Starting phenix.real_space_refine on Fri Mar 6 16:49:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nf2_9359/03_2026/6nf2_9359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf2_9359/03_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_9359/03_2026/6nf2_9359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf2_9359/03_2026/6nf2_9359.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf2_9359/03_2026/6nf2_9359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf2_9359/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.44, per 1000 atoms: 0.23 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: 2.95 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: 1.43 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: 6.74 Time building geometry restraints manager: 3.72 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 - 23.94: 20100 23.94 - 47.87: 1384 47.87 - 71.81: 269 71.81 - 95.75: 225 95.75 - 119.68: 159 Dihedral angle restraints: 22137 sinusoidal: 11082 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 22134 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: 0.04 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: 4.150 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.020 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.130 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 21.014 119.682 14904 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 covalent geometry : bond 0.00918 (33309) covalent geometry : angle 1.27069 (45288) SS BOND : bond 0.00721 ( 51) SS BOND : angle 2.75605 ( 102) hydrogen bonds : bond 0.15517 ( 1053) hydrogen bonds : angle 7.75221 ( 2799) link_ALPHA1-2 : bond 0.00208 ( 9) link_ALPHA1-2 : angle 2.46174 ( 27) link_ALPHA1-3 : bond 0.00843 ( 21) link_ALPHA1-3 : angle 2.80234 ( 63) link_ALPHA1-6 : bond 0.00660 ( 18) link_ALPHA1-6 : angle 2.31249 ( 54) link_BETA1-4 : bond 0.00871 ( 81) link_BETA1-4 : angle 4.02650 ( 243) link_NAG-ASN : bond 0.01297 ( 57) link_NAG-ASN : angle 5.74741 ( 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 : 1.228 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: 0.2486 time to fit residues: 169.5722 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 : 1.070 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: ** 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** D 75 ASN E 58 ASN F 37 GLN G 72 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.086570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058846 restraints weight = 109889.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062094 restraints weight = 64600.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062304 restraints weight = 39665.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.062651 restraints weight = 32893.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062916 restraints weight = 32888.555| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33546 Z= 0.171 Angle : 0.851 10.117 45948 Z= 0.395 Chirality : 0.049 0.305 5589 Planarity : 0.006 0.079 5508 Dihedral : 17.815 109.160 7924 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 2.00 % Allowed : 15.27 % Favored : 82.74 % 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: -1.18 (0.25), residues: 369 sheet: -0.96 (0.13), residues: 1260 loop : -1.84 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG W 75 TYR 0.025 0.002 TYR J 33 PHE 0.022 0.002 PHE M 92 TRP 0.020 0.001 TRP B 571 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00375 (33309) covalent geometry : angle 0.78906 (45288) SS BOND : bond 0.00360 ( 51) SS BOND : angle 1.74234 ( 102) hydrogen bonds : bond 0.04465 ( 1053) hydrogen bonds : angle 6.42100 ( 2799) link_ALPHA1-2 : bond 0.00693 ( 9) link_ALPHA1-2 : angle 2.05368 ( 27) link_ALPHA1-3 : bond 0.01331 ( 21) link_ALPHA1-3 : angle 2.14522 ( 63) link_ALPHA1-6 : bond 0.00563 ( 18) link_ALPHA1-6 : angle 2.09590 ( 54) link_BETA1-4 : bond 0.00434 ( 81) link_BETA1-4 : angle 2.93699 ( 243) link_NAG-ASN : bond 0.00508 ( 57) link_NAG-ASN : angle 3.45204 ( 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 344 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8144 (tm-30) REVERT: F 20 ARG cc_start: 0.7504 (mpt90) cc_final: 0.7225 (mmt-90) REVERT: G 215 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9102 (pt) REVERT: H 34 TRP cc_start: 0.8016 (m-10) cc_final: 0.7525 (m-10) REVERT: I 657 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7973 (tm-30) REVERT: J 46 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: J 100 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8365 (tptt) REVERT: L 24 ARG cc_start: 0.8116 (tmm160) cc_final: 0.7807 (tmm160) REVERT: L 30 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8195 (p0) REVERT: L 82 ASP cc_start: 0.4318 (OUTLIER) cc_final: 0.4054 (p0) REVERT: L 89 MET cc_start: 0.8375 (tmm) cc_final: 0.7914 (tmm) REVERT: L 94 PHE cc_start: 0.7816 (m-80) cc_final: 0.7550 (m-80) REVERT: L 97 THR cc_start: 0.7504 (m) cc_final: 0.7118 (p) REVERT: O 34 TRP cc_start: 0.8075 (m-10) cc_final: 0.7538 (m-10) REVERT: O 47 TRP cc_start: 0.7378 (t60) cc_final: 0.6842 (t60) REVERT: P 27 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8498 (tm-30) REVERT: P 89 MET cc_start: 0.8283 (tmm) cc_final: 0.7759 (tmm) REVERT: P 97 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7309 (p) REVERT: Q 198 THR cc_start: 0.8890 (t) cc_final: 0.8680 (p) REVERT: Q 215 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9154 (pt) REVERT: R 657 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7974 (tm-30) REVERT: S 75 LYS cc_start: 0.8453 (mttt) cc_final: 0.8247 (tttm) REVERT: W 1 GLN cc_start: 0.3775 (pp30) cc_final: 0.3575 (pp30) REVERT: W 34 TRP cc_start: 0.8811 (m-10) cc_final: 0.8282 (m-10) REVERT: X 89 MET cc_start: 0.7532 (tmm) cc_final: 0.7289 (tmm) REVERT: X 91 PHE cc_start: 0.8414 (p90) cc_final: 0.6876 (p90) REVERT: X 97 THR cc_start: 0.7893 (m) cc_final: 0.7455 (p) outliers start: 67 outliers final: 24 residues processed: 327 average time/residue: 0.2356 time to fit residues: 117.5450 Evaluate side-chains 244 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 43 LYS 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 82 ASP 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 P residue 97 THR 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: chunk 301 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 577 GLN D 27 GLN D 36 GLN E 97 HIS H 76 ASN I 543 ASN I 577 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 36 GLN N 101 GLN O 76 ASN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.084169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056234 restraints weight = 109638.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058094 restraints weight = 60095.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059270 restraints weight = 42942.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059991 restraints weight = 35456.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060358 restraints weight = 31704.914| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33546 Z= 0.294 Angle : 0.892 13.712 45948 Z= 0.413 Chirality : 0.051 0.275 5589 Planarity : 0.005 0.066 5508 Dihedral : 15.060 113.828 7920 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 4.38 % Allowed : 15.38 % Favored : 80.23 % 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: -1.77 (0.13), residues: 3801 helix: 0.03 (0.27), residues: 363 sheet: -0.85 (0.14), residues: 1260 loop : -1.60 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 61 TYR 0.020 0.002 TYR C 32 PHE 0.025 0.002 PHE G 382 TRP 0.026 0.002 TRP I 571 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00666 (33309) covalent geometry : angle 0.83569 (45288) SS BOND : bond 0.00478 ( 51) SS BOND : angle 1.73542 ( 102) hydrogen bonds : bond 0.04439 ( 1053) hydrogen bonds : angle 6.17863 ( 2799) link_ALPHA1-2 : bond 0.00406 ( 9) link_ALPHA1-2 : angle 1.97798 ( 27) link_ALPHA1-3 : bond 0.01389 ( 21) link_ALPHA1-3 : angle 2.31521 ( 63) link_ALPHA1-6 : bond 0.00654 ( 18) link_ALPHA1-6 : angle 2.29157 ( 54) link_BETA1-4 : bond 0.00490 ( 81) link_BETA1-4 : angle 2.79977 ( 243) link_NAG-ASN : bond 0.00664 ( 57) link_NAG-ASN : angle 3.38159 ( 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 369 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 222 time to evaluate : 1.252 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: 0.8377 (tm-30) cc_final: 0.8092 (tm-30) REVERT: G 288 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8497 (p90) REVERT: I 657 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7987 (tm-30) REVERT: J 100 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8439 (tptt) REVERT: L 5 THR cc_start: 0.8383 (p) cc_final: 0.7602 (p) REVERT: L 97 THR cc_start: 0.7490 (m) cc_final: 0.7140 (p) REVERT: O 34 TRP cc_start: 0.8303 (m-10) cc_final: 0.7789 (m-10) REVERT: O 63 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5594 (mt) REVERT: P 27 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8367 (tp-100) REVERT: P 82 ASP cc_start: 0.5682 (OUTLIER) cc_final: 0.5382 (p0) REVERT: P 97 THR cc_start: 0.7234 (OUTLIER) cc_final: 0.6778 (p) REVERT: R 657 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7938 (tm-30) REVERT: V 32 TYR cc_start: 0.8738 (m-10) cc_final: 0.8383 (m-10) REVERT: W 1 GLN cc_start: 0.3823 (pp30) cc_final: 0.3567 (pp30) REVERT: W 39 GLN cc_start: 0.6715 (tt0) cc_final: 0.6372 (tm-30) REVERT: X 54 ARG cc_start: 0.7544 (ptp90) cc_final: 0.7272 (mtm-85) REVERT: X 77 ARG cc_start: 0.9239 (tmt170) cc_final: 0.8816 (tmt170) REVERT: X 97 THR cc_start: 0.8011 (m) cc_final: 0.7548 (p) outliers start: 147 outliers final: 58 residues processed: 355 average time/residue: 0.2014 time to fit residues: 115.0150 Evaluate side-chains 251 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 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 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 88 ASN 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 270 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: chunk 4 optimal weight: 0.0670 chunk 366 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN B 543 ASN D 36 GLN G 283 ASN H 76 ASN I 543 ASN L 45 GLN Q 72 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 ASN R 543 ASN S 97 HIS ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.086267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058724 restraints weight = 108226.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060666 restraints weight = 58005.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061904 restraints weight = 40943.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062676 restraints weight = 33496.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063114 restraints weight = 29787.927| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33546 Z= 0.141 Angle : 0.782 14.362 45948 Z= 0.360 Chirality : 0.048 0.283 5589 Planarity : 0.005 0.058 5508 Dihedral : 13.378 108.046 7920 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 3.13 % Allowed : 17.35 % Favored : 79.52 % 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: -1.38 (0.13), residues: 3801 helix: 0.51 (0.28), residues: 363 sheet: -0.49 (0.14), residues: 1206 loop : -1.43 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 24 TYR 0.018 0.001 TYR C 32 PHE 0.040 0.002 PHE P 98 TRP 0.023 0.001 TRP W 103 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (33309) covalent geometry : angle 0.73058 (45288) SS BOND : bond 0.00396 ( 51) SS BOND : angle 1.57096 ( 102) hydrogen bonds : bond 0.03650 ( 1053) hydrogen bonds : angle 5.83727 ( 2799) link_ALPHA1-2 : bond 0.00519 ( 9) link_ALPHA1-2 : angle 1.81390 ( 27) link_ALPHA1-3 : bond 0.01634 ( 21) link_ALPHA1-3 : angle 2.23661 ( 63) link_ALPHA1-6 : bond 0.00697 ( 18) link_ALPHA1-6 : angle 1.72934 ( 54) link_BETA1-4 : bond 0.00506 ( 81) link_BETA1-4 : angle 2.54441 ( 243) link_NAG-ASN : bond 0.00405 ( 57) link_NAG-ASN : angle 3.00909 ( 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 332 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 227 time to evaluate : 1.142 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: 0.8321 (tm-30) cc_final: 0.8035 (tm-30) REVERT: G 288 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8623 (p90) REVERT: H 33 TYR cc_start: 0.6031 (t80) cc_final: 0.5345 (t80) REVERT: H 34 TRP cc_start: 0.8194 (m-10) cc_final: 0.7744 (m-10) REVERT: I 657 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7870 (tm-30) REVERT: J 13 LYS cc_start: 0.8656 (tppt) cc_final: 0.8248 (tppt) REVERT: J 100 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8420 (tmtt) REVERT: L 45 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7539 (pp30) REVERT: L 82 ASP cc_start: 0.5170 (OUTLIER) cc_final: 0.4863 (p0) REVERT: L 96 LEU cc_start: 0.6705 (mp) cc_final: 0.6434 (mp) REVERT: L 97 THR cc_start: 0.7366 (m) cc_final: 0.6898 (p) REVERT: O 1 GLN cc_start: 0.4077 (pp30) cc_final: 0.3806 (pp30) REVERT: O 33 TYR cc_start: 0.5905 (t80) cc_final: 0.5462 (t80) REVERT: O 34 TRP cc_start: 0.8327 (m-10) cc_final: 0.7902 (m-10) REVERT: P 27 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8328 (tp-100) REVERT: R 657 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7887 (tm-30) REVERT: W 1 GLN cc_start: 0.3868 (pp30) cc_final: 0.3610 (pp30) REVERT: W 31 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8297 (ptp90) REVERT: X 70 ASP cc_start: 0.9173 (t0) cc_final: 0.8779 (p0) REVERT: X 77 ARG cc_start: 0.9231 (tmt170) cc_final: 0.8853 (tmt170) REVERT: X 91 PHE cc_start: 0.8155 (p90) cc_final: 0.6774 (p90) REVERT: X 97 THR cc_start: 0.8072 (m) cc_final: 0.7610 (p) outliers start: 105 outliers final: 39 residues processed: 311 average time/residue: 0.2082 time to fit residues: 103.7528 Evaluate side-chains 244 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 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 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 119 CYS 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 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 95 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 82 ASP 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 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 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 100 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 60 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 311 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN O 76 ASN Q 72 HIS 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 = 0.3666 r_free = 0.3666 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054825 restraints weight = 110588.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056651 restraints weight = 60756.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057807 restraints weight = 43741.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058513 restraints weight = 36290.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058910 restraints weight = 32591.431| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 33546 Z= 0.362 Angle : 0.915 11.982 45948 Z= 0.427 Chirality : 0.051 0.278 5589 Planarity : 0.005 0.058 5508 Dihedral : 13.045 114.004 7920 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.43 % Allowed : 18.99 % Favored : 77.58 % 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: -1.57 (0.13), residues: 3801 helix: 0.41 (0.27), residues: 366 sheet: -0.83 (0.14), residues: 1290 loop : -1.44 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 100 TYR 0.041 0.002 TYR P 87 PHE 0.037 0.003 PHE L 62 TRP 0.015 0.002 TRP F 96 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00823 (33309) covalent geometry : angle 0.85977 (45288) SS BOND : bond 0.00631 ( 51) SS BOND : angle 2.27451 ( 102) hydrogen bonds : bond 0.04471 ( 1053) hydrogen bonds : angle 6.06440 ( 2799) link_ALPHA1-2 : bond 0.00371 ( 9) link_ALPHA1-2 : angle 1.93872 ( 27) link_ALPHA1-3 : bond 0.01485 ( 21) link_ALPHA1-3 : angle 2.67770 ( 63) link_ALPHA1-6 : bond 0.00609 ( 18) link_ALPHA1-6 : angle 1.90081 ( 54) link_BETA1-4 : bond 0.00510 ( 81) link_BETA1-4 : angle 2.70425 ( 243) link_NAG-ASN : bond 0.00777 ( 57) link_NAG-ASN : angle 3.38583 ( 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 314 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 199 time to evaluate : 1.084 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: 0.8460 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 13 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8427 (mmmt) REVERT: G 288 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8520 (p90) REVERT: H 33 TYR cc_start: 0.5864 (t80) cc_final: 0.5215 (t80) REVERT: H 86 ASP cc_start: 0.0829 (p0) cc_final: 0.0503 (p0) REVERT: I 657 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8052 (tm-30) REVERT: J 100 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8535 (tptt) REVERT: J 100 ASP cc_start: 0.7984 (p0) cc_final: 0.7671 (p0) REVERT: L 13 VAL cc_start: 0.6309 (OUTLIER) cc_final: 0.6070 (t) REVERT: L 61 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7911 (ttp-170) REVERT: L 97 THR cc_start: 0.6945 (m) cc_final: 0.6632 (p) REVERT: M 32 MET cc_start: 0.8420 (tpp) cc_final: 0.7550 (tpp) REVERT: O 1 GLN cc_start: 0.3970 (pp30) cc_final: 0.3704 (pp30) REVERT: O 33 TYR cc_start: 0.6027 (t80) cc_final: 0.5572 (t80) REVERT: P 13 VAL cc_start: 0.5873 (OUTLIER) cc_final: 0.5583 (t) REVERT: P 89 MET cc_start: 0.8579 (mmm) cc_final: 0.7536 (tpp) REVERT: P 98 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6400 (m-80) REVERT: R 657 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8053 (tm-30) REVERT: S 13 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8503 (mmmt) REVERT: S 16 GLU cc_start: 0.7293 (pt0) cc_final: 0.6885 (mp0) REVERT: V 31 ASP cc_start: 0.8144 (p0) cc_final: 0.7804 (p0) REVERT: V 32 TYR cc_start: 0.8826 (m-10) cc_final: 0.8562 (m-10) REVERT: W 1 GLN cc_start: 0.4180 (pp30) cc_final: 0.3865 (pp30) REVERT: W 39 GLN cc_start: 0.6773 (tt0) cc_final: 0.6405 (tm-30) REVERT: X 77 ARG cc_start: 0.9217 (tmt170) cc_final: 0.8876 (tmt170) outliers start: 115 outliers final: 79 residues processed: 295 average time/residue: 0.1947 time to fit residues: 93.0578 Evaluate side-chains 272 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 188 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 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 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 A residue 346 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR 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 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 416 LEU 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 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain M residue 27 GLN 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 109 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 75 VAL 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 245 VAL Chi-restraints excluded: chain Q residue 287 GLN 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 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 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 257 optimal weight: 8.9990 chunk 376 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 543 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS R 543 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.084488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056639 restraints weight = 108819.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058574 restraints weight = 58468.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059791 restraints weight = 41430.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060535 restraints weight = 34054.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060913 restraints weight = 30416.161| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3212 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= 0.202 Angle : 0.805 13.074 45948 Z= 0.372 Chirality : 0.048 0.284 5589 Planarity : 0.004 0.055 5508 Dihedral : 12.393 111.155 7920 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.34 % Allowed : 19.62 % 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: -1.38 (0.13), residues: 3801 helix: 0.68 (0.27), residues: 363 sheet: -0.74 (0.14), residues: 1293 loop : -1.30 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.032 0.001 TYR L 87 PHE 0.021 0.002 PHE P 98 TRP 0.014 0.001 TRP A 96 HIS 0.002 0.001 HIS Q 66 Details of bonding type rmsd covalent geometry : bond 0.00453 (33309) covalent geometry : angle 0.75205 (45288) SS BOND : bond 0.00428 ( 51) SS BOND : angle 1.93275 ( 102) hydrogen bonds : bond 0.03804 ( 1053) hydrogen bonds : angle 5.85219 ( 2799) link_ALPHA1-2 : bond 0.00441 ( 9) link_ALPHA1-2 : angle 1.81844 ( 27) link_ALPHA1-3 : bond 0.01711 ( 21) link_ALPHA1-3 : angle 2.62552 ( 63) link_ALPHA1-6 : bond 0.00610 ( 18) link_ALPHA1-6 : angle 1.71351 ( 54) link_BETA1-4 : bond 0.00497 ( 81) link_BETA1-4 : angle 2.48537 ( 243) link_NAG-ASN : bond 0.00480 ( 57) link_NAG-ASN : angle 3.06057 ( 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 316 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 204 time to evaluate : 1.220 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: 0.8438 (tm-30) cc_final: 0.8128 (tm-30) REVERT: G 288 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8513 (p90) REVERT: H 33 TYR cc_start: 0.5997 (t80) cc_final: 0.5397 (t80) REVERT: H 86 ASP cc_start: 0.0602 (p0) cc_final: 0.0265 (p0) REVERT: I 657 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8012 (tm-30) REVERT: J 100 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8466 (tptt) REVERT: J 100 ASP cc_start: 0.7864 (p0) cc_final: 0.7521 (p0) REVERT: L 97 THR cc_start: 0.7071 (m) cc_final: 0.6674 (p) REVERT: M 32 MET cc_start: 0.8391 (tpp) cc_final: 0.7551 (tpp) REVERT: N 76 ASP cc_start: 0.8429 (m-30) cc_final: 0.8177 (t70) REVERT: O 1 GLN cc_start: 0.4258 (pp30) cc_final: 0.3953 (pp30) REVERT: O 33 TYR cc_start: 0.5982 (t80) cc_final: 0.5548 (t80) REVERT: O 34 TRP cc_start: 0.8368 (m-10) cc_final: 0.7996 (m-10) REVERT: O 53 ASN cc_start: 0.8806 (t0) cc_final: 0.8454 (p0) REVERT: P 13 VAL cc_start: 0.5850 (OUTLIER) cc_final: 0.5564 (t) REVERT: R 657 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7958 (tm-30) REVERT: S 13 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8480 (mmmt) REVERT: S 16 GLU cc_start: 0.7240 (pt0) cc_final: 0.6940 (mp0) REVERT: V 32 TYR cc_start: 0.8840 (m-10) cc_final: 0.8596 (m-10) REVERT: W 1 GLN cc_start: 0.4085 (pp30) cc_final: 0.3764 (pp30) REVERT: W 63 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5765 (mt) REVERT: X 24 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7068 (mmp80) REVERT: X 77 ARG cc_start: 0.9223 (tmt170) cc_final: 0.8889 (tmt170) outliers start: 112 outliers final: 69 residues processed: 299 average time/residue: 0.1992 time to fit residues: 96.3158 Evaluate side-chains 263 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 GLN 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 E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR 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 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 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 82 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET 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 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN 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 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 604 CYS Chi-restraints excluded: chain S residue 77 LEU 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 W residue 63 LEU 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 Chi-restraints excluded: chain X residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 365 optimal weight: 7.9990 chunk 243 optimal weight: 40.0000 chunk 131 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN M 27 GLN O 76 ASN Q 72 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 543 ASN ** U 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN X 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.085156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057145 restraints weight = 112908.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059054 restraints weight = 61963.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060294 restraints weight = 44306.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061046 restraints weight = 36633.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061455 restraints weight = 32779.007| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33546 Z= 0.136 Angle : 0.772 17.260 45948 Z= 0.352 Chirality : 0.047 0.282 5589 Planarity : 0.004 0.081 5508 Dihedral : 11.583 106.980 7920 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.95 % Allowed : 20.07 % Favored : 76.98 % 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: -1.07 (0.14), residues: 3801 helix: 1.13 (0.29), residues: 345 sheet: -0.45 (0.14), residues: 1233 loop : -1.17 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 24 TYR 0.023 0.001 TYR L 87 PHE 0.035 0.002 PHE P 98 TRP 0.014 0.001 TRP Q 96 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00298 (33309) covalent geometry : angle 0.72282 (45288) SS BOND : bond 0.00381 ( 51) SS BOND : angle 1.59193 ( 102) hydrogen bonds : bond 0.03432 ( 1053) hydrogen bonds : angle 5.64794 ( 2799) link_ALPHA1-2 : bond 0.00428 ( 9) link_ALPHA1-2 : angle 1.75279 ( 27) link_ALPHA1-3 : bond 0.01739 ( 21) link_ALPHA1-3 : angle 2.60286 ( 63) link_ALPHA1-6 : bond 0.00644 ( 18) link_ALPHA1-6 : angle 1.56294 ( 54) link_BETA1-4 : bond 0.00546 ( 81) link_BETA1-4 : angle 2.38643 ( 243) link_NAG-ASN : bond 0.00388 ( 57) link_NAG-ASN : angle 2.87412 ( 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 306 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 207 time to evaluate : 1.010 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: B 657 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 288 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8582 (p90) REVERT: H 33 TYR cc_start: 0.5981 (t80) cc_final: 0.5437 (t80) REVERT: H 34 TRP cc_start: 0.8388 (m-10) cc_final: 0.7969 (m-10) REVERT: I 657 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7956 (tm-30) REVERT: J 100 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8475 (tmtt) REVERT: J 100 ASP cc_start: 0.7841 (p0) cc_final: 0.7469 (p0) REVERT: L 97 THR cc_start: 0.7069 (m) cc_final: 0.6758 (p) REVERT: M 32 MET cc_start: 0.8271 (tpp) cc_final: 0.7472 (tpp) REVERT: N 76 ASP cc_start: 0.8415 (m-30) cc_final: 0.8205 (t70) REVERT: O 1 GLN cc_start: 0.4485 (pp30) cc_final: 0.4153 (pp30) REVERT: O 33 TYR cc_start: 0.5996 (t80) cc_final: 0.5614 (t80) REVERT: O 34 TRP cc_start: 0.8383 (m-10) cc_final: 0.7947 (m-10) REVERT: P 93 GLU cc_start: 0.8384 (tp30) cc_final: 0.8006 (mm-30) REVERT: R 530 MET cc_start: 0.8652 (mmm) cc_final: 0.8232 (mmt) REVERT: R 657 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7915 (tm-30) REVERT: S 13 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8465 (mmmt) REVERT: T 20 ARG cc_start: 0.7197 (mpp-170) cc_final: 0.6801 (mpp-170) REVERT: W 1 GLN cc_start: 0.4065 (pp30) cc_final: 0.3684 (pp30) REVERT: W 31 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.8308 (ptp90) REVERT: W 39 GLN cc_start: 0.6705 (tt0) cc_final: 0.6416 (tm-30) REVERT: W 63 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5642 (mt) REVERT: X 77 ARG cc_start: 0.9211 (tmt170) cc_final: 0.8865 (tmt170) outliers start: 99 outliers final: 64 residues processed: 290 average time/residue: 0.1983 time to fit residues: 93.1779 Evaluate side-chains 260 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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 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 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 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR 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 416 LEU 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 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 27 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 109 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 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 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 V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 161 optimal weight: 0.0060 chunk 31 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 373 optimal weight: 40.0000 chunk 252 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 238 optimal weight: 50.0000 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Q 72 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 293 GLN ** U 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN X 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056316 restraints weight = 112772.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058204 restraints weight = 62280.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059389 restraints weight = 44781.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060127 restraints weight = 37175.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060506 restraints weight = 33331.965| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3495 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= 0.173 Angle : 0.780 13.680 45948 Z= 0.358 Chirality : 0.047 0.284 5589 Planarity : 0.004 0.056 5508 Dihedral : 11.142 109.703 7920 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.89 % Allowed : 20.24 % Favored : 76.86 % 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: -1.04 (0.14), residues: 3801 helix: 0.99 (0.28), residues: 363 sheet: -0.40 (0.14), residues: 1251 loop : -1.16 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 24 TYR 0.021 0.001 TYR L 87 PHE 0.023 0.002 PHE P 36 TRP 0.015 0.001 TRP Q 96 HIS 0.002 0.001 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00389 (33309) covalent geometry : angle 0.72936 (45288) SS BOND : bond 0.00394 ( 51) SS BOND : angle 1.80690 ( 102) hydrogen bonds : bond 0.03484 ( 1053) hydrogen bonds : angle 5.59906 ( 2799) link_ALPHA1-2 : bond 0.00386 ( 9) link_ALPHA1-2 : angle 1.75695 ( 27) link_ALPHA1-3 : bond 0.01665 ( 21) link_ALPHA1-3 : angle 2.69347 ( 63) link_ALPHA1-6 : bond 0.00589 ( 18) link_ALPHA1-6 : angle 1.54331 ( 54) link_BETA1-4 : bond 0.00530 ( 81) link_BETA1-4 : angle 2.40920 ( 243) link_NAG-ASN : bond 0.00422 ( 57) link_NAG-ASN : angle 2.90893 ( 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 296 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 199 time to evaluate : 1.181 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: 0.8426 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 100 ASP cc_start: 0.8043 (m-30) cc_final: 0.7790 (m-30) REVERT: D 32 MET cc_start: 0.8264 (ttm) cc_final: 0.7991 (ttm) REVERT: E 13 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8631 (tppt) REVERT: G 288 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8606 (p90) REVERT: H 33 TYR cc_start: 0.6021 (t80) cc_final: 0.5474 (t80) REVERT: H 34 TRP cc_start: 0.8453 (m-10) cc_final: 0.8030 (m-10) REVERT: H 86 ASP cc_start: 0.0869 (p0) cc_final: 0.0500 (p0) REVERT: I 657 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7986 (tm-30) REVERT: J 100 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8505 (tptt) REVERT: J 100 ASP cc_start: 0.7849 (p0) cc_final: 0.7482 (p0) REVERT: L 61 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7436 (tmm-80) REVERT: M 32 MET cc_start: 0.8245 (tpp) cc_final: 0.7353 (tpp) REVERT: N 76 ASP cc_start: 0.8422 (m-30) cc_final: 0.8106 (t70) REVERT: O 1 GLN cc_start: 0.4398 (pp30) cc_final: 0.4107 (pp30) REVERT: O 33 TYR cc_start: 0.6002 (t80) cc_final: 0.5626 (t80) REVERT: O 53 ASN cc_start: 0.8791 (t0) cc_final: 0.8495 (p0) REVERT: O 71 LYS cc_start: 0.4591 (OUTLIER) cc_final: 0.4350 (mtmt) REVERT: O 86 ASP cc_start: 0.1381 (p0) cc_final: 0.1042 (p0) REVERT: Q 198 THR cc_start: 0.9030 (t) cc_final: 0.8763 (p) REVERT: R 530 MET cc_start: 0.8707 (mmm) cc_final: 0.8325 (mmt) REVERT: R 657 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7956 (tm-30) REVERT: T 20 ARG cc_start: 0.7168 (mpp-170) cc_final: 0.6878 (mpp-170) REVERT: W 31 ARG cc_start: 0.8531 (ttp-170) cc_final: 0.8321 (ptp90) REVERT: W 39 GLN cc_start: 0.6707 (tt0) cc_final: 0.6401 (tm-30) REVERT: W 63 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5672 (mt) REVERT: X 77 ARG cc_start: 0.9216 (tmt170) cc_final: 0.8866 (tmt170) outliers start: 97 outliers final: 76 residues processed: 284 average time/residue: 0.2028 time to fit residues: 92.9264 Evaluate side-chains 272 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 192 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL 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 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 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 202 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 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 82 LEU 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 61 ARG Chi-restraints excluded: chain L residue 89 MET 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 71 LYS Chi-restraints excluded: chain P residue 5 THR 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 202 THR 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 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 U residue 36 GLN Chi-restraints excluded: chain V residue 109 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 184 optimal weight: 3.9990 chunk 298 optimal weight: 0.0000 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 577 GLN D 36 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Q 72 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3683 r_free = 0.3683 target = 0.084396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056180 restraints weight = 112326.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058084 restraints weight = 62257.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059287 restraints weight = 44809.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059915 restraints weight = 37197.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060416 restraints weight = 33606.871| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33546 Z= 0.176 Angle : 0.787 14.413 45948 Z= 0.362 Chirality : 0.047 0.279 5589 Planarity : 0.004 0.056 5508 Dihedral : 10.770 110.345 7920 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.98 % Allowed : 20.36 % Favored : 76.65 % 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: -0.99 (0.14), residues: 3801 helix: 0.99 (0.28), residues: 363 sheet: -0.29 (0.14), residues: 1242 loop : -1.16 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 75 TYR 0.020 0.001 TYR L 87 PHE 0.019 0.002 PHE P 36 TRP 0.017 0.001 TRP A 96 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00398 (33309) covalent geometry : angle 0.73828 (45288) SS BOND : bond 0.00385 ( 51) SS BOND : angle 1.73837 ( 102) hydrogen bonds : bond 0.03517 ( 1053) hydrogen bonds : angle 5.55087 ( 2799) link_ALPHA1-2 : bond 0.00393 ( 9) link_ALPHA1-2 : angle 1.74147 ( 27) link_ALPHA1-3 : bond 0.01713 ( 21) link_ALPHA1-3 : angle 2.68588 ( 63) link_ALPHA1-6 : bond 0.00540 ( 18) link_ALPHA1-6 : angle 1.56791 ( 54) link_BETA1-4 : bond 0.00525 ( 81) link_BETA1-4 : angle 2.40353 ( 243) link_NAG-ASN : bond 0.00418 ( 57) link_NAG-ASN : angle 2.88015 ( 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 304 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 204 time to evaluate : 1.437 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: 0.8420 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 32 MET cc_start: 0.8259 (ttm) cc_final: 0.7931 (ttt) REVERT: G 288 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8605 (p90) REVERT: H 33 TYR cc_start: 0.5942 (t80) cc_final: 0.5488 (t80) REVERT: H 34 TRP cc_start: 0.8480 (m-10) cc_final: 0.8084 (m-10) REVERT: H 86 ASP cc_start: 0.0823 (p0) cc_final: 0.0449 (p0) REVERT: I 657 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7992 (tm-30) REVERT: J 100 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8500 (tptt) REVERT: J 100 ASP cc_start: 0.7836 (p0) cc_final: 0.7506 (p0) REVERT: L 13 VAL cc_start: 0.6217 (OUTLIER) cc_final: 0.5943 (t) REVERT: L 61 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7496 (tmm-80) REVERT: M 32 MET cc_start: 0.8251 (tpp) cc_final: 0.7364 (tpp) REVERT: N 76 ASP cc_start: 0.8408 (m-30) cc_final: 0.8099 (t70) REVERT: O 1 GLN cc_start: 0.4328 (pp30) cc_final: 0.4067 (pp30) REVERT: O 33 TYR cc_start: 0.5993 (t80) cc_final: 0.5642 (t80) REVERT: O 71 LYS cc_start: 0.4622 (OUTLIER) cc_final: 0.4399 (mtmt) REVERT: O 86 ASP cc_start: 0.1376 (p0) cc_final: 0.1022 (p0) REVERT: P 93 GLU cc_start: 0.8357 (tp30) cc_final: 0.8024 (mm-30) REVERT: Q 198 THR cc_start: 0.9029 (t) cc_final: 0.8755 (p) REVERT: R 657 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7947 (tm-30) REVERT: U 32 MET cc_start: 0.7966 (ttt) cc_final: 0.7383 (ttt) REVERT: W 31 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8318 (ptp90) REVERT: W 39 GLN cc_start: 0.6671 (tt0) cc_final: 0.6303 (tm-30) REVERT: W 63 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5678 (mt) REVERT: X 13 VAL cc_start: 0.6165 (OUTLIER) cc_final: 0.5929 (t) outliers start: 100 outliers final: 78 residues processed: 288 average time/residue: 0.2061 time to fit residues: 96.4323 Evaluate side-chains 279 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 195 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL 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 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 202 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 345 VAL 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 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 7 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 89 MET 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 O residue 71 LYS Chi-restraints excluded: chain P residue 5 THR 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 202 THR 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 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 S residue 100 VAL Chi-restraints excluded: chain V residue 109 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 W residue 63 LEU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 53 ASN 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: chunk 376 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 191 optimal weight: 0.0030 chunk 221 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 218 optimal weight: 0.0270 overall best weight: 0.8054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 293 GLN D 36 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Q 72 HIS Q 94 ASN ** U 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN X 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057560 restraints weight = 112228.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059470 restraints weight = 62582.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060677 restraints weight = 45152.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061384 restraints weight = 37472.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061848 restraints weight = 33602.228| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3722 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= 0.134 Angle : 0.775 17.849 45948 Z= 0.354 Chirality : 0.046 0.283 5589 Planarity : 0.004 0.056 5508 Dihedral : 10.223 108.114 7920 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.39 % Allowed : 21.05 % Favored : 76.57 % 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: -0.87 (0.14), residues: 3801 helix: 1.25 (0.29), residues: 345 sheet: -0.19 (0.15), residues: 1215 loop : -1.11 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 75 TYR 0.019 0.001 TYR L 87 PHE 0.021 0.001 PHE P 36 TRP 0.016 0.001 TRP A 96 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (33309) covalent geometry : angle 0.72935 (45288) SS BOND : bond 0.00339 ( 51) SS BOND : angle 1.60361 ( 102) hydrogen bonds : bond 0.03263 ( 1053) hydrogen bonds : angle 5.44637 ( 2799) link_ALPHA1-2 : bond 0.00444 ( 9) link_ALPHA1-2 : angle 1.68780 ( 27) link_ALPHA1-3 : bond 0.01802 ( 21) link_ALPHA1-3 : angle 2.44921 ( 63) link_ALPHA1-6 : bond 0.00535 ( 18) link_ALPHA1-6 : angle 1.51982 ( 54) link_BETA1-4 : bond 0.00554 ( 81) link_BETA1-4 : angle 2.34696 ( 243) link_NAG-ASN : bond 0.00375 ( 57) link_NAG-ASN : angle 2.75490 ( 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 292 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 212 time to evaluate : 1.183 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: A 475 MET cc_start: 0.7986 (mmt) cc_final: 0.7766 (tpp) REVERT: B 657 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 32 MET cc_start: 0.8259 (ttm) cc_final: 0.7938 (ttt) REVERT: E 13 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8638 (tppt) REVERT: G 288 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8592 (p90) REVERT: H 33 TYR cc_start: 0.5914 (t80) cc_final: 0.5334 (t80) REVERT: H 34 TRP cc_start: 0.8480 (m-10) cc_final: 0.8089 (m-10) REVERT: H 86 ASP cc_start: 0.0846 (p0) cc_final: 0.0478 (p0) REVERT: H 95 ARG cc_start: 0.6289 (mtm110) cc_final: 0.6045 (mtm-85) REVERT: I 657 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7999 (tm-30) REVERT: J 100 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8456 (tmtt) REVERT: J 100 ASP cc_start: 0.7842 (p0) cc_final: 0.7501 (p0) REVERT: L 13 VAL cc_start: 0.6286 (OUTLIER) cc_final: 0.6008 (t) REVERT: M 32 MET cc_start: 0.8277 (tpp) cc_final: 0.7402 (tpp) REVERT: N 76 ASP cc_start: 0.8450 (m-30) cc_final: 0.8193 (t70) REVERT: O 1 GLN cc_start: 0.4208 (pp30) cc_final: 0.3968 (pp30) REVERT: O 33 TYR cc_start: 0.5996 (t80) cc_final: 0.5674 (t80) REVERT: O 71 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.4437 (mtmt) REVERT: O 86 ASP cc_start: 0.1591 (p0) cc_final: 0.1242 (p0) REVERT: P 93 GLU cc_start: 0.8412 (tp30) cc_final: 0.8047 (mm-30) REVERT: Q 198 THR cc_start: 0.9017 (t) cc_final: 0.8751 (p) REVERT: R 657 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7963 (tm-30) REVERT: W 31 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8290 (ptp90) REVERT: W 39 GLN cc_start: 0.6695 (tt0) cc_final: 0.6249 (tm-30) REVERT: W 63 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5650 (mt) REVERT: X 13 VAL cc_start: 0.6012 (OUTLIER) cc_final: 0.5803 (t) REVERT: X 77 ARG cc_start: 0.8870 (ttt-90) cc_final: 0.8448 (tmt170) outliers start: 80 outliers final: 67 residues processed: 279 average time/residue: 0.2120 time to fit residues: 94.6161 Evaluate side-chains 266 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 194 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL 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 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 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 202 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 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 13 VAL 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 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 O residue 71 LYS Chi-restraints excluded: chain P residue 5 THR 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 119 CYS Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 202 THR 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 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 57 THR Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 137 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 325 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 366 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 322 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Q 72 HIS R 543 ASN U 6 GLN ** U 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** W 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.085874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058132 restraints weight = 112608.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060066 restraints weight = 62492.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061279 restraints weight = 44879.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062021 restraints weight = 37215.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062397 restraints weight = 33305.164| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33546 Z= 0.128 Angle : 0.755 13.530 45948 Z= 0.350 Chirality : 0.046 0.285 5589 Planarity : 0.004 0.067 5508 Dihedral : 9.825 107.182 7920 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.47 % Allowed : 21.05 % Favored : 76.48 % 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: -0.75 (0.14), residues: 3801 helix: 1.33 (0.29), residues: 345 sheet: -0.05 (0.15), residues: 1197 loop : -1.05 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 24 TYR 0.022 0.001 TYR V 32 PHE 0.021 0.001 PHE O 78 TRP 0.027 0.001 TRP Q 112 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00283 (33309) covalent geometry : angle 0.71046 (45288) SS BOND : bond 0.00321 ( 51) SS BOND : angle 1.57674 ( 102) hydrogen bonds : bond 0.03181 ( 1053) hydrogen bonds : angle 5.35412 ( 2799) link_ALPHA1-2 : bond 0.00464 ( 9) link_ALPHA1-2 : angle 1.64595 ( 27) link_ALPHA1-3 : bond 0.01732 ( 21) link_ALPHA1-3 : angle 2.32050 ( 63) link_ALPHA1-6 : bond 0.00561 ( 18) link_ALPHA1-6 : angle 1.48893 ( 54) link_BETA1-4 : bond 0.00567 ( 81) link_BETA1-4 : angle 2.32845 ( 243) link_NAG-ASN : bond 0.00362 ( 57) link_NAG-ASN : angle 2.68162 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5666.07 seconds wall clock time: 99 minutes 1.68 seconds (5941.68 seconds total)