Starting phenix.real_space_refine on Mon Aug 25 23:58:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cue_7621/08_2025/6cue_7621.map" } resolution = 4.0 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= 0.015 sd= 0.141 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 174 5.16 5 C 19947 2.51 5 N 5289 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31692 Number of models: 1 Model: "" Number of chains: 66 Chain: "c" 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: "2" 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: "C" 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: "1" 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: "3" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "4" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "5" 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: "6" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "7" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "h" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "l" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "A" 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: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "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: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: "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: "e" 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: "f" 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: "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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "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: 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: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" 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: "c" 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: "2" 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: "C" 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 Time building chain proxies: 6.57, per 1000 atoms: 0.21 Number of scatterers: 31692 At special positions: 0 Unit cell: (154, 162.8, 156.2, 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 174 16.00 O 6282 8.00 N 5289 7.00 C 19947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.02 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.02 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 605 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 501 " - pdb=" SG CYS 1 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=1.91 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 93 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 103 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 109 " - pdb=" SG CYS 7 112 " distance=2.00 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=1.94 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.00 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.00 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS q 109 " - pdb=" SG CYS q 112 " distance=1.98 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA a 3 " - " MAN a 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA a 3 " - " MAN a 5 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 9 1 " - " NAG 9 2 " " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN C 332 " " NAG 2 611 " - " ASN 2 197 " " NAG 9 1 " - " ASN C 448 " " NAG A 1 " - " ASN c 133 " " NAG B 1 " - " ASN c 137 " " NAG C 611 " - " ASN C 197 " " NAG E 1 " - " ASN c 156 " " NAG F 1 " - " ASN c 160 " " NAG G 1 " - " ASN c 234 " " NAG I 1 " - " ASN c 262 " " NAG J 1 " - " ASN c 295 " " NAG K 1 " - " ASN c 301 " " NAG O 1 " - " ASN c 363 " " NAG P 1 " - " ASN c 386 " " NAG S 1 " - " ASN c 332 " " NAG T 1 " - " ASN c 448 " " NAG U 1 " - " ASN c 276 " " NAG V 1 " - " ASN 2 133 " " NAG W 1 " - " ASN 2 137 " " NAG X 1 " - " ASN 2 156 " " NAG Y 1 " - " ASN 2 160 " " NAG Z 1 " - " ASN 2 234 " " NAG a 1 " - " ASN 2 262 " " NAG b 1 " - " ASN 2 295 " " NAG c 611 " - " ASN c 197 " " NAG e 1 " - " ASN 2 301 " " NAG f 1 " - " ASN 2 363 " " NAG g 1 " - " ASN 2 386 " " NAG i 1 " - " ASN 2 332 " " NAG j 1 " - " ASN 2 448 " " NAG k 1 " - " ASN 2 276 " " NAG o 1 " - " ASN C 133 " " NAG p 1 " - " ASN C 137 " " NAG s 1 " - " ASN C 156 " " NAG t 1 " - " ASN C 160 " " NAG u 1 " - " ASN C 234 " " NAG v 1 " - " ASN C 262 " " NAG w 1 " - " ASN C 295 " " NAG x 1 " - " ASN C 301 " " NAG y 1 " - " ASN C 363 " " NAG z 1 " - " ASN C 386 " " NAGAA 1 " - " ASN C 276 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 84 sheets defined 13.7% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'c' and resid 101 through 115 removed outlier: 3.998A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN c 114 " --> pdb=" O SER c 110 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.773A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.500A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.271A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 481 removed outlier: 3.684A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 481 " --> pdb=" O ASP c 477 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.832A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN 2 114 " --> pdb=" O SER 2 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 3.535A pdb=" N LEU 2 125 " --> pdb=" O LEU 2 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 122 through 126' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 Processing helix chain '2' and resid 425 through 429 removed outlier: 4.188A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.671A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.728A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.576A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.558A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.728A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.002A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.810A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 528 removed outlier: 4.017A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 543 removed outlier: 3.807A pdb=" N ALA 1 533 " --> pdb=" O THR 1 529 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET 1 535 " --> pdb=" O GLY 1 531 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU 1 537 " --> pdb=" O ALA 1 533 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR 1 538 " --> pdb=" O SER 1 534 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL 1 539 " --> pdb=" O MET 1 535 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN 1 540 " --> pdb=" O THR 1 536 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 removed outlier: 3.704A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 1 589 " --> pdb=" O ARG 1 585 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 616 removed outlier: 4.335A pdb=" N SER 1 615 " --> pdb=" O ASN 1 611 " (cutoff:3.500A) Processing helix chain '1' and resid 619 through 623 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.914A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 640 through 664 removed outlier: 3.702A pdb=" N GLU 1 647 " --> pdb=" O TYR 1 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 1 648 " --> pdb=" O GLY 1 644 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 1 650 " --> pdb=" O LEU 1 646 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 91 removed outlier: 3.511A pdb=" N SER 3 91 " --> pdb=" O SER 3 88 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 88 removed outlier: 3.540A pdb=" N ASP 4 87 " --> pdb=" O GLU 4 84 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.731A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 100D through 100H removed outlier: 3.526A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '7' and resid 62 through 65 Processing helix chain '7' and resid 94 through 98 removed outlier: 3.760A pdb=" N THR 7 98 " --> pdb=" O PRO 7 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.095A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.629A pdb=" N ALA D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.048A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.299A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.767A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.623A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.569A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.891A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.674A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.752A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 3.842A pdb=" N ALA d 533 " --> pdb=" O THR d 529 " (cutoff:3.500A) Processing helix chain 'd' and resid 536 through 544 removed outlier: 4.081A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS d 574 " --> pdb=" O VAL d 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP d 589 " --> pdb=" O ARG d 585 " (cutoff:3.500A) Processing helix chain 'd' and resid 611 through 616 removed outlier: 4.264A pdb=" N SER d 615 " --> pdb=" O ASN d 611 " (cutoff:3.500A) Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.949A pdb=" N LYS d 633 " --> pdb=" O LEU d 629 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU d 634 " --> pdb=" O GLN d 630 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 640 through 663 removed outlier: 3.617A pdb=" N LYS d 655 " --> pdb=" O ASN d 651 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 84 through 88 removed outlier: 3.556A pdb=" N LEU l 88 " --> pdb=" O ALA l 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.680A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 65 Processing helix chain 'q' and resid 94 through 98 removed outlier: 3.685A pdb=" N THR q 98 " --> pdb=" O PRO q 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.949A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.854A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS c 239 " --> pdb=" O GLU c 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY c 237 " --> pdb=" O PHE c 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.516A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS c 374 " --> pdb=" O CYS c 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.197A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'c' and resid 359 through 360 Processing sheet with id=AB1, first strand: chain 'c' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain '2' and resid 495 through 499 removed outlier: 4.628A pdb=" N VAL 2 36 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR 1 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS 1 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 45 through 47 removed outlier: 4.009A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 75 through 76 removed outlier: 3.952A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 91 through 94 removed outlier: 3.555A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE 2 93 " --> pdb=" O GLY 2 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY 2 237 " --> pdb=" O PHE 2 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain '2' and resid 202 through 203 removed outlier: 6.624A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 260 through 261 removed outlier: 7.138A pdb=" N LEU 2 260 " --> pdb=" O THR 2 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 271 through 273 removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain '2' and resid 359 through 361 removed outlier: 3.510A pdb=" N PHE 2 361 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.837A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.557A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.200A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD3, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.550A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 3 through 5 removed outlier: 4.005A pdb=" N THR 3 78 " --> pdb=" O ASP 3 73 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP 3 73 " --> pdb=" O THR 3 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR 3 71 " --> pdb=" O TYR 3 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 10 through 12 removed outlier: 7.301A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE 3 48 " --> pdb=" O TRP 3 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3' and resid 10 through 12 removed outlier: 3.959A pdb=" N ARG 3 98 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL 3 107 " --> pdb=" O ARG 3 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '4' and resid 5 through 7 removed outlier: 3.508A pdb=" N ASP 4 75 " --> pdb=" O SER 4 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 10 through 12 removed outlier: 6.607A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR 4 92 " --> pdb=" O TYR 4 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '5' and resid 5 through 7 Processing sheet with id=AE1, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AE2, first strand: chain '5' and resid 46 through 51 removed outlier: 6.401A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AE4, first strand: chain '6' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain '6' and resid 44 through 48 removed outlier: 6.588A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 3 through 5 Processing sheet with id=AE7, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG 7 38 " --> pdb=" O TRP 7 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP 7 47 " --> pdb=" O ARG 7 38 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE 7 40 " --> pdb=" O PHE 7 45 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE 7 45 " --> pdb=" O ILE 7 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR 7 119 " --> pdb=" O ARG 7 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '8' and resid 4 through 7 removed outlier: 3.591A pdb=" N CYS 8 23 " --> pdb=" O PHE 8 71 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE 8 71 " --> pdb=" O CYS 8 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '8' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain '8' and resid 53 through 54 removed outlier: 5.754A pdb=" N LEU 8 46 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN 8 37 " --> pdb=" O LEU 8 46 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE 8 48 " --> pdb=" O TRP 8 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.360A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 72 through 73 removed outlier: 4.133A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.683A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.696A pdb=" N VAL M 107 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA M 88 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AG4, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.547A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AG7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.693A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Q 40 " --> pdb=" O GLY Q 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 57 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.796A pdb=" N CYS Q 103 " --> pdb=" O TRP Q 120 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP Q 120 " --> pdb=" O CYS Q 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 105 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.741A pdb=" N PHE R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'R' and resid 53 through 54 removed outlier: 5.702A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER h 97 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET h 34 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG h 98 " --> pdb=" O VAL h 107 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL h 107 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'h' and resid 39 through 40 Processing sheet with id=AH7, first strand: chain 'h' and resid 72 through 73 removed outlier: 3.980A pdb=" N ASP h 73 " --> pdb=" O THR h 78 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'l' and resid 5 through 7 removed outlier: 3.620A pdb=" N ASP l 75 " --> pdb=" O SER l 72 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.438A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'l' and resid 40 through 41 removed outlier: 6.575A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AI3, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL m 107 " --> pdb=" O ALA m 88 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA m 88 " --> pdb=" O VAL m 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AI5, first strand: chain 'n' and resid 11 through 13 removed outlier: 3.657A pdb=" N VAL n 11 " --> pdb=" O THR n 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE n 105 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU n 104 " --> pdb=" O ALA n 84 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'n' and resid 18 through 23 Processing sheet with id=AI7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'q' and resid 10 through 12 removed outlier: 5.779A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'q' and resid 10 through 12 removed outlier: 6.958A pdb=" N CYS q 103 " --> pdb=" O TRP q 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP q 120 " --> pdb=" O CYS q 103 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG q 105 " --> pdb=" O GLN q 118 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 4 through 7 removed outlier: 3.591A pdb=" N PHE r 71 " --> pdb=" O CYS r 23 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AJ3, first strand: chain 'r' and resid 53 through 54 removed outlier: 5.688A pdb=" N LEU r 46 " --> pdb=" O GLN r 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN r 37 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE r 48 " --> pdb=" O TRP r 35 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2454 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: 6.61 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9798 1.34 - 1.46: 8565 1.46 - 1.59: 13804 1.59 - 1.71: 2 1.71 - 1.84: 234 Bond restraints: 32403 Sorted by residual: bond pdb=" C LYS C 252 " pdb=" N PRO C 253 " ideal model delta sigma weight residual 1.335 1.304 0.031 8.70e-03 1.32e+04 1.30e+01 bond pdb=" CA TYR L 54 " pdb=" CB TYR L 54 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.20e-02 2.07e+03 1.06e+01 bond pdb=" C1 BMA y 3 " pdb=" C2 BMA y 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.575 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 32398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 42182 2.29 - 4.57: 1558 4.57 - 6.86: 216 6.86 - 9.15: 51 9.15 - 11.44: 18 Bond angle restraints: 44025 Sorted by residual: angle pdb=" C TYR r 49 " pdb=" N ASP r 50 " pdb=" CA ASP r 50 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C ASN C 99 " pdb=" N MET C 100 " pdb=" CA MET C 100 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C TYR R 49 " pdb=" N ASP R 50 " pdb=" CA ASP R 50 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C ASN c 99 " pdb=" N MET c 100 " pdb=" CA MET c 100 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C TYR 8 49 " pdb=" N ASP 8 50 " pdb=" CA ASP 8 50 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 ... (remaining 44020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 19804 23.44 - 46.89: 570 46.89 - 70.33: 128 70.33 - 93.77: 93 93.77 - 117.22: 60 Dihedral angle restraints: 20655 sinusoidal: 9627 harmonic: 11028 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual 93.00 175.73 -82.73 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS 2 201 " pdb=" SG CYS 2 201 " pdb=" SG CYS 2 433 " pdb=" CB CYS 2 433 " ideal model delta sinusoidal sigma weight residual 93.00 169.42 -76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA GLN r 90 " pdb=" C GLN r 90 " pdb=" N PHE r 91 " pdb=" CA PHE r 91 " ideal model delta harmonic sigma weight residual 180.00 -139.91 -40.09 0 5.00e+00 4.00e-02 6.43e+01 ... (remaining 20652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 5157 0.244 - 0.488: 36 0.488 - 0.731: 3 0.731 - 0.975: 1 0.975 - 1.219: 2 Chirality restraints: 5199 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN 2 363 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.71e+01 chirality pdb=" C1 NAG y 1 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG y 1 " pdb=" O5 NAG y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN c 363 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 ... (remaining 5196 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " 0.060 2.00e-02 2.50e+03 8.01e-02 8.03e+01 pdb=" CG ASN C 386 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " -0.138 2.00e-02 2.50e+03 pdb=" C1 NAG z 1 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 386 " -0.043 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN 2 386 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 386 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 386 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 386 " 0.036 2.00e-02 2.50e+03 5.00e-02 3.13e+01 pdb=" CG ASN c 386 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN c 386 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN c 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.058 2.00e-02 2.50e+03 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 869 2.68 - 3.23: 28028 3.23 - 3.79: 48079 3.79 - 4.34: 60139 4.34 - 4.90: 100563 Nonbonded interactions: 237678 Sorted by model distance: nonbonded pdb=" NH2 ARG D 542 " pdb=" OE2 GLU d 647 " model vdw 2.121 3.120 nonbonded pdb=" OD2 ASP c 457 " pdb=" NH1 ARG c 469 " model vdw 2.134 3.120 nonbonded pdb=" NH2 ARG 1 542 " pdb=" OE2 GLU D 647 " model vdw 2.174 3.120 nonbonded pdb=" OE2 GLU 1 647 " pdb=" NH2 ARG d 542 " model vdw 2.177 3.120 nonbonded pdb=" N THR M 83 " pdb=" OD2 ASP M 86 " model vdw 2.180 3.120 ... (remaining 237673 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'I' selection = chain 'S' selection = chain 'a' selection = chain 'i' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '8' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '9' selection = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'o' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'AA' selection = chain 'U' selection = chain 'k' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'O' selection = chain 'W' selection = chain 'X' selection = chain 'f' selection = chain 'p' selection = chain 's' selection = chain 'y' } 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: 0.010 Normalize map: mean=0, sd=1: 4.940 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.770 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.008 0.116 32574 Z= 0.370 Angle : 1.223 58.068 44481 Z= 0.590 Chirality : 0.070 1.219 5199 Planarity : 0.007 0.070 5448 Dihedral : 14.562 117.216 13428 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.12), residues: 3783 helix: -3.21 (0.17), residues: 366 sheet: -1.85 (0.14), residues: 1236 loop : -2.57 (0.11), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 298 TYR 0.028 0.003 TYR D 638 PHE 0.040 0.004 PHE 8 83 TRP 0.047 0.004 TRP 1 614 HIS 0.012 0.003 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00793 (32403) covalent geometry : angle 1.03211 (44025) SS BOND : bond 0.02392 ( 57) SS BOND : angle 7.63968 ( 114) hydrogen bonds : bond 0.17829 ( 933) hydrogen bonds : angle 8.36073 ( 2454) link_ALPHA1-2 : bond 0.00201 ( 3) link_ALPHA1-2 : angle 2.27319 ( 9) link_ALPHA1-3 : bond 0.00899 ( 9) link_ALPHA1-3 : angle 1.94468 ( 27) link_ALPHA1-6 : bond 0.00193 ( 3) link_ALPHA1-6 : angle 1.87293 ( 9) link_BETA1-4 : bond 0.00931 ( 57) link_BETA1-4 : angle 3.97713 ( 171) link_NAG-ASN : bond 0.02247 ( 42) link_NAG-ASN : angle 8.93605 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 647 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 53 PHE cc_start: 0.6337 (t80) cc_final: 0.6132 (t80) REVERT: c 425 ASN cc_start: 0.8642 (t0) cc_final: 0.8300 (t0) REVERT: 2 259 LEU cc_start: 0.8867 (mp) cc_final: 0.8536 (pp) REVERT: 2 416 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8754 (pp) REVERT: 1 535 MET cc_start: 0.8399 (mpt) cc_final: 0.8094 (mpt) REVERT: 3 5 GLN cc_start: 0.8873 (mt0) cc_final: 0.8672 (tm-30) REVERT: 3 65 LYS cc_start: 0.8860 (tttt) cc_final: 0.8310 (pttt) REVERT: 4 40 TRP cc_start: 0.7833 (m100) cc_final: 0.7284 (m100) REVERT: 5 5 GLN cc_start: 0.8733 (tp40) cc_final: 0.8462 (mp10) REVERT: 5 32 ASN cc_start: 0.7408 (t0) cc_final: 0.6481 (p0) REVERT: 5 100 MET cc_start: 0.9470 (mpp) cc_final: 0.9211 (mmm) REVERT: 5 103 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8764 (mptt) REVERT: 7 80 ASP cc_start: 0.7888 (m-30) cc_final: 0.7596 (p0) REVERT: 7 88 MET cc_start: 0.8320 (ttp) cc_final: 0.7217 (ttp) REVERT: D 581 LEU cc_start: 0.9345 (tp) cc_final: 0.9130 (tt) REVERT: H 23 LYS cc_start: 0.8956 (mttt) cc_final: 0.8722 (tptt) REVERT: H 102 TYR cc_start: 0.8327 (m-80) cc_final: 0.8091 (m-10) REVERT: L 31 TYR cc_start: 0.7245 (t80) cc_final: 0.6821 (t80) REVERT: L 53 ILE cc_start: 0.6774 (mt) cc_final: 0.5792 (mt) REVERT: M 5 GLN cc_start: 0.9207 (tp40) cc_final: 0.8095 (mp10) REVERT: M 13 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8488 (mmtm) REVERT: M 100 MET cc_start: 0.9199 (mpp) cc_final: 0.8777 (mmm) REVERT: N 11 VAL cc_start: 0.7440 (t) cc_final: 0.7201 (t) REVERT: Q 32 TYR cc_start: 0.8794 (m-80) cc_final: 0.8317 (m-10) REVERT: Q 88 MET cc_start: 0.8421 (ttp) cc_final: 0.7827 (ttp) REVERT: Q 110 ASP cc_start: 0.8082 (p0) cc_final: 0.7740 (p0) REVERT: Q 122 GLN cc_start: 0.8895 (pm20) cc_final: 0.8654 (pp30) REVERT: R 33 MET cc_start: 0.6922 (mtm) cc_final: 0.6639 (mtp) REVERT: R 83 PHE cc_start: 0.7714 (t80) cc_final: 0.7038 (t80) REVERT: d 633 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8759 (mttt) REVERT: h 81 MET cc_start: 0.6982 (mmm) cc_final: 0.5738 (tpp) REVERT: h 104 TYR cc_start: 0.8325 (p90) cc_final: 0.7973 (p90) REVERT: l 40 TRP cc_start: 0.7471 (m100) cc_final: 0.6730 (m100) REVERT: m 5 GLN cc_start: 0.8880 (tp40) cc_final: 0.8679 (mp10) REVERT: m 27 THR cc_start: 0.7440 (m) cc_final: 0.7208 (m) REVERT: m 31 ASP cc_start: 0.8695 (t0) cc_final: 0.8303 (t0) REVERT: m 32 ASN cc_start: 0.8357 (t0) cc_final: 0.7290 (p0) REVERT: m 86 ASP cc_start: 0.7549 (m-30) cc_final: 0.6767 (m-30) REVERT: m 100 MET cc_start: 0.9375 (mpp) cc_final: 0.8930 (mmm) REVERT: n 42 GLN cc_start: 0.7948 (mt0) cc_final: 0.7699 (mp10) REVERT: n 53 ASP cc_start: 0.8891 (m-30) cc_final: 0.8661 (m-30) REVERT: n 87 TYR cc_start: 0.8210 (m-80) cc_final: 0.7916 (m-80) REVERT: r 56 SER cc_start: 0.9077 (m) cc_final: 0.8761 (p) REVERT: r 70 ASP cc_start: 0.8385 (m-30) cc_final: 0.8068 (m-30) REVERT: r 106 VAL cc_start: 0.7778 (t) cc_final: 0.7140 (m) outliers start: 7 outliers final: 3 residues processed: 654 average time/residue: 0.1782 time to fit residues: 178.2003 Evaluate side-chains 289 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 285 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain C residue 373 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN c 315 GLN c 356 ASN 2 33 ASN 2 356 ASN C 33 ASN C 72 HIS C 85 HIS 1 625 ASN 4 27 GLN 4 58 ASN 5 52 HIS 7 3 GLN 7 6 GLN 7 118 GLN D 625 ASN L 27 GLN L 58 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 6 GLN Q 118 GLN l 58 ASN l 95 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN q 6 GLN q 118 GLN r 90 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055193 restraints weight = 137883.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056289 restraints weight = 82168.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056469 restraints weight = 57984.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056678 restraints weight = 54432.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056706 restraints weight = 47477.479| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 32574 Z= 0.196 Angle : 0.817 13.055 44481 Z= 0.395 Chirality : 0.047 0.215 5199 Planarity : 0.005 0.055 5448 Dihedral : 13.084 81.857 6497 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.34 % Allowed : 10.03 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.13), residues: 3783 helix: -1.29 (0.23), residues: 408 sheet: -1.63 (0.14), residues: 1293 loop : -2.16 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 61 TYR 0.032 0.002 TYR 6 87 PHE 0.019 0.002 PHE C 353 TRP 0.022 0.002 TRP 7 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00434 (32403) covalent geometry : angle 0.76933 (44025) SS BOND : bond 0.00401 ( 57) SS BOND : angle 2.35177 ( 114) hydrogen bonds : bond 0.04630 ( 933) hydrogen bonds : angle 6.77662 ( 2454) link_ALPHA1-2 : bond 0.00340 ( 3) link_ALPHA1-2 : angle 1.75426 ( 9) link_ALPHA1-3 : bond 0.01270 ( 9) link_ALPHA1-3 : angle 1.93896 ( 27) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.86362 ( 9) link_BETA1-4 : bond 0.00686 ( 57) link_BETA1-4 : angle 3.02289 ( 171) link_NAG-ASN : bond 0.00531 ( 42) link_NAG-ASN : angle 3.20156 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 0.891 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: c 86 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8649 (tt) REVERT: c 125 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9326 (tt) REVERT: c 425 ASN cc_start: 0.8601 (t0) cc_final: 0.8299 (t0) REVERT: 2 86 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8642 (tt) REVERT: 2 425 ASN cc_start: 0.8706 (t0) cc_final: 0.8461 (t0) REVERT: 2 475 MET cc_start: 0.8355 (mmt) cc_final: 0.7977 (mmm) REVERT: 1 530 MET cc_start: 0.8939 (mmt) cc_final: 0.8715 (mmm) REVERT: 1 624 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8429 (p0) REVERT: 3 3 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: 3 65 LYS cc_start: 0.8865 (tttt) cc_final: 0.8325 (pttt) REVERT: 4 40 TRP cc_start: 0.7749 (m100) cc_final: 0.7304 (m100) REVERT: 4 44 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7288 (mmt180) REVERT: 4 50 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.6886 (mmtm) REVERT: 5 13 LYS cc_start: 0.8664 (tppp) cc_final: 0.8304 (mmmm) REVERT: 5 86 ASP cc_start: 0.7416 (m-30) cc_final: 0.7098 (m-30) REVERT: 5 100 LYS cc_start: 0.9299 (mmmt) cc_final: 0.9093 (mmmt) REVERT: 5 103 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8744 (mptt) REVERT: 6 104 LEU cc_start: 0.7862 (tt) cc_final: 0.7468 (mm) REVERT: 7 89 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7923 (mm-30) REVERT: 7 97 ASP cc_start: 0.8920 (m-30) cc_final: 0.8533 (m-30) REVERT: 8 89 GLN cc_start: 0.9002 (tt0) cc_final: 0.8720 (tt0) REVERT: D 570 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8729 (p) REVERT: D 589 ASP cc_start: 0.8662 (m-30) cc_final: 0.8430 (m-30) REVERT: D 632 ASP cc_start: 0.8348 (t0) cc_final: 0.7804 (t0) REVERT: D 633 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8544 (mmtt) REVERT: D 655 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9049 (ptmt) REVERT: H 69 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5333 (tpt) REVERT: H 81 MET cc_start: 0.6477 (mmm) cc_final: 0.5861 (mmm) REVERT: H 102 TYR cc_start: 0.8438 (m-80) cc_final: 0.8236 (m-10) REVERT: L 4 MET cc_start: 0.5638 (tpp) cc_final: 0.5285 (tpp) REVERT: M 5 GLN cc_start: 0.9158 (tp40) cc_final: 0.8066 (mp10) REVERT: M 100 MET cc_start: 0.9434 (mpp) cc_final: 0.8940 (mmm) REVERT: N 100 GLU cc_start: 0.8288 (pm20) cc_final: 0.7938 (pp20) REVERT: Q 97 ASP cc_start: 0.8666 (m-30) cc_final: 0.8427 (t70) REVERT: Q 110 ASP cc_start: 0.8432 (p0) cc_final: 0.8158 (p0) REVERT: R 36 TYR cc_start: 0.9254 (m-80) cc_final: 0.9024 (m-10) REVERT: d 595 ILE cc_start: 0.9649 (pt) cc_final: 0.9408 (mp) REVERT: d 621 GLU cc_start: 0.8154 (pt0) cc_final: 0.7670 (pp20) REVERT: h 81 MET cc_start: 0.6878 (mmm) cc_final: 0.5461 (tpp) REVERT: h 104 TYR cc_start: 0.8167 (p90) cc_final: 0.7738 (p90) REVERT: l 38 LEU cc_start: 0.6213 (tt) cc_final: 0.5951 (mt) REVERT: l 40 TRP cc_start: 0.6905 (m100) cc_final: 0.6601 (m100) REVERT: l 76 PHE cc_start: 0.6791 (m-80) cc_final: 0.6361 (m-10) REVERT: m 31 ASP cc_start: 0.8746 (t0) cc_final: 0.8320 (t0) REVERT: m 32 ASN cc_start: 0.8237 (t0) cc_final: 0.7264 (p0) REVERT: m 100 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9061 (mmmt) REVERT: n 42 GLN cc_start: 0.7942 (mt0) cc_final: 0.7676 (mp10) REVERT: n 52 ASN cc_start: 0.9287 (t0) cc_final: 0.8953 (t0) REVERT: n 53 ASP cc_start: 0.8840 (m-30) cc_final: 0.8547 (m-30) REVERT: n 100 GLU cc_start: 0.8475 (pm20) cc_final: 0.7814 (pp20) REVERT: r 56 SER cc_start: 0.9176 (m) cc_final: 0.8895 (p) REVERT: r 70 ASP cc_start: 0.8421 (m-30) cc_final: 0.8213 (p0) outliers start: 78 outliers final: 34 residues processed: 409 average time/residue: 0.1586 time to fit residues: 104.9809 Evaluate side-chains 317 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain 2 residue 86 LEU Chi-restraints excluded: chain 2 residue 95 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 624 ASP Chi-restraints excluded: chain 3 residue 3 GLN Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 95 GLN Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain q residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 121 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN C 183 GLN 4 35 ASN 5 44 GLN D 625 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.078464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055751 restraints weight = 137265.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056050 restraints weight = 82869.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056538 restraints weight = 61393.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056686 restraints weight = 54627.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056734 restraints weight = 47961.667| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32574 Z= 0.160 Angle : 0.746 12.228 44481 Z= 0.358 Chirality : 0.047 0.233 5199 Planarity : 0.005 0.048 5448 Dihedral : 10.639 71.755 6496 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.09 % Allowed : 10.63 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -2.30 (0.13), residues: 3783 helix: -0.26 (0.26), residues: 393 sheet: -1.39 (0.14), residues: 1398 loop : -1.86 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 61 TYR 0.036 0.001 TYR 6 87 PHE 0.029 0.002 PHE Q 102 TRP 0.034 0.001 TRP 3 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00355 (32403) covalent geometry : angle 0.70732 (44025) SS BOND : bond 0.00320 ( 57) SS BOND : angle 1.59875 ( 114) hydrogen bonds : bond 0.03929 ( 933) hydrogen bonds : angle 6.14085 ( 2454) link_ALPHA1-2 : bond 0.00184 ( 3) link_ALPHA1-2 : angle 1.66451 ( 9) link_ALPHA1-3 : bond 0.01106 ( 9) link_ALPHA1-3 : angle 1.79427 ( 27) link_ALPHA1-6 : bond 0.00474 ( 3) link_ALPHA1-6 : angle 1.67935 ( 9) link_BETA1-4 : bond 0.00608 ( 57) link_BETA1-4 : angle 2.85889 ( 171) link_NAG-ASN : bond 0.00477 ( 42) link_NAG-ASN : angle 2.72120 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 323 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 125 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9319 (tt) REVERT: c 425 ASN cc_start: 0.8533 (t0) cc_final: 0.8319 (t0) REVERT: 2 34 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7866 (mm) REVERT: 2 104 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7898 (tmm) REVERT: 2 125 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9318 (tt) REVERT: 2 255 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8899 (p) REVERT: 2 259 LEU cc_start: 0.8886 (mp) cc_final: 0.8507 (pp) REVERT: 2 475 MET cc_start: 0.8426 (mmt) cc_final: 0.8098 (mmm) REVERT: C 34 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8022 (mm) REVERT: C 416 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8705 (pp) REVERT: 1 624 ASP cc_start: 0.8952 (m-30) cc_final: 0.8488 (p0) REVERT: 3 65 LYS cc_start: 0.8833 (tttt) cc_final: 0.8272 (pttt) REVERT: 3 80 TYR cc_start: 0.7257 (m-80) cc_final: 0.6822 (m-80) REVERT: 3 103 TRP cc_start: 0.8902 (m100) cc_final: 0.8598 (m-10) REVERT: 4 4 MET cc_start: 0.5521 (tpt) cc_final: 0.5168 (tpt) REVERT: 4 29 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7352 (tp) REVERT: 4 40 TRP cc_start: 0.7826 (m100) cc_final: 0.7573 (m-10) REVERT: 5 86 ASP cc_start: 0.7341 (m-30) cc_final: 0.6912 (m-30) REVERT: 5 100 LYS cc_start: 0.9318 (mmmt) cc_final: 0.9112 (mmmt) REVERT: 5 103 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8696 (mptt) REVERT: 6 25 GLU cc_start: 0.8731 (tp30) cc_final: 0.8507 (tp30) REVERT: 6 104 LEU cc_start: 0.7676 (tt) cc_final: 0.7298 (mm) REVERT: 7 89 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7852 (mm-30) REVERT: 7 97 ASP cc_start: 0.8880 (m-30) cc_final: 0.8488 (m-30) REVERT: D 589 ASP cc_start: 0.8619 (m-30) cc_final: 0.8397 (m-30) REVERT: D 657 GLU cc_start: 0.9031 (tp30) cc_final: 0.8516 (pt0) REVERT: H 69 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5621 (tpt) REVERT: M 5 GLN cc_start: 0.9189 (tp40) cc_final: 0.8157 (mp10) REVERT: M 13 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8607 (mmmm) REVERT: M 53 ASP cc_start: 0.8461 (t0) cc_final: 0.8250 (t0) REVERT: M 75 LYS cc_start: 0.9443 (pttp) cc_final: 0.8779 (tptt) REVERT: M 81 ARG cc_start: 0.8818 (ttp-110) cc_final: 0.8488 (ptp90) REVERT: M 100 LYS cc_start: 0.9360 (mmmt) cc_final: 0.9099 (mmmt) REVERT: M 100 MET cc_start: 0.9506 (mpp) cc_final: 0.8979 (mmm) REVERT: N 61 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7415 (mtm-85) REVERT: Q 80 ASP cc_start: 0.8548 (t0) cc_final: 0.7961 (p0) REVERT: Q 97 ASP cc_start: 0.8701 (m-30) cc_final: 0.8375 (t0) REVERT: Q 110 ASP cc_start: 0.8533 (p0) cc_final: 0.8279 (p0) REVERT: Q 122 GLN cc_start: 0.8685 (pm20) cc_final: 0.8310 (pp30) REVERT: d 595 ILE cc_start: 0.9609 (pt) cc_final: 0.9396 (mp) REVERT: h 81 MET cc_start: 0.6520 (mmm) cc_final: 0.5293 (tpp) REVERT: h 104 TYR cc_start: 0.8199 (p90) cc_final: 0.7940 (p90) REVERT: l 40 TRP cc_start: 0.7092 (m100) cc_final: 0.6798 (m100) REVERT: l 76 PHE cc_start: 0.6901 (m-80) cc_final: 0.6589 (m-10) REVERT: m 31 ASP cc_start: 0.8812 (t0) cc_final: 0.8386 (t0) REVERT: m 32 ASN cc_start: 0.8223 (t0) cc_final: 0.7264 (p0) REVERT: m 100 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9128 (mmmt) REVERT: n 42 GLN cc_start: 0.8049 (mt0) cc_final: 0.7808 (mp10) REVERT: n 53 ASP cc_start: 0.8729 (m-30) cc_final: 0.8520 (m-30) REVERT: q 89 GLU cc_start: 0.8551 (tp30) cc_final: 0.8305 (mm-30) REVERT: q 97 ASP cc_start: 0.8805 (m-30) cc_final: 0.8432 (m-30) REVERT: r 56 SER cc_start: 0.9156 (m) cc_final: 0.8845 (p) REVERT: r 61 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8243 (mtm180) outliers start: 103 outliers final: 53 residues processed: 400 average time/residue: 0.1624 time to fit residues: 105.8066 Evaluate side-chains 339 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 42 ASP Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 530 MET Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 61 ARG Chi-restraints excluded: chain r residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 119 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 286 optimal weight: 0.0060 chunk 283 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 366 optimal weight: 0.0270 chunk 360 optimal weight: 6.9990 overall best weight: 1.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN 4 35 ASN Q 3 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN r 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056461 restraints weight = 137860.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056415 restraints weight = 84155.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.056871 restraints weight = 65791.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056990 restraints weight = 57494.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057397 restraints weight = 51541.355| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32574 Z= 0.136 Angle : 0.705 12.021 44481 Z= 0.337 Chirality : 0.045 0.220 5199 Planarity : 0.004 0.066 5448 Dihedral : 9.113 61.297 6496 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.24 % Allowed : 11.77 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.98 (0.13), residues: 3783 helix: 0.08 (0.26), residues: 396 sheet: -1.13 (0.14), residues: 1389 loop : -1.72 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG r 61 TYR 0.019 0.001 TYR l 92 PHE 0.018 0.001 PHE Q 102 TRP 0.024 0.001 TRP 3 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00304 (32403) covalent geometry : angle 0.66663 (44025) SS BOND : bond 0.00295 ( 57) SS BOND : angle 1.46763 ( 114) hydrogen bonds : bond 0.03568 ( 933) hydrogen bonds : angle 5.82271 ( 2454) link_ALPHA1-2 : bond 0.00251 ( 3) link_ALPHA1-2 : angle 1.61795 ( 9) link_ALPHA1-3 : bond 0.00931 ( 9) link_ALPHA1-3 : angle 1.87664 ( 27) link_ALPHA1-6 : bond 0.00640 ( 3) link_ALPHA1-6 : angle 1.46424 ( 9) link_BETA1-4 : bond 0.00548 ( 57) link_BETA1-4 : angle 2.75673 ( 171) link_NAG-ASN : bond 0.00471 ( 42) link_NAG-ASN : angle 2.57131 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 1.065 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: c 125 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9289 (tt) REVERT: 2 34 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7822 (mm) REVERT: 2 104 MET cc_start: 0.8744 (ttp) cc_final: 0.7961 (tmm) REVERT: 2 125 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9277 (tt) REVERT: 2 255 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8917 (p) REVERT: 2 259 LEU cc_start: 0.8730 (mp) cc_final: 0.8404 (pp) REVERT: 2 475 MET cc_start: 0.8319 (mmt) cc_final: 0.8037 (mmm) REVERT: C 34 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7883 (mm) REVERT: C 416 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8724 (pp) REVERT: 1 624 ASP cc_start: 0.8888 (m-30) cc_final: 0.8480 (p0) REVERT: 3 39 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7136 (tp40) REVERT: 3 65 LYS cc_start: 0.8845 (tttt) cc_final: 0.8366 (pttt) REVERT: 4 50 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7362 (mmtm) REVERT: 5 103 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8662 (mptt) REVERT: 6 104 LEU cc_start: 0.7500 (tt) cc_final: 0.7220 (mm) REVERT: 7 79 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7723 (t0) REVERT: 7 97 ASP cc_start: 0.8871 (m-30) cc_final: 0.8453 (m-30) REVERT: D 530 MET cc_start: 0.9048 (mmt) cc_final: 0.8455 (mmp) REVERT: D 657 GLU cc_start: 0.9021 (tp30) cc_final: 0.8491 (pt0) REVERT: H 69 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5489 (tpt) REVERT: H 81 MET cc_start: 0.6411 (mmm) cc_final: 0.5818 (mmm) REVERT: H 103 TRP cc_start: 0.8701 (m100) cc_final: 0.8001 (m-90) REVERT: M 5 GLN cc_start: 0.9197 (tp40) cc_final: 0.8175 (mp10) REVERT: M 75 LYS cc_start: 0.9415 (pttp) cc_final: 0.8673 (tptt) REVERT: M 81 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8536 (ptp90) REVERT: M 100 MET cc_start: 0.9307 (mpp) cc_final: 0.8869 (mmm) REVERT: Q 80 ASP cc_start: 0.8581 (t0) cc_final: 0.8278 (t0) REVERT: Q 97 ASP cc_start: 0.8736 (m-30) cc_final: 0.8382 (t0) REVERT: Q 110 ASP cc_start: 0.8588 (p0) cc_final: 0.8365 (p0) REVERT: Q 122 GLN cc_start: 0.8673 (pm20) cc_final: 0.8274 (pp30) REVERT: R 37 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: d 664 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: h 27 TYR cc_start: 0.8776 (t80) cc_final: 0.8413 (t80) REVERT: h 81 MET cc_start: 0.6553 (mmm) cc_final: 0.5314 (tpp) REVERT: h 104 TYR cc_start: 0.8078 (p90) cc_final: 0.7709 (p90) REVERT: l 40 TRP cc_start: 0.7403 (m100) cc_final: 0.7037 (m100) REVERT: l 76 PHE cc_start: 0.6690 (m-80) cc_final: 0.6301 (m-10) REVERT: m 31 ASP cc_start: 0.8794 (t0) cc_final: 0.8330 (t0) REVERT: m 32 ASN cc_start: 0.8170 (t0) cc_final: 0.7313 (p0) REVERT: m 48 ILE cc_start: 0.9418 (tp) cc_final: 0.9087 (mp) REVERT: m 77 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (tt) REVERT: m 86 ASP cc_start: 0.6799 (t0) cc_final: 0.6027 (m-30) REVERT: m 100 MET cc_start: 0.9477 (mpp) cc_final: 0.8773 (mmm) REVERT: n 42 GLN cc_start: 0.7984 (mt0) cc_final: 0.7721 (mp10) REVERT: n 52 ASN cc_start: 0.9379 (t0) cc_final: 0.9120 (t0) REVERT: n 83 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: q 89 GLU cc_start: 0.8465 (tp30) cc_final: 0.8177 (mm-30) REVERT: q 97 ASP cc_start: 0.8822 (m-30) cc_final: 0.8393 (m-30) REVERT: r 56 SER cc_start: 0.9129 (m) cc_final: 0.8834 (p) outliers start: 108 outliers final: 60 residues processed: 387 average time/residue: 0.1575 time to fit residues: 100.3204 Evaluate side-chains 341 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 268 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 424 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 6 residue 23 CYS Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 42 ASP Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 83 GLU Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 4 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 362 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN 5 68 HIS 6 89 HIS L 35 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.077450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055131 restraints weight = 138325.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054692 restraints weight = 90085.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055132 restraints weight = 67251.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055406 restraints weight = 56700.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055503 restraints weight = 51874.814| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32574 Z= 0.202 Angle : 0.729 12.861 44481 Z= 0.348 Chirality : 0.046 0.227 5199 Planarity : 0.004 0.065 5448 Dihedral : 8.556 54.611 6496 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.48 % Allowed : 12.34 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.82 (0.13), residues: 3783 helix: 0.32 (0.27), residues: 396 sheet: -1.00 (0.14), residues: 1365 loop : -1.67 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 61 TYR 0.031 0.001 TYR N 87 PHE 0.019 0.002 PHE Q 102 TRP 0.031 0.001 TRP 3 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00455 (32403) covalent geometry : angle 0.69365 (44025) SS BOND : bond 0.00322 ( 57) SS BOND : angle 1.33900 ( 114) hydrogen bonds : bond 0.03682 ( 933) hydrogen bonds : angle 5.69822 ( 2454) link_ALPHA1-2 : bond 0.00227 ( 3) link_ALPHA1-2 : angle 1.81416 ( 9) link_ALPHA1-3 : bond 0.00970 ( 9) link_ALPHA1-3 : angle 1.85622 ( 27) link_ALPHA1-6 : bond 0.00648 ( 3) link_ALPHA1-6 : angle 1.44403 ( 9) link_BETA1-4 : bond 0.00495 ( 57) link_BETA1-4 : angle 2.70661 ( 171) link_NAG-ASN : bond 0.00483 ( 42) link_NAG-ASN : angle 2.65293 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 279 time to evaluate : 1.048 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: c 125 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9313 (tt) REVERT: c 425 ASN cc_start: 0.8750 (t0) cc_final: 0.8517 (t0) REVERT: 2 34 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (mm) REVERT: 2 104 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: 2 125 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9267 (tt) REVERT: 2 255 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9057 (p) REVERT: C 34 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8037 (mm) REVERT: C 104 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (tpp) REVERT: C 161 MET cc_start: 0.8882 (tpp) cc_final: 0.8592 (tpt) REVERT: C 416 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8688 (pp) REVERT: 1 633 LYS cc_start: 0.9003 (mttp) cc_final: 0.8798 (mttp) REVERT: 3 39 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7214 (tp40) REVERT: 3 47 TRP cc_start: 0.5543 (OUTLIER) cc_final: 0.5102 (t60) REVERT: 3 65 LYS cc_start: 0.8960 (tttt) cc_final: 0.8398 (pttt) REVERT: 4 29 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7444 (tp) REVERT: 4 50 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7605 (mmtm) REVERT: 5 16 GLU cc_start: 0.8157 (mp0) cc_final: 0.7937 (pm20) REVERT: 5 103 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8712 (mptt) REVERT: 6 79 GLU cc_start: 0.7666 (mp0) cc_final: 0.7297 (pm20) REVERT: 6 104 LEU cc_start: 0.7558 (tt) cc_final: 0.7145 (mm) REVERT: 7 97 ASP cc_start: 0.8868 (m-30) cc_final: 0.8411 (m-30) REVERT: D 530 MET cc_start: 0.9017 (mmt) cc_final: 0.8309 (mmp) REVERT: D 657 GLU cc_start: 0.9016 (tp30) cc_final: 0.8494 (pt0) REVERT: H 81 MET cc_start: 0.6676 (mmm) cc_final: 0.6162 (mmm) REVERT: H 100 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8383 (mtp180) REVERT: H 103 TRP cc_start: 0.8851 (m100) cc_final: 0.7954 (m-10) REVERT: L 4 MET cc_start: 0.5399 (tpp) cc_final: 0.5147 (tpp) REVERT: M 5 GLN cc_start: 0.9212 (tp40) cc_final: 0.8215 (mp10) REVERT: M 75 LYS cc_start: 0.9431 (pttp) cc_final: 0.8769 (tptt) REVERT: M 81 ARG cc_start: 0.8911 (ttp-110) cc_final: 0.8543 (ptp90) REVERT: M 94 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8724 (p) REVERT: M 100 LYS cc_start: 0.9393 (mmmt) cc_final: 0.9145 (mmmt) REVERT: M 100 MET cc_start: 0.9364 (mpp) cc_final: 0.8887 (mmm) REVERT: N 61 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7442 (mtm-85) REVERT: Q 80 ASP cc_start: 0.8730 (t0) cc_final: 0.8309 (t0) REVERT: Q 97 ASP cc_start: 0.8784 (m-30) cc_final: 0.8400 (t0) REVERT: Q 122 GLN cc_start: 0.8773 (pm20) cc_final: 0.8431 (pp30) REVERT: R 37 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: h 81 MET cc_start: 0.6594 (mmm) cc_final: 0.5289 (tpp) REVERT: h 104 TYR cc_start: 0.8154 (p90) cc_final: 0.7683 (p90) REVERT: l 40 TRP cc_start: 0.7586 (m100) cc_final: 0.7364 (m100) REVERT: l 76 PHE cc_start: 0.6562 (m-80) cc_final: 0.6311 (m-10) REVERT: m 31 ASP cc_start: 0.8878 (t0) cc_final: 0.8439 (t0) REVERT: m 32 ASN cc_start: 0.8083 (t0) cc_final: 0.7291 (p0) REVERT: m 48 ILE cc_start: 0.9447 (tp) cc_final: 0.9123 (mp) REVERT: m 77 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (tt) REVERT: m 86 ASP cc_start: 0.7076 (t0) cc_final: 0.6766 (m-30) REVERT: m 94 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.6830 (p) REVERT: m 100 MET cc_start: 0.9460 (mpp) cc_final: 0.8534 (mmm) REVERT: q 89 GLU cc_start: 0.8479 (tp30) cc_final: 0.8196 (mm-30) REVERT: q 97 ASP cc_start: 0.8815 (m-30) cc_final: 0.8345 (m-30) REVERT: r 56 SER cc_start: 0.9165 (m) cc_final: 0.8899 (p) outliers start: 116 outliers final: 85 residues processed: 367 average time/residue: 0.1566 time to fit residues: 95.1488 Evaluate side-chains 363 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 263 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 424 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 6 residue 23 CYS Chi-restraints excluded: chain 7 residue 42 ASP Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 573 ILE Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 616 ASN Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 0.0570 chunk 200 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 371 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.9712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS Q 3 GLN l 27 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.078376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.055947 restraints weight = 136954.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056074 restraints weight = 78880.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056557 restraints weight = 59774.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056685 restraints weight = 55440.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056690 restraints weight = 48077.691| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32574 Z= 0.124 Angle : 0.681 11.940 44481 Z= 0.325 Chirality : 0.045 0.225 5199 Planarity : 0.004 0.065 5448 Dihedral : 8.009 56.330 6496 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.45 % Allowed : 12.70 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.72 (0.14), residues: 3783 helix: 0.48 (0.27), residues: 396 sheet: -0.97 (0.14), residues: 1335 loop : -1.58 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 39 TYR 0.023 0.001 TYR 6 87 PHE 0.017 0.001 PHE Q 102 TRP 0.026 0.001 TRP 3 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00276 (32403) covalent geometry : angle 0.64611 (44025) SS BOND : bond 0.00303 ( 57) SS BOND : angle 1.25173 ( 114) hydrogen bonds : bond 0.03340 ( 933) hydrogen bonds : angle 5.48860 ( 2454) link_ALPHA1-2 : bond 0.00243 ( 3) link_ALPHA1-2 : angle 1.58209 ( 9) link_ALPHA1-3 : bond 0.00945 ( 9) link_ALPHA1-3 : angle 1.98146 ( 27) link_ALPHA1-6 : bond 0.00954 ( 3) link_ALPHA1-6 : angle 1.21420 ( 9) link_BETA1-4 : bond 0.00539 ( 57) link_BETA1-4 : angle 2.57848 ( 171) link_NAG-ASN : bond 0.00469 ( 42) link_NAG-ASN : angle 2.48895 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 289 time to evaluate : 0.911 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: c 125 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9300 (tt) REVERT: c 425 ASN cc_start: 0.8693 (t0) cc_final: 0.8476 (t0) REVERT: 2 34 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7848 (mm) REVERT: 2 104 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8258 (tmm) REVERT: 2 125 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9275 (tt) REVERT: 2 255 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9039 (p) REVERT: 2 259 LEU cc_start: 0.8822 (mp) cc_final: 0.8417 (pp) REVERT: C 34 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7971 (mm) REVERT: C 416 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8687 (pp) REVERT: 1 633 LYS cc_start: 0.8980 (mttp) cc_final: 0.8719 (mttp) REVERT: 3 39 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7294 (tp40) REVERT: 3 47 TRP cc_start: 0.5634 (OUTLIER) cc_final: 0.5209 (t60) REVERT: 3 65 LYS cc_start: 0.8986 (tttt) cc_final: 0.8412 (pttt) REVERT: 3 81 MET cc_start: 0.6893 (mmt) cc_final: 0.6580 (mmm) REVERT: 4 29 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7290 (tp) REVERT: 4 50 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7809 (mmtp) REVERT: 5 16 GLU cc_start: 0.8265 (mp0) cc_final: 0.7991 (pm20) REVERT: 5 86 ASP cc_start: 0.6960 (m-30) cc_final: 0.6425 (m-30) REVERT: 5 103 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8725 (mptt) REVERT: 6 52 ASN cc_start: 0.9435 (t0) cc_final: 0.9172 (m-40) REVERT: 6 79 GLU cc_start: 0.7711 (mp0) cc_final: 0.7474 (pm20) REVERT: 6 104 LEU cc_start: 0.7615 (tt) cc_final: 0.7273 (mm) REVERT: 7 97 ASP cc_start: 0.8830 (m-30) cc_final: 0.8396 (m-30) REVERT: D 530 MET cc_start: 0.8925 (mmt) cc_final: 0.8254 (mmp) REVERT: H 103 TRP cc_start: 0.8847 (m100) cc_final: 0.8125 (m-90) REVERT: M 5 GLN cc_start: 0.9198 (tp40) cc_final: 0.8203 (mp10) REVERT: M 75 LYS cc_start: 0.9418 (pttp) cc_final: 0.8842 (tptt) REVERT: M 81 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.8570 (ptp90) REVERT: M 94 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (p) REVERT: M 100 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9128 (mmmt) REVERT: M 100 MET cc_start: 0.9371 (mpp) cc_final: 0.8893 (mmm) REVERT: N 61 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7609 (mtm-85) REVERT: N 90 ILE cc_start: 0.9463 (pt) cc_final: 0.9149 (tp) REVERT: Q 80 ASP cc_start: 0.8699 (t0) cc_final: 0.8268 (t0) REVERT: Q 97 ASP cc_start: 0.8777 (m-30) cc_final: 0.8369 (t0) REVERT: Q 122 GLN cc_start: 0.8731 (pm20) cc_final: 0.8303 (pp30) REVERT: R 37 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: h 81 MET cc_start: 0.6675 (mmm) cc_final: 0.5222 (tpp) REVERT: h 104 TYR cc_start: 0.8051 (p90) cc_final: 0.7689 (p90) REVERT: l 76 PHE cc_start: 0.6815 (m-80) cc_final: 0.6508 (m-10) REVERT: m 31 ASP cc_start: 0.8886 (t0) cc_final: 0.8445 (t0) REVERT: m 32 ASN cc_start: 0.7997 (t0) cc_final: 0.7261 (p0) REVERT: m 48 ILE cc_start: 0.9410 (tp) cc_final: 0.9105 (mp) REVERT: m 77 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8133 (tp) REVERT: m 86 ASP cc_start: 0.6983 (t0) cc_final: 0.6670 (m-30) REVERT: m 94 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.6680 (p) REVERT: m 100 MET cc_start: 0.9471 (mpp) cc_final: 0.8491 (mmm) REVERT: n 42 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7049 (pp30) REVERT: n 52 ASN cc_start: 0.9308 (t0) cc_final: 0.9002 (t0) REVERT: q 89 GLU cc_start: 0.8472 (tp30) cc_final: 0.8182 (mm-30) REVERT: q 97 ASP cc_start: 0.8797 (m-30) cc_final: 0.8545 (m-30) REVERT: r 33 MET cc_start: 0.8061 (ppp) cc_final: 0.7355 (ppp) REVERT: r 36 TYR cc_start: 0.8817 (m-10) cc_final: 0.8371 (m-10) REVERT: r 56 SER cc_start: 0.9129 (m) cc_final: 0.8870 (p) REVERT: r 70 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7887 (p0) outliers start: 115 outliers final: 81 residues processed: 380 average time/residue: 0.1682 time to fit residues: 105.3441 Evaluate side-chains 361 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 264 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 46 GLU Chi-restraints excluded: chain 6 residue 23 CYS Chi-restraints excluded: chain 7 residue 42 ASP Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 70 ASP Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 263 optimal weight: 0.0870 chunk 296 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN l 27 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.078345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055538 restraints weight = 137205.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056174 restraints weight = 81586.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056280 restraints weight = 60318.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056440 restraints weight = 57117.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056487 restraints weight = 49612.022| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32574 Z= 0.127 Angle : 0.671 13.821 44481 Z= 0.319 Chirality : 0.044 0.228 5199 Planarity : 0.004 0.054 5448 Dihedral : 7.618 56.143 6496 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.48 % Allowed : 13.18 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.59 (0.14), residues: 3783 helix: 0.60 (0.27), residues: 396 sheet: -0.78 (0.14), residues: 1365 loop : -1.58 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 429 TYR 0.019 0.001 TYR 4 31 PHE 0.019 0.001 PHE c 53 TRP 0.034 0.001 TRP l 40 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00284 (32403) covalent geometry : angle 0.63755 (44025) SS BOND : bond 0.00337 ( 57) SS BOND : angle 1.15510 ( 114) hydrogen bonds : bond 0.03256 ( 933) hydrogen bonds : angle 5.32774 ( 2454) link_ALPHA1-2 : bond 0.00237 ( 3) link_ALPHA1-2 : angle 1.61624 ( 9) link_ALPHA1-3 : bond 0.00926 ( 9) link_ALPHA1-3 : angle 1.93954 ( 27) link_ALPHA1-6 : bond 0.01026 ( 3) link_ALPHA1-6 : angle 1.13716 ( 9) link_BETA1-4 : bond 0.00520 ( 57) link_BETA1-4 : angle 2.50935 ( 171) link_NAG-ASN : bond 0.00456 ( 42) link_NAG-ASN : angle 2.46166 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 279 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 125 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9325 (tt) REVERT: c 425 ASN cc_start: 0.8731 (t0) cc_final: 0.8523 (t0) REVERT: 2 34 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7851 (mm) REVERT: 2 104 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8143 (tmm) REVERT: 2 125 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9257 (tt) REVERT: 2 255 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9073 (p) REVERT: 2 259 LEU cc_start: 0.8732 (mp) cc_final: 0.8329 (pp) REVERT: C 34 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7918 (mm) REVERT: C 416 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 475 MET cc_start: 0.7923 (mtt) cc_final: 0.7652 (ttm) REVERT: 1 633 LYS cc_start: 0.8975 (mttp) cc_final: 0.8775 (mttp) REVERT: 3 39 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7277 (tp40) REVERT: 3 47 TRP cc_start: 0.5807 (OUTLIER) cc_final: 0.5463 (t60) REVERT: 3 65 LYS cc_start: 0.9059 (tttt) cc_final: 0.8502 (pttt) REVERT: 3 81 MET cc_start: 0.6959 (mmt) cc_final: 0.6512 (mmm) REVERT: 4 29 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7517 (tp) REVERT: 4 50 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7844 (mmtp) REVERT: 5 16 GLU cc_start: 0.8241 (mp0) cc_final: 0.7978 (pm20) REVERT: 5 86 ASP cc_start: 0.7015 (m-30) cc_final: 0.6364 (m-30) REVERT: 5 103 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8697 (mptt) REVERT: 6 25 GLU cc_start: 0.8488 (tp30) cc_final: 0.8013 (mm-30) REVERT: 6 52 ASN cc_start: 0.9482 (t0) cc_final: 0.9187 (m-40) REVERT: 6 79 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: 6 104 LEU cc_start: 0.7595 (tt) cc_final: 0.7052 (tp) REVERT: 7 97 ASP cc_start: 0.8841 (m-30) cc_final: 0.8391 (m-30) REVERT: 8 36 TYR cc_start: 0.8931 (m-10) cc_final: 0.8668 (m-10) REVERT: D 530 MET cc_start: 0.8936 (mmt) cc_final: 0.8323 (mmp) REVERT: H 81 MET cc_start: 0.6012 (mmm) cc_final: 0.5362 (mmm) REVERT: M 5 GLN cc_start: 0.9208 (tp40) cc_final: 0.8259 (mp10) REVERT: M 75 LYS cc_start: 0.9401 (pttp) cc_final: 0.8814 (tptt) REVERT: M 81 ARG cc_start: 0.8953 (ttp-110) cc_final: 0.8569 (ptp90) REVERT: M 94 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (p) REVERT: M 100 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8653 (tmtt) REVERT: M 100 MET cc_start: 0.9410 (mpp) cc_final: 0.8914 (mmm) REVERT: N 61 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7620 (mtm-85) REVERT: N 90 ILE cc_start: 0.9443 (pt) cc_final: 0.9164 (tp) REVERT: Q 80 ASP cc_start: 0.8753 (t0) cc_final: 0.8263 (t0) REVERT: Q 97 ASP cc_start: 0.8786 (m-30) cc_final: 0.8384 (t0) REVERT: Q 122 GLN cc_start: 0.8754 (pm20) cc_final: 0.8307 (pp30) REVERT: R 37 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: h 81 MET cc_start: 0.6707 (mmm) cc_final: 0.5219 (tpp) REVERT: h 104 TYR cc_start: 0.7999 (p90) cc_final: 0.7508 (p90) REVERT: m 31 ASP cc_start: 0.8809 (t0) cc_final: 0.8360 (t0) REVERT: m 32 ASN cc_start: 0.7910 (t0) cc_final: 0.7280 (p0) REVERT: m 48 ILE cc_start: 0.9446 (tp) cc_final: 0.9146 (mp) REVERT: m 77 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8254 (tt) REVERT: m 86 ASP cc_start: 0.6972 (t0) cc_final: 0.6675 (m-30) REVERT: m 94 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.6826 (p) REVERT: m 100 MET cc_start: 0.9486 (mpp) cc_final: 0.8517 (mmm) REVERT: n 52 ASN cc_start: 0.9343 (t0) cc_final: 0.9044 (t0) REVERT: q 97 ASP cc_start: 0.8799 (m-30) cc_final: 0.8549 (m-30) REVERT: r 33 MET cc_start: 0.7968 (ppp) cc_final: 0.7552 (ppp) REVERT: r 36 TYR cc_start: 0.8765 (m-10) cc_final: 0.8228 (m-10) REVERT: r 56 SER cc_start: 0.9124 (m) cc_final: 0.8875 (p) REVERT: r 70 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8028 (p0) outliers start: 116 outliers final: 83 residues processed: 371 average time/residue: 0.1655 time to fit residues: 100.9874 Evaluate side-chains 360 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 261 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 90 VAL Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 6 residue 79 GLU Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 42 ASP Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 70 ASP Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 89 GLN Chi-restraints excluded: chain r residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 354 optimal weight: 0.8980 chunk 324 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 367 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 103 GLN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 HIS D 625 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Q 3 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.076791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054411 restraints weight = 139165.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054185 restraints weight = 88566.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054707 restraints weight = 66582.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054788 restraints weight = 60434.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054860 restraints weight = 53529.800| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 32574 Z= 0.223 Angle : 0.732 12.041 44481 Z= 0.350 Chirality : 0.046 0.221 5199 Planarity : 0.004 0.068 5448 Dihedral : 7.669 54.939 6496 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.93 % Allowed : 13.30 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.60 (0.14), residues: 3783 helix: 0.37 (0.26), residues: 414 sheet: -0.78 (0.15), residues: 1320 loop : -1.56 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG n 39 TYR 0.024 0.001 TYR 4 37 PHE 0.018 0.002 PHE Q 102 TRP 0.042 0.002 TRP l 40 HIS 0.005 0.001 HIS 2 105 Details of bonding type rmsd covalent geometry : bond 0.00504 (32403) covalent geometry : angle 0.69985 (44025) SS BOND : bond 0.00342 ( 57) SS BOND : angle 1.24350 ( 114) hydrogen bonds : bond 0.03628 ( 933) hydrogen bonds : angle 5.44299 ( 2454) link_ALPHA1-2 : bond 0.00035 ( 3) link_ALPHA1-2 : angle 1.79878 ( 9) link_ALPHA1-3 : bond 0.01039 ( 9) link_ALPHA1-3 : angle 1.96723 ( 27) link_ALPHA1-6 : bond 0.00992 ( 3) link_ALPHA1-6 : angle 1.18498 ( 9) link_BETA1-4 : bond 0.00479 ( 57) link_BETA1-4 : angle 2.53304 ( 171) link_NAG-ASN : bond 0.00535 ( 42) link_NAG-ASN : angle 2.63070 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 263 time to evaluate : 1.033 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: c 125 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9338 (tt) REVERT: 2 34 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7857 (mm) REVERT: 2 103 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8250 (pp30) REVERT: 2 104 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8068 (tmm) REVERT: 2 125 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9232 (tt) REVERT: 2 255 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 34 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 416 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8738 (pp) REVERT: C 475 MET cc_start: 0.8050 (mtt) cc_final: 0.7815 (ttm) REVERT: 1 638 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7193 (p90) REVERT: 3 39 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7247 (tp40) REVERT: 3 65 LYS cc_start: 0.9061 (tttt) cc_final: 0.8520 (pttt) REVERT: 4 29 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7534 (tp) REVERT: 4 31 TYR cc_start: 0.7704 (t80) cc_final: 0.7394 (t80) REVERT: 4 50 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7869 (mmtp) REVERT: 5 103 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8717 (mptt) REVERT: 6 79 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: 6 104 LEU cc_start: 0.7488 (tt) cc_final: 0.6986 (tp) REVERT: 7 97 ASP cc_start: 0.8891 (m-30) cc_final: 0.8420 (m-30) REVERT: D 530 MET cc_start: 0.8976 (mmt) cc_final: 0.8451 (mmp) REVERT: D 655 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8912 (tppp) REVERT: H 81 MET cc_start: 0.6411 (mmm) cc_final: 0.5949 (mmm) REVERT: M 5 GLN cc_start: 0.9188 (tp40) cc_final: 0.8235 (mp10) REVERT: M 75 LYS cc_start: 0.9390 (pttp) cc_final: 0.8818 (tptt) REVERT: M 81 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8588 (ptp90) REVERT: M 100 LYS cc_start: 0.9400 (mmmt) cc_final: 0.8636 (tmtt) REVERT: M 100 MET cc_start: 0.9448 (mpp) cc_final: 0.8977 (mmm) REVERT: N 25 GLU cc_start: 0.7969 (tp30) cc_final: 0.7652 (mm-30) REVERT: Q 80 ASP cc_start: 0.8802 (t0) cc_final: 0.8339 (t0) REVERT: Q 97 ASP cc_start: 0.8813 (m-30) cc_final: 0.8260 (t0) REVERT: Q 122 GLN cc_start: 0.8847 (pm20) cc_final: 0.8505 (pp30) REVERT: R 37 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: d 535 MET cc_start: 0.8524 (mpt) cc_final: 0.8030 (mpt) REVERT: d 626 MET cc_start: 0.7763 (mmm) cc_final: 0.7404 (mmm) REVERT: d 638 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.5296 (p90) REVERT: h 81 MET cc_start: 0.6886 (mmm) cc_final: 0.5384 (tpp) REVERT: h 104 TYR cc_start: 0.8118 (p90) cc_final: 0.7712 (p90) REVERT: m 48 ILE cc_start: 0.9495 (tp) cc_final: 0.9206 (mp) REVERT: m 77 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8220 (tp) REVERT: m 86 ASP cc_start: 0.6858 (t0) cc_final: 0.6443 (m-30) REVERT: m 94 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.6989 (p) REVERT: m 100 MET cc_start: 0.9452 (mpp) cc_final: 0.8472 (mmm) REVERT: q 97 ASP cc_start: 0.8792 (m-30) cc_final: 0.8517 (m-30) REVERT: r 33 MET cc_start: 0.8050 (ppp) cc_final: 0.7257 (ppp) REVERT: r 36 TYR cc_start: 0.8820 (m-10) cc_final: 0.8216 (m-10) outliers start: 131 outliers final: 92 residues processed: 364 average time/residue: 0.1668 time to fit residues: 102.2843 Evaluate side-chains 361 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 253 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 245 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 632 ASP Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 638 TYR Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 90 VAL Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 6 residue 79 GLU Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 573 ILE Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 593 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 616 ASN Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 235 optimal weight: 10.0000 chunk 251 optimal weight: 0.0870 chunk 359 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN H 62 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN l 27 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.076948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054575 restraints weight = 138526.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054210 restraints weight = 89712.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054997 restraints weight = 70265.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054991 restraints weight = 59474.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055058 restraints weight = 54203.634| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32574 Z= 0.176 Angle : 0.720 12.530 44481 Z= 0.343 Chirality : 0.045 0.220 5199 Planarity : 0.004 0.051 5448 Dihedral : 7.523 55.608 6496 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.63 % Allowed : 13.75 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: -1.54 (0.14), residues: 3783 helix: 0.47 (0.26), residues: 414 sheet: -0.69 (0.15), residues: 1311 loop : -1.57 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 429 TYR 0.015 0.001 TYR H 32 PHE 0.033 0.002 PHE l 76 TRP 0.033 0.002 TRP l 40 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00398 (32403) covalent geometry : angle 0.68764 (44025) SS BOND : bond 0.00358 ( 57) SS BOND : angle 1.42023 ( 114) hydrogen bonds : bond 0.03493 ( 933) hydrogen bonds : angle 5.39746 ( 2454) link_ALPHA1-2 : bond 0.00119 ( 3) link_ALPHA1-2 : angle 1.68734 ( 9) link_ALPHA1-3 : bond 0.00862 ( 9) link_ALPHA1-3 : angle 1.91236 ( 27) link_ALPHA1-6 : bond 0.01056 ( 3) link_ALPHA1-6 : angle 1.12767 ( 9) link_BETA1-4 : bond 0.00484 ( 57) link_BETA1-4 : angle 2.47504 ( 171) link_NAG-ASN : bond 0.00473 ( 42) link_NAG-ASN : angle 2.53045 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 270 time to evaluate : 1.247 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: c 125 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9325 (tt) REVERT: 2 34 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7827 (mm) REVERT: 2 103 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (pp30) REVERT: 2 104 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8065 (tmm) REVERT: 2 125 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9220 (tt) REVERT: 2 255 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8918 (p) REVERT: 2 259 LEU cc_start: 0.8823 (mp) cc_final: 0.8483 (pp) REVERT: C 34 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7892 (mm) REVERT: C 161 MET cc_start: 0.9033 (tpp) cc_final: 0.8721 (tpt) REVERT: C 416 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8746 (pp) REVERT: C 475 MET cc_start: 0.8022 (mtt) cc_final: 0.7802 (ttm) REVERT: 3 39 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7230 (tp40) REVERT: 3 65 LYS cc_start: 0.9053 (tttt) cc_final: 0.8516 (pttt) REVERT: 3 81 MET cc_start: 0.7053 (mmm) cc_final: 0.6658 (mmm) REVERT: 4 29 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7569 (tp) REVERT: 4 50 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: 5 16 GLU cc_start: 0.8282 (mp0) cc_final: 0.8020 (pm20) REVERT: 5 103 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8710 (mptt) REVERT: 6 25 GLU cc_start: 0.8365 (tp30) cc_final: 0.8125 (mm-30) REVERT: 6 52 ASN cc_start: 0.9448 (t0) cc_final: 0.9141 (m-40) REVERT: 6 79 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: 6 104 LEU cc_start: 0.7483 (tt) cc_final: 0.6935 (tp) REVERT: 7 97 ASP cc_start: 0.8888 (m-30) cc_final: 0.8411 (m-30) REVERT: 8 36 TYR cc_start: 0.8923 (m-10) cc_final: 0.8657 (m-10) REVERT: D 530 MET cc_start: 0.8943 (mmt) cc_final: 0.8450 (mmp) REVERT: H 81 MET cc_start: 0.6445 (mmm) cc_final: 0.5941 (mmm) REVERT: M 5 GLN cc_start: 0.9186 (tp40) cc_final: 0.8244 (mp10) REVERT: M 81 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8575 (ptp90) REVERT: M 100 LYS cc_start: 0.9400 (mmmt) cc_final: 0.8643 (tmtt) REVERT: M 100 MET cc_start: 0.9383 (mpp) cc_final: 0.8905 (mmm) REVERT: N 25 GLU cc_start: 0.7977 (tp30) cc_final: 0.7633 (mm-30) REVERT: Q 80 ASP cc_start: 0.8781 (t0) cc_final: 0.8358 (t0) REVERT: Q 97 ASP cc_start: 0.8815 (m-30) cc_final: 0.8219 (t0) REVERT: Q 122 GLN cc_start: 0.8831 (pm20) cc_final: 0.8472 (pp30) REVERT: R 37 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: d 535 MET cc_start: 0.8527 (mpt) cc_final: 0.8086 (mpt) REVERT: d 626 MET cc_start: 0.7660 (mmm) cc_final: 0.7287 (mmm) REVERT: d 638 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5416 (p90) REVERT: h 81 MET cc_start: 0.6666 (mmm) cc_final: 0.5229 (tpp) REVERT: h 83 LEU cc_start: 0.4407 (mt) cc_final: 0.3438 (mt) REVERT: h 104 TYR cc_start: 0.8011 (p90) cc_final: 0.7626 (p90) REVERT: l 38 LEU cc_start: 0.6087 (tp) cc_final: 0.5829 (mt) REVERT: m 48 ILE cc_start: 0.9503 (tp) cc_final: 0.9214 (mp) REVERT: m 77 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8208 (tp) REVERT: m 86 ASP cc_start: 0.6889 (t0) cc_final: 0.6485 (m-30) REVERT: m 94 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7074 (p) REVERT: m 100 MET cc_start: 0.9473 (mpp) cc_final: 0.8501 (mmm) REVERT: n 52 ASN cc_start: 0.9348 (t0) cc_final: 0.9065 (t0) REVERT: q 97 ASP cc_start: 0.8784 (m-30) cc_final: 0.8492 (m-30) REVERT: r 33 MET cc_start: 0.7981 (ppp) cc_final: 0.7203 (ppp) REVERT: r 36 TYR cc_start: 0.8795 (m-10) cc_final: 0.8095 (m-10) REVERT: r 89 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8319 (tt0) outliers start: 121 outliers final: 88 residues processed: 364 average time/residue: 0.1749 time to fit residues: 106.2686 Evaluate side-chains 363 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 259 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 518 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 90 VAL Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 46 GLU Chi-restraints excluded: chain 5 residue 86 ASP Chi-restraints excluded: chain 6 residue 79 GLU Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 354 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN H 62 GLN l 27 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.077509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055027 restraints weight = 137126.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055046 restraints weight = 82100.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.055233 restraints weight = 67198.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055432 restraints weight = 58217.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055917 restraints weight = 52467.128| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32574 Z= 0.136 Angle : 0.702 17.423 44481 Z= 0.335 Chirality : 0.045 0.223 5199 Planarity : 0.004 0.051 5448 Dihedral : 7.352 55.930 6496 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.24 % Allowed : 14.05 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.14), residues: 3783 helix: 0.58 (0.26), residues: 414 sheet: -0.68 (0.15), residues: 1308 loop : -1.51 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 429 TYR 0.018 0.001 TYR 4 31 PHE 0.019 0.001 PHE 8 83 TRP 0.033 0.001 TRP l 40 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (32403) covalent geometry : angle 0.67072 (44025) SS BOND : bond 0.00369 ( 57) SS BOND : angle 1.42032 ( 114) hydrogen bonds : bond 0.03300 ( 933) hydrogen bonds : angle 5.28775 ( 2454) link_ALPHA1-2 : bond 0.00196 ( 3) link_ALPHA1-2 : angle 1.63670 ( 9) link_ALPHA1-3 : bond 0.00923 ( 9) link_ALPHA1-3 : angle 1.93343 ( 27) link_ALPHA1-6 : bond 0.01097 ( 3) link_ALPHA1-6 : angle 1.13976 ( 9) link_BETA1-4 : bond 0.00510 ( 57) link_BETA1-4 : angle 2.42568 ( 171) link_NAG-ASN : bond 0.00462 ( 42) link_NAG-ASN : angle 2.46286 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 273 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 125 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9345 (tt) REVERT: 2 34 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7864 (mm) REVERT: 2 103 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8265 (pp30) REVERT: 2 104 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: 2 125 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9281 (tt) REVERT: 2 255 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8906 (p) REVERT: 2 259 LEU cc_start: 0.8782 (mp) cc_final: 0.8469 (pp) REVERT: C 34 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7901 (mm) REVERT: C 161 MET cc_start: 0.8992 (tpp) cc_final: 0.8644 (tpt) REVERT: C 415 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9103 (m) REVERT: C 416 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8738 (pp) REVERT: 3 39 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7211 (tp40) REVERT: 3 65 LYS cc_start: 0.9046 (tttt) cc_final: 0.8501 (pttt) REVERT: 3 81 MET cc_start: 0.7077 (mmm) cc_final: 0.6741 (mmm) REVERT: 4 29 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7697 (tp) REVERT: 4 50 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7906 (mmtp) REVERT: 5 16 GLU cc_start: 0.8277 (mp0) cc_final: 0.8037 (pm20) REVERT: 5 103 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8700 (mptt) REVERT: 6 25 GLU cc_start: 0.8419 (tp30) cc_final: 0.8197 (mm-30) REVERT: 6 52 ASN cc_start: 0.9464 (t0) cc_final: 0.9167 (m-40) REVERT: 6 79 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: 6 104 LEU cc_start: 0.7487 (tt) cc_final: 0.6941 (tp) REVERT: 7 97 ASP cc_start: 0.8879 (m-30) cc_final: 0.8392 (m-30) REVERT: 8 36 TYR cc_start: 0.8922 (m-10) cc_final: 0.8648 (m-10) REVERT: D 530 MET cc_start: 0.8911 (mmt) cc_final: 0.8436 (mmp) REVERT: H 81 MET cc_start: 0.6450 (mmm) cc_final: 0.5801 (mmm) REVERT: M 5 GLN cc_start: 0.9186 (tp40) cc_final: 0.8258 (mp10) REVERT: M 81 ARG cc_start: 0.8985 (ttp-110) cc_final: 0.8591 (ptp90) REVERT: M 100 LYS cc_start: 0.9391 (mmmt) cc_final: 0.8685 (tmtt) REVERT: M 100 MET cc_start: 0.9406 (mpp) cc_final: 0.8908 (mmm) REVERT: N 25 GLU cc_start: 0.7958 (tp30) cc_final: 0.7616 (mm-30) REVERT: Q 80 ASP cc_start: 0.8783 (t0) cc_final: 0.8330 (t0) REVERT: Q 97 ASP cc_start: 0.8794 (m-30) cc_final: 0.8239 (t0) REVERT: R 33 MET cc_start: 0.8112 (ppp) cc_final: 0.7095 (ppp) REVERT: R 37 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: d 535 MET cc_start: 0.8571 (mpt) cc_final: 0.8087 (mpt) REVERT: d 626 MET cc_start: 0.7745 (mmm) cc_final: 0.7397 (mmm) REVERT: d 638 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.5490 (p90) REVERT: h 81 MET cc_start: 0.6653 (mmm) cc_final: 0.5190 (tpp) REVERT: h 83 LEU cc_start: 0.4395 (mt) cc_final: 0.3438 (mt) REVERT: h 104 TYR cc_start: 0.7995 (p90) cc_final: 0.7604 (p90) REVERT: m 48 ILE cc_start: 0.9499 (tp) cc_final: 0.9213 (mp) REVERT: m 77 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8262 (tp) REVERT: m 86 ASP cc_start: 0.6844 (t0) cc_final: 0.6438 (m-30) REVERT: m 94 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7180 (p) REVERT: m 100 MET cc_start: 0.9480 (mpp) cc_final: 0.8528 (mmm) REVERT: n 52 ASN cc_start: 0.9366 (t0) cc_final: 0.9054 (t0) REVERT: q 97 ASP cc_start: 0.8792 (m-30) cc_final: 0.8504 (m-30) REVERT: r 33 MET cc_start: 0.7788 (ppp) cc_final: 0.7068 (ppp) REVERT: r 36 TYR cc_start: 0.8801 (m-10) cc_final: 0.8099 (m-80) REVERT: r 89 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8271 (tt0) outliers start: 108 outliers final: 85 residues processed: 352 average time/residue: 0.1773 time to fit residues: 103.9182 Evaluate side-chains 365 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 263 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 518 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 90 VAL Chi-restraints excluded: chain 5 residue 46 GLU Chi-restraints excluded: chain 5 residue 86 ASP Chi-restraints excluded: chain 6 residue 79 GLU Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 83 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 616 ASN Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 340 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 369 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN H 62 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.077676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055148 restraints weight = 137369.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055386 restraints weight = 80615.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055516 restraints weight = 64931.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055656 restraints weight = 58848.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055767 restraints weight = 52454.104| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32574 Z= 0.129 Angle : 0.695 17.244 44481 Z= 0.331 Chirality : 0.045 0.228 5199 Planarity : 0.004 0.051 5448 Dihedral : 7.219 55.739 6496 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.24 % Allowed : 14.29 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.14), residues: 3783 helix: 0.65 (0.26), residues: 414 sheet: -0.61 (0.15), residues: 1317 loop : -1.47 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 429 TYR 0.018 0.001 TYR 6 87 PHE 0.025 0.001 PHE c 53 TRP 0.034 0.001 TRP L 40 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00290 (32403) covalent geometry : angle 0.66528 (44025) SS BOND : bond 0.00309 ( 57) SS BOND : angle 1.22275 ( 114) hydrogen bonds : bond 0.03212 ( 933) hydrogen bonds : angle 5.20230 ( 2454) link_ALPHA1-2 : bond 0.00221 ( 3) link_ALPHA1-2 : angle 1.62244 ( 9) link_ALPHA1-3 : bond 0.00869 ( 9) link_ALPHA1-3 : angle 1.90595 ( 27) link_ALPHA1-6 : bond 0.01129 ( 3) link_ALPHA1-6 : angle 1.14496 ( 9) link_BETA1-4 : bond 0.00519 ( 57) link_BETA1-4 : angle 2.39164 ( 171) link_NAG-ASN : bond 0.00461 ( 42) link_NAG-ASN : angle 2.43047 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.66 seconds wall clock time: 78 minutes 30.08 seconds (4710.08 seconds total)