdb=" O THR Q 455 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR Q 455 " --> pdb=" O VAL Q 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE Q 288 " --> pdb=" O ILE Q 453 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N ILE Q 453 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR Q 290 " --> pdb=" O GLY Q 451 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY Q 451 " --> pdb=" O THR Q 290 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN Q 301 " --> pdb=" O ILE Q 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE Q 322 " --> pdb=" O ASN Q 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR Q 303 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 423 through 424 Processing sheet with id=AG8, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.657A pdb=" N VAL W 12 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP W 34 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY W 50 " --> pdb=" O TRP W 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 30 through 31B removed outlier: 6.312A pdb=" N GLY R 516 " --> pdb=" O LYS W 97 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER S 70 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR S 33 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR S 100O" --> pdb=" O LYS S 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 99 through 100A Processing sheet with id=AH5, first strand: chain 'T' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL T 11 " --> pdb=" O ILE T 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR T 86 " --> pdb=" O THR T 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP T 35 " --> pdb=" O ILE T 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 19 through 23 Processing sheet with id=AH7, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR U 5 " --> pdb=" O LYS U 24 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU U 11 " --> pdb=" O GLU U 100 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN U 36 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU U 45 " --> pdb=" O GLN U 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 3 through 6 removed outlier: 3.523A pdb=" N THR V 70 " --> pdb=" O TYR V 79 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG V 38 " --> pdb=" O TRP V 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP V 47 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE V 40 " --> pdb=" O PHE V 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE V 45 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AI4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR X 97 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 2799 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: 10.83 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9457 1.33 - 1.46: 9333 1.46 - 1.59: 14294 1.59 - 1.72: 0 1.72 - 1.85: 225 Bond restraints: 33309 Sorted by residual: bond pdb=" C1 MAN 6 4 " pdb=" O5 MAN 6 4 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 MAN q 4 " pdb=" O5 MAN q 4 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG 5 1 " pdb=" O5 NAG 5 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 NAG p 1 " pdb=" O5 NAG p 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 33304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 44451 3.90 - 7.80: 759 7.80 - 11.70: 72 11.70 - 15.60: 0 15.60 - 19.50: 6 Bond angle restraints: 45288 Sorted by residual: angle pdb=" C ASN P 53 " pdb=" N ARG P 54 " pdb=" CA ARG P 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.34e+01 angle pdb=" C ASN X 53 " pdb=" N ARG X 54 " pdb=" CA ARG X 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.33e+01 angle pdb=" C ASN L 53 " pdb=" N ARG L 54 " pdb=" CA ARG L 54 " ideal model delta sigma weight residual 122.09 130.61 -8.52 1.48e+00 4.57e-01 3.31e+01 angle pdb=" CA LEU W 79 " pdb=" CB LEU W 79 " pdb=" CG LEU W 79 " ideal model delta sigma weight residual 116.30 135.80 -19.50 3.50e+00 8.16e-02 3.10e+01 angle pdb=" CA LEU O 79 " pdb=" CB LEU O 79 " pdb=" CG LEU O 79 " ideal model delta sigma weight residual 116.30 135.75 -19.45 3.50e+00 8.16e-02 3.09e+01 ... (remaining 45283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16386 17.94 - 35.89: 1633 35.89 - 53.83: 293 53.83 - 71.77: 60 71.77 - 89.72: 21 Dihedral angle restraints: 18393 sinusoidal: 7338 harmonic: 11055 Sorted by residual: dihedral pdb=" CA ASP L 50 " pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual -180.00 -119.37 -60.63 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP P 50 " pdb=" C ASP P 50 " pdb=" N VAL P 51 " pdb=" CA VAL P 51 " ideal model delta harmonic sigma weight residual -180.00 -119.38 -60.62 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP X 50 " pdb=" C ASP X 50 " pdb=" N VAL X 51 " pdb=" CA VAL X 51 " ideal model delta harmonic sigma weight residual -180.00 -119.47 -60.53 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 18390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4401 0.079 - 0.159: 990 0.159 - 0.238: 135 0.238 - 0.318: 45 0.318 - 0.397: 18 Chirality restraints: 5589 Sorted by residual: chirality pdb=" C1 MAN q 4 " pdb=" O3 BMA q 3 " pdb=" C2 MAN q 4 " pdb=" O5 MAN q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.11e+00 chirality pdb=" C1 MAN 6 4 " pdb=" O3 BMA 6 3 " pdb=" C2 MAN 6 4 " pdb=" O5 MAN 6 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.34e+00 chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.00e+00 ... (remaining 5586 not shown) Planarity restraints: 5565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO H 29 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO H 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO H 29 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR W 28 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO W 29 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO W 29 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO W 29 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO O 29 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO O 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO O 29 " 0.071 5.00e-02 4.00e+02 ... (remaining 5562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7003 2.77 - 3.31: 28556 3.31 - 3.84: 53775 3.84 - 4.37: 59169 4.37 - 4.90: 103109 Nonbonded interactions: 251612 Sorted by model distance: nonbonded pdb=" NH2 ARG W 100F" pdb=" OD2 ASP X 50 " model vdw 2.242 3.120 nonbonded pdb=" OG SER J 70 " pdb=" OG SER J 79 " model vdw 2.244 3.040 nonbonded pdb=" OG SER E 70 " pdb=" OG SER E 79 " model vdw 2.244 3.040 nonbonded pdb=" OG SER S 70 " pdb=" OG SER S 79 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR G 318 " pdb=" OD2 ASP N 76B" model vdw 2.249 3.040 ... (remaining 251607 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: 0.09 Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '5' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain 'HA' selection = chain 'l' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'AA' selection = chain 'EA' selection = chain 'IA' selection = chain 'c' selection = chain 'e' selection = chain 'i' selection = chain 'm' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '3' selection = chain '6' selection = chain '9' selection = chain 'JA' selection = chain 'a' selection = chain 'd' selection = chain 'n' selection = chain 'q' selection = chain 't' } ncs_group { reference = chain '7' selection = chain 'FA' selection = chain 'b' selection = chain 'j' selection = chain 'r' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'BA' selection = chain 'f' selection = chain 'v' } ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'X' } 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.540 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.009 0.082 33546 Z= 0.436 Angle : 1.356 19.499 45948 Z= 0.672 Chirality : 0.072 0.397 5589 Planarity : 0.008 0.140 5508 Dihedral : 14.652 89.716 11160 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 0.45 % Allowed : 10.44 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.90 (0.12), residues: 3801 helix: -2.83 (0.18), residues: 369 sheet: -1.25 (0.13), residues: 1269 loop : -2.22 (0.11), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 100 TYR 0.023 0.003 TYR A 486 PHE 0.031 0.003 PHE P 91 TRP 0.026 0.003 TRP L 35 HIS 0.007 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.44 (33309) covalent geometry : angle 1.27069 / 0.65 (45288) SS BOND : bond 0.00721 / 0.48 ( 51) SS BOND : angle 2.75605 / 1.98 ( 102) hydrogen bonds : bond 0.15517 / 10.21 ( 1053) hydrogen bonds : angle 7.75221 / 5.37 ( 2799) link_ALPHA1-2 : bond 0.00208 / 0.13 ( 9) link_ALPHA1-2 : angle 2.46174 / 1.50 ( 27) link_ALPHA1-3 : bond 0.00843 / 0.54 ( 21) link_ALPHA1-3 : angle 2.80234 / 1.95 ( 63) link_ALPHA1-6 : bond 0.00660 / 0.45 ( 18) link_ALPHA1-6 : angle 2.31249 / 1.62 ( 54) link_BETA1-4 : bond 0.00871 / 0.57 ( 81) link_BETA1-4 : angle 4.02650 / 2.71 ( 243) link_NAG-ASN : bond 0.01297 / 0.95 ( 57) link_NAG-ASN : angle 5.74741 / 3.85 ( 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 460 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 445 time to evaluate : 1.246 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: B 530 MET cc_start: 0.8750 (mtp) cc_final: 0.8536 (mtm) REVERT: B 657 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 20 ARG cc_start: 0.7532 (mpt90) cc_final: 0.7247 (mmt-90) REVERT: F 26 GLU cc_start: 0.8043 (tp30) cc_final: 0.7775 (tp30) REVERT: G 166 ARG cc_start: 0.7313 (mtm110) cc_final: 0.7101 (ttp80) REVERT: G 337 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9155 (t) REVERT: I 657 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8129 (tm-30) REVERT: J 75 LYS cc_start: 0.8511 (mttt) cc_final: 0.8219 (tttm) REVERT: J 100 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8289 (tptt) REVERT: K 26 GLU cc_start: 0.8197 (tp30) cc_final: 0.7826 (tp30) REVERT: L 61 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7787 (ttm110) REVERT: L 96 LEU cc_start: 0.7932 (mt) cc_final: 0.6967 (mp) REVERT: L 97 THR cc_start: 0.7604 (m) cc_final: 0.6642 (m) REVERT: O 34 TRP cc_start: 0.8321 (m-10) cc_final: 0.7996 (m-10) REVERT: O 47 TRP cc_start: 0.7803 (t60) cc_final: 0.7029 (t60) REVERT: O 52 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6294 (m) REVERT: P 96 LEU cc_start: 0.7721 (mt) cc_final: 0.6847 (mp) REVERT: Q 166 ARG cc_start: 0.7323 (mtm110) cc_final: 0.7106 (ttp80) REVERT: Q 337 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9191 (t) REVERT: R 657 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8053 (tm-30) REVERT: S 75 LYS cc_start: 0.8518 (mttt) cc_final: 0.8259 (tttm) REVERT: T 26 GLU cc_start: 0.8232 (tp30) cc_final: 0.7827 (tp30) REVERT: W 34 TRP cc_start: 0.8816 (m-10) cc_final: 0.8441 (m-10) REVERT: W 52 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7217 (m) REVERT: X 91 PHE cc_start: 0.8515 (p90) cc_final: 0.7909 (p90) REVERT: X 96 LEU cc_start: 0.7876 (mt) cc_final: 0.7086 (mt) REVERT: X 98 PHE cc_start: 0.7157 (m-80) cc_final: 0.6871 (m-80) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.2503 time to fit residues: 173.4011 Evaluate side-chains 240 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain W residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 246 GLN A 328 GLN B 543 ASN C 6 GLN C 64 GLN C 72 GLN C 101 GLN D 27 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN F 37 GLN G 72 HIS G 183 GLN G 203 GLN G 246 GLN G 328 GLN H 76 ASN I 543 ASN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 58 ASN J 97 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 6 GLN N 64 GLN N 72 GLN P 27 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN Q 246 GLN Q 328 GLN Q 411 ASN R 543 ASN S 58 ASN U 27 GLN U 36 GLN V 6 GLN V 64 GLN V 72 GLN V 101 GLN W 76 ASN X 27 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.086001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057799 restraints weight = 111468.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060815 restraints weight = 67562.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061013 restraints weight = 43262.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061477 restraints weight = 36367.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061623 restraints weight = 36172.774| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33546 Z= 0.171 Angle : 0.807 10.158 45948 Z= 0.385 Chirality : 0.047 0.338 5589 Planarity : 0.006 0.080 5508 Dihedral : 6.041 55.772 4180 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 1.91 % Allowed : 15.32 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.20 (0.12), residues: 3801 helix: -1.20 (0.25), residues: 369 sheet: -0.97 (0.13), residues: 1260 loop : -1.83 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG W 75 TYR 0.026 0.002 TYR J 33 PHE 0.022 0.002 PHE M 92 TRP 0.019 0.001 TRP B 571 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (33309) covalent geometry : angle 0.75247 / 0.37 (45288) SS BOND : bond 0.00348 / 0.21 ( 51) SS BOND : angle 1.79416 / 1.23 ( 102) hydrogen bonds : bond 0.04462 / 2.95 ( 1053) hydrogen bonds : angle 6.41082 / 4.45 ( 2799) link_ALPHA1-2 : bond 0.00622 / 0.37 ( 9) link_ALPHA1-2 : angle 2.02569 / 1.29 ( 27) link_ALPHA1-3 : bond 0.00910 / 0.58 ( 21) link_ALPHA1-3 : angle 2.00651 / 1.38 ( 63) link_ALPHA1-6 : bond 0.00533 / 0.36 ( 18) link_ALPHA1-6 : angle 1.57036 / 1.08 ( 54) link_BETA1-4 : bond 0.00459 / 0.30 ( 81) link_BETA1-4 : angle 2.44689 / 1.64 ( 243) link_NAG-ASN : bond 0.00546 / 0.34 ( 57) link_NAG-ASN : angle 3.40088 / 2.28 ( 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 337 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 1.210 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 657 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8165 (tm-30) REVERT: F 20 ARG cc_start: 0.7498 (mpt90) cc_final: 0.7222 (mmt-90) REVERT: G 215 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9110 (pt) REVERT: H 34 TRP cc_start: 0.8006 (m-10) cc_final: 0.7518 (m-10) REVERT: I 657 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7977 (tm-30) REVERT: J 46 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: J 100 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8384 (tptt) REVERT: L 24 ARG cc_start: 0.8105 (tmm160) cc_final: 0.7801 (tmm160) REVERT: L 30 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (p0) REVERT: L 89 MET cc_start: 0.8386 (tmm) cc_final: 0.7956 (tmm) REVERT: L 94 PHE cc_start: 0.7830 (m-80) cc_final: 0.7573 (m-80) REVERT: L 97 THR cc_start: 0.7536 (m) cc_final: 0.7116 (p) REVERT: O 34 TRP cc_start: 0.8070 (m-10) cc_final: 0.7541 (m-10) REVERT: O 47 TRP cc_start: 0.7345 (t60) cc_final: 0.6825 (t60) REVERT: P 27 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8485 (tm-30) REVERT: P 89 MET cc_start: 0.8280 (tmm) cc_final: 0.7756 (tmm) REVERT: P 97 THR cc_start: 0.7657 (m) cc_final: 0.7311 (p) REVERT: Q 215 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9165 (pt) REVERT: R 657 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7979 (tm-30) REVERT: S 75 LYS cc_start: 0.8455 (mttt) cc_final: 0.8246 (tttm) REVERT: W 1 GLN cc_start: 0.3780 (pp30) cc_final: 0.3576 (pp30) REVERT: W 34 TRP cc_start: 0.8809 (m-10) cc_final: 0.8277 (m-10) REVERT: X 77 ARG cc_start: 0.9120 (tmt170) cc_final: 0.8889 (tmt170) REVERT: X 97 THR cc_start: 0.7903 (m) cc_final: 0.7448 (p) outliers start: 64 outliers final: 24 residues processed: 323 average time/residue: 0.2354 time to fit residues: 117.0471 Evaluate side-chains 238 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain Q residue 215 ILE Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [301, 57, 207, 120, 78, 17, 38, 297, 173, 373, 131] chunk 301 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 373 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 27 GLN D 36 GLN H 76 ASN I 543 ASN I 577 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 36 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 183 GLN Q 411 ASN R 543 ASN R 577 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056206 restraints weight = 109580.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058099 restraints weight = 58722.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059315 restraints weight = 41650.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060039 restraints weight = 34183.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060410 restraints weight = 30534.337| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 33546 Z= 0.302 Angle : 0.844 10.670 45948 Z= 0.401 Chirality : 0.048 0.295 5589 Planarity : 0.005 0.066 5508 Dihedral : 5.958 53.867 4176 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 4.05 % Allowed : 15.12 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.82 (0.13), residues: 3801 helix: -0.07 (0.27), residues: 363 sheet: -0.87 (0.14), residues: 1266 loop : -1.64 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 20 TYR 0.019 0.002 TYR V 32 PHE 0.026 0.002 PHE G 382 TRP 0.024 0.002 TRP I 571 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.30 (33309) covalent geometry : angle 0.79490 / 0.39 (45288) SS BOND : bond 0.00486 / 0.30 ( 51) SS BOND : angle 1.73587 / 1.18 ( 102) hydrogen bonds : bond 0.04459 / 2.95 ( 1053) hydrogen bonds : angle 6.21500 / 4.34 ( 2799) link_ALPHA1-2 : bond 0.00487 / 0.29 ( 9) link_ALPHA1-2 : angle 1.89858 / 1.20 ( 27) link_ALPHA1-3 : bond 0.00679 / 0.44 ( 21) link_ALPHA1-3 : angle 2.06354 / 1.42 ( 63) link_ALPHA1-6 : bond 0.00552 / 0.38 ( 18) link_ALPHA1-6 : angle 1.56226 / 1.05 ( 54) link_BETA1-4 : bond 0.00461 / 0.29 ( 81) link_BETA1-4 : angle 2.41356 / 1.60 ( 243) link_NAG-ASN : bond 0.00678 / 0.45 ( 57) link_NAG-ASN : angle 3.32943 / 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 357 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 221 time to evaluate : 1.260 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 657 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 288 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8547 (p90) REVERT: I 657 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 100 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8400 (tptt) REVERT: L 97 THR cc_start: 0.7428 (m) cc_final: 0.7047 (p) REVERT: O 34 TRP cc_start: 0.8257 (m-10) cc_final: 0.7739 (m-10) REVERT: O 63 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5601 (mt) REVERT: P 27 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8416 (tp-100) REVERT: P 82 ASP cc_start: 0.5523 (OUTLIER) cc_final: 0.5189 (p0) REVERT: P 89 MET cc_start: 0.8462 (tmm) cc_final: 0.7957 (tmm) REVERT: P 97 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6768 (p) REVERT: R 657 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7960 (tm-30) REVERT: S 13 LYS cc_start: 0.9101 (tptp) cc_final: 0.8424 (mmmt) REVERT: S 16 GLU cc_start: 0.7063 (pt0) cc_final: 0.6544 (mp0) REVERT: W 1 GLN cc_start: 0.3799 (pp30) cc_final: 0.3558 (pp30) REVERT: W 39 GLN cc_start: 0.6715 (tt0) cc_final: 0.6369 (tm-30) REVERT: X 61 ARG cc_start: 0.8657 (ptp90) cc_final: 0.8408 (ptp90) REVERT: X 77 ARG cc_start: 0.9218 (tmt170) cc_final: 0.8782 (tmt170) REVERT: X 97 THR cc_start: 0.8067 (m) cc_final: 0.7463 (p) outliers start: 136 outliers final: 55 residues processed: 341 average time/residue: 0.1966 time to fit residues: 108.6748 Evaluate side-chains 244 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 411 ASN Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [4, 366, 10, 65, 314, 174, 60, 210, 81, 313, 125] chunk 4 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 36 GLN E 97 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 543 ASN L 45 GLN O 76 ASN Q 72 HIS R 543 ASN S 97 HIS ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.085372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.057453 restraints weight = 109536.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059416 restraints weight = 58565.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060665 restraints weight = 41414.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061419 restraints weight = 33957.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061871 restraints weight = 30252.941| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33546 Z= 0.175 Angle : 0.757 12.612 45948 Z= 0.358 Chirality : 0.046 0.273 5589 Planarity : 0.005 0.058 5508 Dihedral : 5.689 52.167 4176 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 3.25 % Allowed : 17.26 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.13), residues: 3801 helix: 0.37 (0.28), residues: 363 sheet: -0.67 (0.14), residues: 1236 loop : -1.48 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 24 TYR 0.020 0.001 TYR C 32 PHE 0.018 0.002 PHE O 78 TRP 0.020 0.001 TRP W 103 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (33309) covalent geometry : angle 0.71089 / 0.35 (45288) SS BOND : bond 0.00391 / 0.24 ( 51) SS BOND : angle 1.63456 / 1.09 ( 102) hydrogen bonds : bond 0.03870 / 2.55 ( 1053) hydrogen bonds : angle 5.93630 / 4.13 ( 2799) link_ALPHA1-2 : bond 0.00539 / 0.32 ( 9) link_ALPHA1-2 : angle 1.79885 / 1.13 ( 27) link_ALPHA1-3 : bond 0.00715 / 0.46 ( 21) link_ALPHA1-3 : angle 1.92895 / 1.32 ( 63) link_ALPHA1-6 : bond 0.00536 / 0.36 ( 18) link_ALPHA1-6 : angle 1.50794 / 1.02 ( 54) link_BETA1-4 : bond 0.00456 / 0.29 ( 81) link_BETA1-4 : angle 2.22221 / 1.48 ( 243) link_NAG-ASN : bond 0.00464 / 0.29 ( 57) link_NAG-ASN : angle 2.97772 / 2.00 ( 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 317 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 208 time to evaluate : 1.257 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 657 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 13 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8477 (mmmt) REVERT: G 288 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8659 (p90) REVERT: H 34 TRP cc_start: 0.8173 (m-10) cc_final: 0.7668 (m-10) REVERT: I 657 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 100 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8428 (tptt) REVERT: L 45 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: L 97 THR cc_start: 0.7362 (m) cc_final: 0.6913 (p) REVERT: O 1 GLN cc_start: 0.3832 (pp30) cc_final: 0.3586 (pp30) REVERT: O 34 TRP cc_start: 0.8312 (m-10) cc_final: 0.7845 (m-10) REVERT: O 63 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5587 (mt) REVERT: P 27 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8355 (tp-100) REVERT: P 39 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6557 (pttm) REVERT: P 89 MET cc_start: 0.8531 (tmm) cc_final: 0.8193 (tmm) REVERT: P 97 THR cc_start: 0.7219 (OUTLIER) cc_final: 0.6779 (p) REVERT: R 657 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7941 (tm-30) REVERT: S 13 LYS cc_start: 0.9034 (tptp) cc_final: 0.8423 (mmmt) REVERT: S 16 GLU cc_start: 0.7164 (pt0) cc_final: 0.6780 (mp0) REVERT: V 76 ASP cc_start: 0.8345 (m-30) cc_final: 0.8110 (t70) REVERT: W 1 GLN cc_start: 0.3960 (pp30) cc_final: 0.3722 (pp30) REVERT: X 70 ASP cc_start: 0.9199 (t0) cc_final: 0.8801 (p0) REVERT: X 77 ARG cc_start: 0.9197 (tmt170) cc_final: 0.8809 (tmt170) outliers start: 109 outliers final: 45 residues processed: 303 average time/residue: 0.1947 time to fit residues: 95.9613 Evaluate side-chains 241 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [311, 9, 257, 283, 81, 7, 64, 268, 69, 130, 5] chunk 311 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN B 543 ASN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 543 ASN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS Q 411 ASN R 543 ASN ** R 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055310 restraints weight = 110568.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057164 restraints weight = 60730.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058350 restraints weight = 43597.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059076 restraints weight = 36137.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059413 restraints weight = 32490.477| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 33546 Z= 0.310 Angle : 0.835 10.957 45948 Z= 0.397 Chirality : 0.048 0.268 5589 Planarity : 0.005 0.058 5508 Dihedral : 5.839 51.012 4176 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.52 % Allowed : 18.43 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.55 (0.13), residues: 3801 helix: 0.44 (0.27), residues: 366 sheet: -0.79 (0.14), residues: 1281 loop : -1.44 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 75 TYR 0.020 0.002 TYR P 87 PHE 0.033 0.002 PHE P 98 TRP 0.016 0.002 TRP T 96 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.31 (33309) covalent geometry : angle 0.78882 / 0.39 (45288) SS BOND : bond 0.00505 / 0.31 ( 51) SS BOND : angle 1.94838 / 1.31 ( 102) hydrogen bonds : bond 0.04285 / 2.85 ( 1053) hydrogen bonds : angle 6.02408 / 4.20 ( 2799) link_ALPHA1-2 : bond 0.00449 / 0.27 ( 9) link_ALPHA1-2 : angle 1.85286 / 1.16 ( 27) link_ALPHA1-3 : bond 0.00529 / 0.35 ( 21) link_ALPHA1-3 : angle 1.95959 / 1.34 ( 63) link_ALPHA1-6 : bond 0.00562 / 0.38 ( 18) link_ALPHA1-6 : angle 1.52149 / 1.01 ( 54) link_BETA1-4 : bond 0.00454 / 0.30 ( 81) link_BETA1-4 : angle 2.30140 / 1.52 ( 243) link_NAG-ASN : bond 0.00685 / 0.46 ( 57) link_NAG-ASN : angle 3.17783 / 2.12 ( 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 323 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 205 time to evaluate : 1.492 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 657 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8155 (tm-30) REVERT: G 288 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8491 (p90) REVERT: H 86 ASP cc_start: 0.0956 (p0) cc_final: 0.0612 (p0) REVERT: I 657 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8038 (tm-30) REVERT: J 100 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8528 (tptt) REVERT: J 100 ASP cc_start: 0.7927 (p0) cc_final: 0.7592 (p0) REVERT: L 89 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: L 97 THR cc_start: 0.6952 (m) cc_final: 0.6639 (p) REVERT: N 76 ASP cc_start: 0.8413 (m-30) cc_final: 0.7976 (t0) REVERT: O 1 GLN cc_start: 0.3949 (pp30) cc_final: 0.3683 (pp30) REVERT: O 33 TYR cc_start: 0.5919 (t80) cc_final: 0.5455 (t80) REVERT: P 13 VAL cc_start: 0.5979 (OUTLIER) cc_final: 0.5684 (t) REVERT: R 657 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8041 (tm-30) REVERT: S 13 LYS cc_start: 0.9097 (tptp) cc_final: 0.8543 (mmmt) REVERT: S 16 GLU cc_start: 0.7318 (pt0) cc_final: 0.6967 (mp0) REVERT: W 1 GLN cc_start: 0.4156 (pp30) cc_final: 0.3857 (pp30) REVERT: W 39 GLN cc_start: 0.6871 (tt0) cc_final: 0.6480 (tm-30) REVERT: X 24 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8369 (mmt-90) outliers start: 118 outliers final: 83 residues processed: 305 average time/residue: 0.2026 time to fit residues: 100.2701 Evaluate side-chains 274 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain M residue 36 GLN Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 287 GLN Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [257, 376, 271, 36, 289, 197, 162, 269, 243, 62, 255] chunk 257 optimal weight: 0.7980 chunk 376 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 0.0870 chunk 162 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 243 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS B 543 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN G 293 GLN I 543 ASN L 45 GLN Q 72 HIS Q 411 ASN R 543 ASN U 36 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.085346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057194 restraints weight = 111987.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059140 restraints weight = 61589.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060377 restraints weight = 44111.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061121 restraints weight = 36476.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061527 restraints weight = 32660.004| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33546 Z= 0.125 Angle : 0.726 15.421 45948 Z= 0.343 Chirality : 0.045 0.260 5589 Planarity : 0.004 0.056 5508 Dihedral : 5.435 50.732 4176 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.71 % Allowed : 19.53 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.26 (0.14), residues: 3801 helix: 0.78 (0.28), residues: 366 sheet: -0.55 (0.14), residues: 1254 loop : -1.30 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 24 TYR 0.027 0.001 TYR P 87 PHE 0.024 0.001 PHE L 98 TRP 0.015 0.001 TRP O 47 HIS 0.002 0.001 HIS Q 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (33309) covalent geometry : angle 0.68439 / 0.33 (45288) SS BOND : bond 0.00337 / 0.22 ( 51) SS BOND : angle 1.63442 / 1.10 ( 102) hydrogen bonds : bond 0.03470 / 2.30 ( 1053) hydrogen bonds : angle 5.73845 / 4.00 ( 2799) link_ALPHA1-2 : bond 0.00593 / 0.35 ( 9) link_ALPHA1-2 : angle 1.69016 / 1.07 ( 27) link_ALPHA1-3 : bond 0.00736 / 0.47 ( 21) link_ALPHA1-3 : angle 1.75016 / 1.19 ( 63) link_ALPHA1-6 : bond 0.00551 / 0.37 ( 18) link_ALPHA1-6 : angle 1.48629 / 1.01 ( 54) link_BETA1-4 : bond 0.00500 / 0.32 ( 81) link_BETA1-4 : angle 2.08221 / 1.38 ( 243) link_NAG-ASN : bond 0.00416 / 0.24 ( 57) link_NAG-ASN : angle 2.73954 / 1.84 ( 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 309 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 218 time to evaluate : 1.239 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: B 657 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8106 (tm-30) REVERT: G 288 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8695 (p90) REVERT: H 33 TYR cc_start: 0.6006 (t80) cc_final: 0.5422 (t80) REVERT: I 657 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7943 (tm-30) REVERT: J 100 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8471 (tmtt) REVERT: J 100 ASP cc_start: 0.7852 (p0) cc_final: 0.7429 (p0) REVERT: L 89 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8280 (tpp) REVERT: O 1 GLN cc_start: 0.4214 (pp30) cc_final: 0.3872 (pp30) REVERT: O 33 TYR cc_start: 0.5910 (t80) cc_final: 0.5456 (t80) REVERT: O 34 TRP cc_start: 0.8364 (m-10) cc_final: 0.7992 (m-10) REVERT: P 13 VAL cc_start: 0.5792 (OUTLIER) cc_final: 0.5512 (t) REVERT: R 657 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7927 (tm-30) REVERT: S 13 LYS cc_start: 0.9008 (tptp) cc_final: 0.8500 (mmmt) REVERT: U 32 MET cc_start: 0.8187 (tpp) cc_final: 0.7499 (tpp) REVERT: W 1 GLN cc_start: 0.4096 (pp30) cc_final: 0.3769 (pp30) REVERT: W 31 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8315 (ptp90) REVERT: W 39 GLN cc_start: 0.6713 (tt0) cc_final: 0.6488 (tm-30) REVERT: W 63 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5736 (mt) REVERT: X 24 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8433 (mmp80) outliers start: 91 outliers final: 49 residues processed: 293 average time/residue: 0.1997 time to fit residues: 95.2819 Evaluate side-chains 249 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 411 ASN Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [25, 43, 1, 125, 365, 243, 131, 44, 76, 284, 292] chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 365 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 284 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 293 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN Q 72 HIS Q 293 GLN R 543 ASN U 27 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.085209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057238 restraints weight = 112853.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059238 restraints weight = 60350.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060511 restraints weight = 42661.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061269 restraints weight = 34968.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061711 restraints weight = 31208.667| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33546 Z= 0.156 Angle : 0.728 14.685 45948 Z= 0.344 Chirality : 0.044 0.262 5589 Planarity : 0.004 0.058 5508 Dihedral : 5.349 49.615 4176 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.22 % Allowed : 19.17 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.16 (0.14), residues: 3801 helix: 0.94 (0.28), residues: 363 sheet: -0.54 (0.14), residues: 1263 loop : -1.20 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 75 TYR 0.021 0.001 TYR P 87 PHE 0.031 0.002 PHE M 70 TRP 0.015 0.001 TRP G 96 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (33309) covalent geometry : angle 0.68640 / 0.33 (45288) SS BOND : bond 0.00384 / 0.24 ( 51) SS BOND : angle 1.70954 / 1.15 ( 102) hydrogen bonds : bond 0.03544 / 2.35 ( 1053) hydrogen bonds : angle 5.64491 / 3.94 ( 2799) link_ALPHA1-2 : bond 0.00487 / 0.29 ( 9) link_ALPHA1-2 : angle 1.69488 / 1.06 ( 27) link_ALPHA1-3 : bond 0.00675 / 0.43 ( 21) link_ALPHA1-3 : angle 1.72823 / 1.18 ( 63) link_ALPHA1-6 : bond 0.00554 / 0.37 ( 18) link_ALPHA1-6 : angle 1.45195 / 0.98 ( 54) link_BETA1-4 : bond 0.00457 / 0.29 ( 81) link_BETA1-4 : angle 2.07642 / 1.37 ( 243) link_NAG-ASN : bond 0.00447 / 0.27 ( 57) link_NAG-ASN : angle 2.75682 / 1.85 ( 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 312 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 204 time to evaluate : 1.254 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: B 657 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8128 (tm-30) REVERT: G 288 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8589 (p90) REVERT: H 33 TYR cc_start: 0.6029 (t80) cc_final: 0.5456 (t80) REVERT: H 34 TRP cc_start: 0.8382 (m-10) cc_final: 0.7954 (m-10) REVERT: I 657 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7994 (tm-30) REVERT: J 100 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8469 (tptt) REVERT: J 100 ASP cc_start: 0.7927 (p0) cc_final: 0.7545 (p0) REVERT: L 61 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7862 (ttp-170) REVERT: L 89 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7674 (tpp) REVERT: L 98 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: N 76 ASP cc_start: 0.8432 (m-30) cc_final: 0.8227 (t70) REVERT: O 1 GLN cc_start: 0.4453 (pp30) cc_final: 0.4103 (pp30) REVERT: O 33 TYR cc_start: 0.5994 (t80) cc_final: 0.5581 (t80) REVERT: O 34 TRP cc_start: 0.8340 (m-10) cc_final: 0.7965 (m-10) REVERT: P 13 VAL cc_start: 0.5756 (OUTLIER) cc_final: 0.5460 (t) REVERT: R 530 MET cc_start: 0.8748 (mmt) cc_final: 0.8378 (mmt) REVERT: R 657 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7968 (tm-30) REVERT: U 32 MET cc_start: 0.8323 (tpp) cc_final: 0.7611 (tpp) REVERT: V 76 ASP cc_start: 0.8071 (t70) cc_final: 0.7846 (t70) REVERT: W 1 GLN cc_start: 0.4213 (pp30) cc_final: 0.3871 (pp30) REVERT: W 31 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8309 (ptp90) REVERT: W 39 GLN cc_start: 0.6847 (tt0) cc_final: 0.6510 (tm-30) REVERT: W 63 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5587 (mt) REVERT: X 24 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8496 (mmp80) outliers start: 108 outliers final: 69 residues processed: 294 average time/residue: 0.1937 time to fit residues: 93.7583 Evaluate side-chains 272 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 434 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [161, 31, 212, 257, 335, 373, 252, 179, 21, 183, 238] chunk 161 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 238 optimal weight: 50.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN O 76 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055848 restraints weight = 112381.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057740 restraints weight = 62127.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058939 restraints weight = 44700.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059657 restraints weight = 37077.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060025 restraints weight = 33288.020| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33546 Z= 0.194 Angle : 0.752 14.170 45948 Z= 0.355 Chirality : 0.045 0.260 5589 Planarity : 0.004 0.055 5508 Dihedral : 5.367 50.139 4176 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.07 % Allowed : 19.62 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.12 (0.14), residues: 3801 helix: 0.90 (0.28), residues: 363 sheet: -0.41 (0.14), residues: 1224 loop : -1.23 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.018 0.001 TYR P 87 PHE 0.019 0.002 PHE M 70 TRP 0.016 0.001 TRP G 96 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (33309) covalent geometry : angle 0.70960 / 0.34 (45288) SS BOND : bond 0.00456 / 0.28 ( 51) SS BOND : angle 1.89841 / 1.27 ( 102) hydrogen bonds : bond 0.03606 / 2.38 ( 1053) hydrogen bonds : angle 5.65366 / 3.95 ( 2799) link_ALPHA1-2 : bond 0.00470 / 0.28 ( 9) link_ALPHA1-2 : angle 1.70506 / 1.07 ( 27) link_ALPHA1-3 : bond 0.00623 / 0.40 ( 21) link_ALPHA1-3 : angle 1.74663 / 1.18 ( 63) link_ALPHA1-6 : bond 0.00553 / 0.37 ( 18) link_ALPHA1-6 : angle 1.46545 / 0.98 ( 54) link_BETA1-4 : bond 0.00452 / 0.29 ( 81) link_BETA1-4 : angle 2.08632 / 1.38 ( 243) link_NAG-ASN : bond 0.00472 / 0.29 ( 57) link_NAG-ASN : angle 2.80893 / 1.90 ( 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 306 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 203 time to evaluate : 1.057 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 657 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8139 (tm-30) REVERT: E 13 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8613 (tppt) REVERT: G 288 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8452 (p90) REVERT: H 33 TYR cc_start: 0.6026 (t80) cc_final: 0.5484 (t80) REVERT: H 34 TRP cc_start: 0.8430 (m-10) cc_final: 0.7885 (m-10) REVERT: H 86 ASP cc_start: 0.0827 (p0) cc_final: 0.0456 (p0) REVERT: I 657 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8012 (tm-30) REVERT: J 100 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8494 (tptt) REVERT: J 100 ASP cc_start: 0.7904 (p0) cc_final: 0.7558 (p0) REVERT: L 89 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7633 (tpp) REVERT: L 98 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5641 (m-80) REVERT: N 76 ASP cc_start: 0.8419 (m-30) cc_final: 0.8214 (t70) REVERT: O 1 GLN cc_start: 0.4437 (pp30) cc_final: 0.4130 (pp30) REVERT: O 33 TYR cc_start: 0.6005 (t80) cc_final: 0.5610 (t80) REVERT: O 86 ASP cc_start: 0.1376 (p0) cc_final: 0.1037 (p0) REVERT: P 13 VAL cc_start: 0.5762 (OUTLIER) cc_final: 0.5453 (t) REVERT: P 89 MET cc_start: 0.9280 (tpt) cc_final: 0.8589 (ttt) REVERT: R 530 MET cc_start: 0.8724 (mmt) cc_final: 0.8293 (mmt) REVERT: R 657 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7960 (tm-30) REVERT: W 31 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (ptp90) REVERT: W 39 GLN cc_start: 0.6720 (tt0) cc_final: 0.6442 (tm-30) REVERT: W 63 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5610 (mt) REVERT: X 24 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8569 (mmp80) REVERT: X 77 ARG cc_start: 0.8877 (ttt-90) cc_final: 0.8484 (tmt170) outliers start: 103 outliers final: 77 residues processed: 288 average time/residue: 0.2031 time to fit residues: 95.5956 Evaluate side-chains 277 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 194 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 434 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [184, 298, 110, 10, 160, 223, 170, 339, 188, 78, 44] chunk 184 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN Q 72 HIS ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.083583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055195 restraints weight = 112217.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057069 restraints weight = 62376.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058271 restraints weight = 44953.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058963 restraints weight = 37370.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.059303 restraints weight = 33608.898| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33546 Z= 0.222 Angle : 0.775 13.040 45948 Z= 0.367 Chirality : 0.046 0.260 5589 Planarity : 0.005 0.057 5508 Dihedral : 5.433 51.183 4176 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.86 % Allowed : 20.10 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.16 (0.14), residues: 3801 helix: 0.59 (0.27), residues: 384 sheet: -0.38 (0.14), residues: 1224 loop : -1.26 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 24 TYR 0.023 0.001 TYR P 87 PHE 0.017 0.002 PHE O 78 TRP 0.014 0.002 TRP N 50 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (33309) covalent geometry : angle 0.73330 / 0.36 (45288) SS BOND : bond 0.00435 / 0.27 ( 51) SS BOND : angle 1.82510 / 1.23 ( 102) hydrogen bonds : bond 0.03726 / 2.48 ( 1053) hydrogen bonds : angle 5.66695 / 3.96 ( 2799) link_ALPHA1-2 : bond 0.00467 / 0.28 ( 9) link_ALPHA1-2 : angle 1.73851 / 1.08 ( 27) link_ALPHA1-3 : bond 0.00591 / 0.38 ( 21) link_ALPHA1-3 : angle 1.76155 / 1.18 ( 63) link_ALPHA1-6 : bond 0.00557 / 0.38 ( 18) link_ALPHA1-6 : angle 1.47283 / 0.98 ( 54) link_BETA1-4 : bond 0.00440 / 0.28 ( 81) link_BETA1-4 : angle 2.11320 / 1.39 ( 243) link_NAG-ASN : bond 0.00526 / 0.34 ( 57) link_NAG-ASN : angle 2.87783 / 1.93 ( 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 290 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 194 time to evaluate : 1.341 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 657 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 288 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8534 (p90) REVERT: H 33 TYR cc_start: 0.5979 (t80) cc_final: 0.5454 (t80) REVERT: H 34 TRP cc_start: 0.8517 (m-10) cc_final: 0.8049 (m-10) REVERT: H 86 ASP cc_start: 0.1022 (p0) cc_final: 0.0642 (p0) REVERT: I 657 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8048 (tm-30) REVERT: J 100 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8464 (tptt) REVERT: J 100 ASP cc_start: 0.7909 (p0) cc_final: 0.7581 (p0) REVERT: L 89 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7647 (tpp) REVERT: L 98 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: N 76 ASP cc_start: 0.8442 (m-30) cc_final: 0.8224 (t70) REVERT: O 86 ASP cc_start: 0.1482 (p0) cc_final: 0.1136 (p0) REVERT: P 13 VAL cc_start: 0.5669 (OUTLIER) cc_final: 0.5352 (t) REVERT: P 89 MET cc_start: 0.9263 (tpt) cc_final: 0.8631 (ttt) REVERT: Q 198 THR cc_start: 0.9026 (t) cc_final: 0.8754 (p) REVERT: R 657 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7977 (tm-30) REVERT: S 13 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8644 (tppt) REVERT: T 20 ARG cc_start: 0.6911 (mmt-90) cc_final: 0.6665 (mmt-90) REVERT: W 31 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8324 (ptp90) REVERT: W 39 GLN cc_start: 0.6765 (tt0) cc_final: 0.6296 (tm-30) REVERT: W 63 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5876 (mt) REVERT: X 70 ASP cc_start: 0.9221 (t0) cc_final: 0.9004 (p0) REVERT: X 77 ARG cc_start: 0.8800 (ttt-90) cc_final: 0.8440 (tmt170) outliers start: 96 outliers final: 77 residues processed: 273 average time/residue: 0.2056 time to fit residues: 90.7975 Evaluate side-chains 272 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 189 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 434 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [376, 28, 34, 191, 221, 20, 180, 126, 302, 64, 218] chunk 376 optimal weight: 4.9990 chunk 28 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS D 36 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN M 36 GLN Q 72 HIS R 577 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 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 = 0.3812 r_free = 0.3812 target = 0.088877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060738 restraints weight = 118315.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.062747 restraints weight = 63135.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064031 restraints weight = 44620.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064785 restraints weight = 36574.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065171 restraints weight = 32665.871| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33546 Z= 0.128 Angle : 0.732 14.873 45948 Z= 0.345 Chirality : 0.044 0.259 5589 Planarity : 0.004 0.075 5508 Dihedral : 5.203 51.790 4176 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.44 % Allowed : 20.63 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.91 (0.14), residues: 3801 helix: 1.13 (0.29), residues: 348 sheet: -0.23 (0.14), residues: 1230 loop : -1.12 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG X 24 TYR 0.021 0.001 TYR P 87 PHE 0.021 0.001 PHE O 78 TRP 0.015 0.001 TRP G 96 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (33309) covalent geometry : angle 0.69483 / 0.34 (45288) SS BOND : bond 0.00361 / 0.23 ( 51) SS BOND : angle 1.55239 / 1.04 ( 102) hydrogen bonds : bond 0.03289 / 2.18 ( 1053) hydrogen bonds : angle 5.49627 / 3.84 ( 2799) link_ALPHA1-2 : bond 0.00607 / 0.36 ( 9) link_ALPHA1-2 : angle 1.64951 / 1.04 ( 27) link_ALPHA1-3 : bond 0.00682 / 0.43 ( 21) link_ALPHA1-3 : angle 1.66154 / 1.12 ( 63) link_ALPHA1-6 : bond 0.00551 / 0.36 ( 18) link_ALPHA1-6 : angle 1.46603 / 0.99 ( 54) link_BETA1-4 : bond 0.00503 / 0.32 ( 81) link_BETA1-4 : angle 1.99591 / 1.32 ( 243) link_NAG-ASN : bond 0.00400 / 0.23 ( 57) link_NAG-ASN : angle 2.63564 / 1.78 ( 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 295 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 213 time to evaluate : 1.259 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: A 161 MET cc_start: 0.8312 (tpt) cc_final: 0.7706 (tpt) REVERT: B 530 MET cc_start: 0.8854 (tpp) cc_final: 0.8111 (mmm) REVERT: B 657 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8191 (tm-30) REVERT: G 288 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8619 (p90) REVERT: H 33 TYR cc_start: 0.5950 (t80) cc_final: 0.5278 (t80) REVERT: H 34 TRP cc_start: 0.8493 (m-10) cc_final: 0.8029 (m-10) REVERT: H 86 ASP cc_start: 0.1015 (p0) cc_final: 0.0642 (p0) REVERT: H 95 ARG cc_start: 0.6184 (mtm110) cc_final: 0.5841 (mtm-85) REVERT: I 657 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8060 (tm-30) REVERT: J 100 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8432 (tmtt) REVERT: J 100 ASP cc_start: 0.7910 (p0) cc_final: 0.7603 (p0) REVERT: L 89 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7609 (tpp) REVERT: L 91 PHE cc_start: 0.8442 (p90) cc_final: 0.7244 (p90) REVERT: L 98 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6046 (m-80) REVERT: N 76 ASP cc_start: 0.8499 (m-30) cc_final: 0.8189 (t70) REVERT: O 71 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4278 (mtmt) REVERT: O 86 ASP cc_start: 0.1621 (p0) cc_final: 0.1258 (p0) REVERT: P 89 MET cc_start: 0.9215 (tpt) cc_final: 0.8664 (ttt) REVERT: P 93 GLU cc_start: 0.8321 (tp30) cc_final: 0.7965 (mm-30) REVERT: Q 198 THR cc_start: 0.9068 (t) cc_final: 0.8790 (p) REVERT: R 543 ASN cc_start: 0.8609 (t0) cc_final: 0.8399 (p0) REVERT: R 657 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8046 (tm-30) REVERT: S 13 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8673 (tppt) REVERT: W 31 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8284 (ptp90) REVERT: W 39 GLN cc_start: 0.6587 (tt0) cc_final: 0.6166 (tm-30) REVERT: W 63 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5846 (mt) REVERT: X 70 ASP cc_start: 0.9284 (t0) cc_final: 0.9019 (p0) REVERT: X 77 ARG cc_start: 0.8769 (ttt-90) cc_final: 0.8409 (tmt170) REVERT: X 82 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4779 (p0) REVERT: X 91 PHE cc_start: 0.7797 (p90) cc_final: 0.6712 (p90) outliers start: 82 outliers final: 63 residues processed: 279 average time/residue: 0.2032 time to fit residues: 91.8242 Evaluate side-chains 269 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 199 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [137, 51, 143, 155, 325, 22, 15, 193, 366, 159, 322] chunk 137 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 50.0000 chunk 325 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 366 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 322 optimal weight: 0.2980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS D 36 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 ASN U 6 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.088999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060994 restraints weight = 118601.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063006 restraints weight = 62883.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.064275 restraints weight = 44446.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065015 restraints weight = 36528.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065384 restraints weight = 32627.221| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33546 Z= 0.127 Angle : 0.720 11.623 45948 Z= 0.341 Chirality : 0.044 0.256 5589 Planarity : 0.005 0.095 5508 Dihedral : 5.080 52.317 4176 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.30 % Allowed : 20.99 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.85 (0.14), residues: 3801 helix: 1.17 (0.29), residues: 351 sheet: -0.16 (0.15), residues: 1197 loop : -1.09 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG O 75 TYR 0.024 0.001 TYR V 27 PHE 0.021 0.001 PHE O 78 TRP 0.025 0.001 TRP Q 112 HIS 0.005 0.001 HIS Q 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (33309) covalent geometry : angle 0.68173 / 0.33 (45288) SS BOND : bond 0.00350 / 0.22 ( 51) SS BOND : angle 1.68514 / 1.12 ( 102) hydrogen bonds : bond 0.03201 / 2.12 ( 1053) hydrogen bonds : angle 5.38234 / 3.76 ( 2799) link_ALPHA1-2 : bond 0.00501 / 0.30 ( 9) link_ALPHA1-2 : angle 1.60693 / 1.01 ( 27) link_ALPHA1-3 : bond 0.00690 / 0.44 ( 21) link_ALPHA1-3 : angle 1.65538 / 1.12 ( 63) link_ALPHA1-6 : bond 0.00555 / 0.37 ( 18) link_ALPHA1-6 : angle 1.44002 / 0.97 ( 54) link_BETA1-4 : bond 0.00475 / 0.31 ( 81) link_BETA1-4 : angle 1.98321 / 1.31 ( 243) link_NAG-ASN : bond 0.00399 / 0.24 ( 57) link_NAG-ASN : angle 2.58381 / 1.74 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.07 seconds wall clock time: 101 minutes 43.54 seconds (6103.54 seconds total)