Starting phenix.real_space_refine on Wed Sep 25 12:16:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/09_2024/7jjj_22354.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.001 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 240 5.16 5 C 34638 2.51 5 N 8886 2.21 5 O 10850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 300 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54614 Number of models: 1 Model: "" Number of chains: 92 Chain: "A" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8739 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 1 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "C" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8648 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 53, 'TRANS': 1054} Chain breaks: 2 Chain: "D" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8739 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 1 Chain: "E" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "F" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8648 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 53, 'TRANS': 1054} Chain breaks: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "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: "L" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: 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: 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: 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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: "l" 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: "m" 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 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: 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: 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: 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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 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: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 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: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 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: "IA" 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: "JA" 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: "KA" 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: "LA" 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: "MA" 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: "NA" 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: "OA" 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: "PA" 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: "QA" 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: "RA" 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: "SA" 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: "TA" 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: "UA" 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: "VA" 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: "WA" 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: "XA" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 27.92, per 1000 atoms: 0.51 Number of scatterers: 54614 At special positions: 0 Unit cell: (205.85, 226.55, 172.5, 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 240 16.00 O 10850 8.00 N 8886 7.00 C 34638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=90, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.06 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.17 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.06 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.06 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.14 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 840 " - pdb=" SG CYS D 851 " distance=2.02 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.17 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.05 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.02 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 840 " - pdb=" SG CYS E 851 " distance=2.02 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.06 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.13 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.02 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.02 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.02 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 840 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.02 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 BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGQA 1 " - " NAGQA 2 " " NAGRA 1 " - " NAGRA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGTA 1 " - " NAGTA 2 " " NAGUA 1 " - " NAGUA 2 " " NAGVA 1 " - " NAGVA 2 " " NAGWA 1 " - " NAGWA 2 " " NAGXA 1 " - " NAGXA 2 " " NAGXA 2 " - " BMAXA 3 " BETA1-6 " NAG 6 1 " - " FUC 6 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG t 1 " - " FUC t 4 " " NAGXA 1 " - " FUCXA 4 " NAG-ASN " NAG 0 1 " - " ASN D 122 " " NAG 1 1 " - " ASN D 234 " " NAG 2 1 " - " ASN D 282 " " NAG 3 1 " - " ASN D 165 " " NAG 4 1 " - " ASN D 17 " " NAG 5 1 " - " ASN D 149 " " NAG 6 1 " - " ASN D 616 " " NAG 7 1 " - " ASN E 61 " " NAG 8 1 " - " ASN E 616 " " NAG 9 1 " - " ASN E 343 " " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 282 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 709 " " NAG D1303 " - " ASN D1134 " " NAG E1301 " - " ASN E 331 " " NAG E1302 " - " ASN E 282 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 331 " " NAG F1303 " - " ASN F 343 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A 122 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 282 " " NAG P 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 17 " " NAG R 1 " - " ASN A 149 " " NAG S 1 " - " ASN A 616 " " NAG T 1 " - " ASN B 61 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN B 122 " " NAG d 1 " - " ASN B 234 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN B 17 " " NAG g 1 " - " ASN B 149 " " NAG h 1 " - " ASN C 616 " " NAG i 1 " - " ASN C 709 " " NAG j 1 " - " ASN C 717 " " NAG k 1 " - " ASN C 801 " " NAG l 1 " - " ASN C1074 " " NAG m 1 " - " ASN C1098 " " NAG n 1 " - " ASN C1134 " " NAG o 1 " - " ASN C 122 " " NAG p 1 " - " ASN C 234 " " NAG q 1 " - " ASN C 165 " " NAG r 1 " - " ASN C 17 " " NAG s 1 " - " ASN C 149 " " NAG t 1 " - " ASN C 282 " " NAG u 1 " - " ASN D 61 " " NAG v 1 " - " ASN D 343 " " NAG w 1 " - " ASN D 717 " " NAG x 1 " - " ASN D 801 " " NAG y 1 " - " ASN D1074 " " NAG z 1 " - " ASN D1098 " " NAGAA 1 " - " ASN E 709 " " NAGBA 1 " - " ASN E 717 " " NAGCA 1 " - " ASN E 801 " " NAGDA 1 " - " ASN E1074 " " NAGEA 1 " - " ASN E1098 " " NAGFA 1 " - " ASN E1134 " " NAGGA 1 " - " ASN E 122 " " NAGHA 1 " - " ASN E 234 " " NAGIA 1 " - " ASN E 165 " " NAGJA 1 " - " ASN E 17 " " NAGKA 1 " - " ASN E 149 " " NAGLA 1 " - " ASN F 616 " " NAGMA 1 " - " ASN F 709 " " NAGNA 1 " - " ASN F 717 " " NAGOA 1 " - " ASN F 801 " " NAGPA 1 " - " ASN F1074 " " NAGQA 1 " - " ASN F1098 " " NAGRA 1 " - " ASN F1134 " " NAGSA 1 " - " ASN F 122 " " NAGTA 1 " - " ASN F 234 " " NAGUA 1 " - " ASN F 165 " " NAGVA 1 " - " ASN F 17 " " NAGWA 1 " - " ASN F 149 " " NAGXA 1 " - " ASN F 282 " Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 5.2 seconds 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12460 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 100 sheets defined 25.7% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.679A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.768A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.719A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.522A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.990A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.038A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.721A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.105A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.919A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.952A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.472A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.743A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.815A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.506A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.679A pdb=" N TRP D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.768A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 757 through 783 removed outlier: 3.719A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 836 through 841 Processing helix chain 'D' and resid 842 through 847 Processing helix chain 'D' and resid 848 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 885 through 889 removed outlier: 3.522A pdb=" N GLY D 889 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 913 through 919 Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.990A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.038A pdb=" N ASN E 370 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.721A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.105A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 739 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 756 through 783 removed outlier: 3.919A pdb=" N CYS E 760 " --> pdb=" O TYR E 756 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 836 through 841 Processing helix chain 'E' and resid 842 through 847 Processing helix chain 'E' and resid 848 through 855 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 910 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.952A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 337 through 343 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 364 through 366 No H-bonds generated for 'chain 'F' and resid 364 through 366' Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.472A pdb=" N SER F 371 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.743A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 739 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 756 through 783 removed outlier: 3.815A pdb=" N CYS F 760 " --> pdb=" O TYR F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 836 through 841 Processing helix chain 'F' and resid 842 through 847 Processing helix chain 'F' and resid 848 through 855 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 885 through 889 removed outlier: 3.506A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 910 Processing helix chain 'F' and resid 913 through 919 Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.977A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.487A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.609A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.520A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.579A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.453A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.191A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.587A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.646A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.339A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.076A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.976A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.275A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.573A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.567A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.549A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 714 removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.012A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.619A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.883A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.249A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.611A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.148A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.414A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 714 removed outlier: 4.201A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 27 through 30 removed outlier: 7.977A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 27 through 30 Processing sheet with id=AF8, first strand: chain 'D' and resid 48 through 55 removed outlier: 7.487A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.609A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU D 132 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AG2, first strand: chain 'D' and resid 311 through 315 removed outlier: 4.520A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AG4, first strand: chain 'D' and resid 354 through 357 removed outlier: 3.579A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 354 through 357 removed outlier: 5.453A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU D 516 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AG7, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AG8, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.191A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.587A pdb=" N ALA D 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 787 through 789 Processing sheet with id=AH5, first strand: chain 'D' and resid 1120 through 1123 Processing sheet with id=AH6, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.646A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AH8, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.339A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 83 through 85 removed outlier: 13.076A pdb=" N PHE E 135 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 12.976A pdb=" N THR E 240 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASN E 137 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N LEU E 242 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU E 244 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.275A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.573A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AI4, first strand: chain 'E' and resid 354 through 357 removed outlier: 3.567A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 354 through 357 removed outlier: 5.549A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AI7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AI8, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.267A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 711 through 714 removed outlier: 4.312A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 717 through 728 removed outlier: 6.012A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AJ3, first strand: chain 'E' and resid 787 through 790 Processing sheet with id=AJ4, first strand: chain 'E' and resid 1120 through 1123 Processing sheet with id=AJ5, first strand: chain 'F' and resid 27 through 30 removed outlier: 7.619A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 83 through 85 removed outlier: 6.883A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS F 136 " --> pdb=" O TYR F 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR F 160 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP F 138 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG F 158 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE F 140 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU F 156 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 142 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 154 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 83 through 85 removed outlier: 13.249A pdb=" N PHE F 238 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N PHE F 135 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N THR F 240 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASN F 137 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N LEU F 242 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU F 244 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS F 136 " --> pdb=" O TYR F 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR F 160 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP F 138 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG F 158 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE F 140 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU F 156 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 142 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 154 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.611A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AK2, first strand: chain 'F' and resid 348 through 349 removed outlier: 7.148A pdb=" N ALA F 348 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ARG F 403 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 524 " --> pdb=" O PHE F 392 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 354 through 357 removed outlier: 5.414A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AK5, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AK6, first strand: chain 'F' and resid 654 through 660 removed outlier: 6.244A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 711 through 714 removed outlier: 4.201A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 717 through 728 removed outlier: 6.005A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) 2224 hydrogen bonds defined for protein. 5910 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: 29.05 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 11884 1.32 - 1.46: 18834 1.46 - 1.60: 24782 1.60 - 1.74: 42 1.74 - 1.88: 292 Bond restraints: 55834 Sorted by residual: bond pdb=" CB HIS D 146 " pdb=" CG HIS D 146 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CB HIS A 146 " pdb=" CG HIS A 146 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CB TYR A 351 " pdb=" CG TYR A 351 " ideal model delta sigma weight residual 1.512 1.396 0.116 2.20e-02 2.07e+03 2.79e+01 bond pdb=" CB TYR D 351 " pdb=" CG TYR D 351 " ideal model delta sigma weight residual 1.512 1.396 0.116 2.20e-02 2.07e+03 2.79e+01 bond pdb=" NE ARG D1019 " pdb=" CZ ARG D1019 " ideal model delta sigma weight residual 1.326 1.384 -0.058 1.10e-02 8.26e+03 2.75e+01 ... (remaining 55829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.44: 75824 7.44 - 14.89: 178 14.89 - 22.33: 0 22.33 - 29.78: 0 29.78 - 37.22: 4 Bond angle restraints: 76006 Sorted by residual: angle pdb=" C2 NAG C1302 " pdb=" N2 NAG C1302 " pdb=" C7 NAG C1302 " ideal model delta sigma weight residual 124.56 161.78 -37.22 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG F1302 " pdb=" N2 NAG F1302 " pdb=" C7 NAG F1302 " ideal model delta sigma weight residual 124.56 161.78 -37.22 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " pdb=" C7 NAG A1301 " ideal model delta sigma weight residual 124.56 161.20 -36.64 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C2 NAG D1301 " pdb=" N2 NAG D1301 " pdb=" C7 NAG D1301 " ideal model delta sigma weight residual 124.56 161.20 -36.64 3.00e+00 1.11e-01 1.49e+02 angle pdb=" N PRO E 600 " pdb=" CA PRO E 600 " pdb=" C PRO E 600 " ideal model delta sigma weight residual 111.57 98.96 12.61 1.52e+00 4.33e-01 6.88e+01 ... (remaining 76001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 34576 20.86 - 41.73: 716 41.73 - 62.59: 208 62.59 - 83.46: 56 83.46 - 104.32: 26 Dihedral angle restraints: 35582 sinusoidal: 16170 harmonic: 19412 Sorted by residual: dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual 93.00 158.28 -65.28 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 158.28 -65.28 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS F 840 " pdb=" SG CYS F 840 " pdb=" SG CYS F 851 " pdb=" CB CYS F 851 " ideal model delta sinusoidal sigma weight residual 93.00 153.60 -60.60 1 1.00e+01 1.00e-02 4.89e+01 ... (remaining 35579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 6394 0.110 - 0.221: 1828 0.221 - 0.331: 590 0.331 - 0.441: 210 0.441 - 0.551: 90 Chirality restraints: 9112 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.43e+02 chirality pdb=" C1 NAG 6 2 " pdb=" O4 NAG 6 1 " pdb=" C2 NAG 6 2 " pdb=" O5 NAG 6 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.37e+02 chirality pdb=" C1 NAG 0 2 " pdb=" O4 NAG 0 1 " pdb=" C2 NAG 0 2 " pdb=" O5 NAG 0 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 ... (remaining 9109 not shown) Planarity restraints: 9716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.149 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C7 NAG S 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.201 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " 0.149 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C7 NAG 6 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " 0.109 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " -0.201 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " 0.089 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" CG ASN E 122 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAGGA 1 " 0.118 2.00e-02 2.50e+03 ... (remaining 9713 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 20848 2.88 - 3.39: 51504 3.39 - 3.89: 95628 3.89 - 4.40: 110095 4.40 - 4.90: 174467 Nonbonded interactions: 452542 Sorted by model distance: nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.377 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.377 2.496 nonbonded pdb=" N ASP F 843 " pdb=" OD1 ASP F 843 " model vdw 2.383 3.120 nonbonded pdb=" N ASP C 843 " pdb=" OD1 ASP C 843 " model vdw 2.383 3.120 nonbonded pdb=" N ASP E 663 " pdb=" O ASP E 663 " model vdw 2.415 2.496 ... (remaining 452537 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: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '6' selection = chain 'S' } ncs_group { reference = (chain 'A' and (resid 14 through 618 or resid 632 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'B' and (resid 14 through 689 or resid 692 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'C' and (resid 14 through 676 or resid 690 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'D' and (resid 14 through 618 or resid 632 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'E' and (resid 14 through 689 or resid 692 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'F' and (resid 14 through 676 or resid 690 through 1146 or resid 1301 thr \ ough 1302)) } ncs_group { reference = chain 'XA' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.590 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 111.660 Find NCS groups from input model: 5.000 Set up NCS constraints: 0.990 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: 0.020 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.156 55834 Z= 1.312 Angle : 1.790 37.224 76006 Z= 1.188 Chirality : 0.133 0.551 9112 Planarity : 0.009 0.123 9620 Dihedral : 10.008 104.320 22852 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.07 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 6642 helix: 0.46 (0.12), residues: 1366 sheet: 1.20 (0.14), residues: 1252 loop : 0.32 (0.09), residues: 4024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.010 TRP D 64 HIS 0.011 0.003 HIS C 69 PHE 0.038 0.007 PHE A 55 TYR 0.098 0.009 TYR C 145 ARG 0.008 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1089 time to evaluate : 4.465 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: 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: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7647 (mtm110) REVERT: A 177 MET cc_start: 0.5902 (ttm) cc_final: 0.5399 (tpt) REVERT: A 358 ILE cc_start: 0.9139 (mm) cc_final: 0.8927 (mm) REVERT: A 434 ILE cc_start: 0.9057 (mt) cc_final: 0.8649 (tt) REVERT: A 523 THR cc_start: 0.9089 (p) cc_final: 0.8704 (t) REVERT: A 740 MET cc_start: 0.9188 (mmm) cc_final: 0.8870 (mtm) REVERT: A 742 ILE cc_start: 0.9134 (mt) cc_final: 0.8817 (tt) REVERT: A 781 VAL cc_start: 0.9600 (t) cc_final: 0.9304 (m) REVERT: A 869 MET cc_start: 0.9101 (mtp) cc_final: 0.8784 (mpp) REVERT: A 911 VAL cc_start: 0.9015 (t) cc_final: 0.8622 (t) REVERT: A 996 LEU cc_start: 0.9068 (mt) cc_final: 0.8666 (tt) REVERT: A 1037 SER cc_start: 0.8814 (t) cc_final: 0.8120 (m) REVERT: A 1038 LYS cc_start: 0.9271 (mmtp) cc_final: 0.9018 (tptt) REVERT: B 101 ILE cc_start: 0.8056 (mm) cc_final: 0.7846 (mm) REVERT: B 193 VAL cc_start: 0.9306 (p) cc_final: 0.9093 (m) REVERT: B 300 LYS cc_start: 0.9015 (mttt) cc_final: 0.8493 (mttm) REVERT: B 317 ASN cc_start: 0.8545 (m-40) cc_final: 0.7949 (m-40) REVERT: B 326 ILE cc_start: 0.9181 (mt) cc_final: 0.8787 (pt) REVERT: B 461 LEU cc_start: 0.9409 (mt) cc_final: 0.8760 (mt) REVERT: B 465 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8672 (tm-30) REVERT: B 658 ASN cc_start: 0.8629 (m-40) cc_final: 0.7874 (t0) REVERT: B 731 MET cc_start: 0.8635 (mtp) cc_final: 0.8272 (mtp) REVERT: B 737 ASP cc_start: 0.8398 (t0) cc_final: 0.7303 (m-30) REVERT: B 741 TYR cc_start: 0.9435 (t80) cc_final: 0.9213 (t80) REVERT: B 759 PHE cc_start: 0.8092 (t80) cc_final: 0.7438 (t80) REVERT: B 819 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 867 ASP cc_start: 0.8459 (m-30) cc_final: 0.8092 (t0) REVERT: B 938 LEU cc_start: 0.7320 (tp) cc_final: 0.6985 (tp) REVERT: B 1050 MET cc_start: 0.8545 (ptt) cc_final: 0.8313 (ttt) REVERT: C 97 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8337 (ptmt) REVERT: C 111 ASP cc_start: 0.9190 (t0) cc_final: 0.8816 (m-30) REVERT: C 133 PHE cc_start: 0.8553 (m-80) cc_final: 0.8330 (m-80) REVERT: C 223 LEU cc_start: 0.8626 (mt) cc_final: 0.8357 (mp) REVERT: C 285 ILE cc_start: 0.9395 (mt) cc_final: 0.9138 (tp) REVERT: C 306 PHE cc_start: 0.7887 (m-80) cc_final: 0.7518 (m-80) REVERT: C 389 ASP cc_start: 0.9033 (m-30) cc_final: 0.8196 (t70) REVERT: C 467 ASP cc_start: 0.7469 (t0) cc_final: 0.7232 (p0) REVERT: C 513 LEU cc_start: 0.9211 (tp) cc_final: 0.8827 (mp) REVERT: C 746 SER cc_start: 0.9001 (t) cc_final: 0.8752 (m) REVERT: C 867 ASP cc_start: 0.8755 (m-30) cc_final: 0.8297 (t70) REVERT: C 909 ILE cc_start: 0.8592 (mt) cc_final: 0.8330 (mm) REVERT: C 936 ASP cc_start: 0.8799 (m-30) cc_final: 0.8503 (t70) REVERT: C 996 LEU cc_start: 0.9001 (mt) cc_final: 0.8616 (tt) REVERT: C 1028 LYS cc_start: 0.9261 (mttt) cc_final: 0.9001 (tppt) REVERT: C 1064 HIS cc_start: 0.6907 (m-70) cc_final: 0.5416 (m170) REVERT: C 1102 TRP cc_start: 0.6557 (m100) cc_final: 0.5030 (m100) REVERT: D 102 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7649 (mtm110) REVERT: D 177 MET cc_start: 0.5897 (ttm) cc_final: 0.5398 (tpt) REVERT: D 358 ILE cc_start: 0.9141 (mm) cc_final: 0.8929 (mm) REVERT: D 434 ILE cc_start: 0.9061 (mt) cc_final: 0.8656 (tt) REVERT: D 523 THR cc_start: 0.9090 (p) cc_final: 0.8700 (t) REVERT: D 740 MET cc_start: 0.9186 (mmm) cc_final: 0.8869 (mtm) REVERT: D 742 ILE cc_start: 0.9135 (mt) cc_final: 0.8826 (tt) REVERT: D 781 VAL cc_start: 0.9600 (t) cc_final: 0.9301 (m) REVERT: D 869 MET cc_start: 0.9101 (mtp) cc_final: 0.8784 (mpp) REVERT: D 911 VAL cc_start: 0.9015 (t) cc_final: 0.8618 (t) REVERT: D 996 LEU cc_start: 0.9067 (mt) cc_final: 0.8685 (tt) REVERT: D 1037 SER cc_start: 0.8806 (t) cc_final: 0.8102 (m) REVERT: D 1038 LYS cc_start: 0.9268 (mmtp) cc_final: 0.9014 (tptt) REVERT: E 101 ILE cc_start: 0.8059 (mm) cc_final: 0.7848 (mm) REVERT: E 193 VAL cc_start: 0.9304 (p) cc_final: 0.9090 (m) REVERT: E 300 LYS cc_start: 0.9014 (mttt) cc_final: 0.8495 (mttm) REVERT: E 317 ASN cc_start: 0.8542 (m-40) cc_final: 0.7943 (m-40) REVERT: E 326 ILE cc_start: 0.9183 (mt) cc_final: 0.8787 (pt) REVERT: E 461 LEU cc_start: 0.9407 (mt) cc_final: 0.8761 (mt) REVERT: E 465 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8672 (tm-30) REVERT: E 658 ASN cc_start: 0.8626 (m-40) cc_final: 0.7871 (t0) REVERT: E 731 MET cc_start: 0.8636 (mtp) cc_final: 0.8277 (mtp) REVERT: E 737 ASP cc_start: 0.8394 (t0) cc_final: 0.7301 (m-30) REVERT: E 741 TYR cc_start: 0.9437 (t80) cc_final: 0.9221 (t80) REVERT: E 759 PHE cc_start: 0.8093 (t80) cc_final: 0.7448 (t80) REVERT: E 819 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 867 ASP cc_start: 0.8456 (m-30) cc_final: 0.8093 (t0) REVERT: E 938 LEU cc_start: 0.7321 (tp) cc_final: 0.6988 (tp) REVERT: E 1050 MET cc_start: 0.8553 (ptt) cc_final: 0.8318 (ttt) REVERT: F 97 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8335 (ptmt) REVERT: F 111 ASP cc_start: 0.9187 (t0) cc_final: 0.8813 (m-30) REVERT: F 133 PHE cc_start: 0.8550 (m-80) cc_final: 0.8330 (m-80) REVERT: F 223 LEU cc_start: 0.8625 (mt) cc_final: 0.8358 (mp) REVERT: F 285 ILE cc_start: 0.9397 (mt) cc_final: 0.9139 (tp) REVERT: F 290 ASP cc_start: 0.8411 (t0) cc_final: 0.8211 (t0) REVERT: F 306 PHE cc_start: 0.7883 (m-80) cc_final: 0.7516 (m-80) REVERT: F 389 ASP cc_start: 0.9027 (m-30) cc_final: 0.8198 (t70) REVERT: F 467 ASP cc_start: 0.7472 (t0) cc_final: 0.7234 (p0) REVERT: F 513 LEU cc_start: 0.9208 (tp) cc_final: 0.8825 (mp) REVERT: F 746 SER cc_start: 0.9004 (t) cc_final: 0.8754 (m) REVERT: F 867 ASP cc_start: 0.8758 (m-30) cc_final: 0.8296 (t70) REVERT: F 909 ILE cc_start: 0.8594 (mt) cc_final: 0.8332 (mm) REVERT: F 936 ASP cc_start: 0.8797 (m-30) cc_final: 0.8505 (t70) REVERT: F 996 LEU cc_start: 0.9001 (mt) cc_final: 0.8621 (tt) REVERT: F 1028 LYS cc_start: 0.9260 (mttt) cc_final: 0.9005 (tppt) REVERT: F 1064 HIS cc_start: 0.6906 (m-70) cc_final: 0.5413 (m170) REVERT: F 1102 TRP cc_start: 0.6552 (m100) cc_final: 0.5037 (m100) outliers start: 4 outliers final: 2 residues processed: 1093 average time/residue: 0.5263 time to fit residues: 975.3591 Evaluate side-chains 475 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 473 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 5.9990 chunk 503 optimal weight: 4.9990 chunk 279 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 520 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 387 optimal weight: 0.9980 chunk 602 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 641 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 955 ASN B1054 GLN C 146 HIS C 188 ASN C 901 GLN C 928 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1010 GLN C1023 ASN D 69 HIS ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 354 ASN D 641 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1054 GLN F 146 HIS F 188 ASN F 901 GLN F 928 ASN ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN F1010 GLN F1023 ASN F1048 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 55834 Z= 0.287 Angle : 0.734 10.397 76006 Z= 0.386 Chirality : 0.050 0.402 9112 Planarity : 0.005 0.063 9620 Dihedral : 6.728 63.225 10982 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.21 % Allowed : 1.76 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 6642 helix: 1.79 (0.14), residues: 1348 sheet: 0.65 (0.14), residues: 1308 loop : -0.00 (0.09), residues: 3986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 152 HIS 0.006 0.002 HIS A 625 PHE 0.024 0.002 PHE D 802 TYR 0.043 0.002 TYR A 37 ARG 0.008 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 609 time to evaluate : 4.645 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5841 (ttm) cc_final: 0.5410 (tpt) REVERT: A 271 GLN cc_start: 0.9185 (mt0) cc_final: 0.8598 (mt0) REVERT: A 434 ILE cc_start: 0.9163 (mt) cc_final: 0.8810 (tt) REVERT: A 523 THR cc_start: 0.9089 (p) cc_final: 0.8731 (t) REVERT: A 584 ILE cc_start: 0.9177 (mm) cc_final: 0.8967 (mm) REVERT: A 781 VAL cc_start: 0.9492 (t) cc_final: 0.9192 (p) REVERT: A 869 MET cc_start: 0.9344 (mtp) cc_final: 0.8974 (mtt) REVERT: A 872 GLN cc_start: 0.8210 (mt0) cc_final: 0.7718 (mm-40) REVERT: A 900 MET cc_start: 0.9332 (mmt) cc_final: 0.8752 (mmt) REVERT: A 996 LEU cc_start: 0.9122 (mt) cc_final: 0.8780 (tp) REVERT: A 1037 SER cc_start: 0.8885 (t) cc_final: 0.8147 (m) REVERT: A 1038 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8941 (tptt) REVERT: B 233 ILE cc_start: 0.8498 (pt) cc_final: 0.8287 (mm) REVERT: B 300 LYS cc_start: 0.9100 (mttt) cc_final: 0.8490 (mmtt) REVERT: B 317 ASN cc_start: 0.8655 (m-40) cc_final: 0.8399 (m-40) REVERT: B 326 ILE cc_start: 0.8691 (mt) cc_final: 0.8350 (pt) REVERT: B 360 ASN cc_start: 0.9105 (m-40) cc_final: 0.8393 (p0) REVERT: B 461 LEU cc_start: 0.9514 (mt) cc_final: 0.9309 (mt) REVERT: B 581 THR cc_start: 0.8254 (m) cc_final: 0.7887 (p) REVERT: B 586 ASP cc_start: 0.8735 (t70) cc_final: 0.8488 (t0) REVERT: B 592 PHE cc_start: 0.9149 (t80) cc_final: 0.8844 (t80) REVERT: B 658 ASN cc_start: 0.8569 (m-40) cc_final: 0.7837 (t0) REVERT: B 661 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8812 (mt-10) REVERT: B 737 ASP cc_start: 0.8959 (t0) cc_final: 0.8376 (m-30) REVERT: B 788 ILE cc_start: 0.8417 (tt) cc_final: 0.7958 (pt) REVERT: B 867 ASP cc_start: 0.8549 (m-30) cc_final: 0.8017 (t0) REVERT: B 1031 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: B 1050 MET cc_start: 0.8479 (ptt) cc_final: 0.8170 (ttt) REVERT: C 97 LYS cc_start: 0.8974 (ptpt) cc_final: 0.8583 (ptpt) REVERT: C 111 ASP cc_start: 0.9169 (t0) cc_final: 0.8755 (m-30) REVERT: C 133 PHE cc_start: 0.8672 (m-80) cc_final: 0.8420 (m-80) REVERT: C 153 MET cc_start: 0.8540 (tpp) cc_final: 0.8188 (tpp) REVERT: C 185 ASN cc_start: 0.9141 (m-40) cc_final: 0.8455 (t0) REVERT: C 265 TYR cc_start: 0.7948 (p90) cc_final: 0.7146 (p90) REVERT: C 285 ILE cc_start: 0.9495 (mt) cc_final: 0.9201 (tp) REVERT: C 358 ILE cc_start: 0.9545 (mp) cc_final: 0.9197 (tt) REVERT: C 389 ASP cc_start: 0.9071 (m-30) cc_final: 0.8174 (t70) REVERT: C 513 LEU cc_start: 0.9192 (tp) cc_final: 0.8825 (mp) REVERT: C 867 ASP cc_start: 0.8622 (m-30) cc_final: 0.8301 (t70) REVERT: C 936 ASP cc_start: 0.8666 (m-30) cc_final: 0.8252 (t70) REVERT: C 1028 LYS cc_start: 0.9108 (mttt) cc_final: 0.8638 (tppp) REVERT: D 177 MET cc_start: 0.5833 (ttm) cc_final: 0.5405 (tpt) REVERT: D 271 GLN cc_start: 0.9184 (mt0) cc_final: 0.8598 (mt0) REVERT: D 434 ILE cc_start: 0.9165 (mt) cc_final: 0.8811 (tt) REVERT: D 523 THR cc_start: 0.9088 (p) cc_final: 0.8729 (t) REVERT: D 584 ILE cc_start: 0.9169 (mm) cc_final: 0.8957 (mm) REVERT: D 781 VAL cc_start: 0.9494 (t) cc_final: 0.9192 (p) REVERT: D 869 MET cc_start: 0.9347 (mtp) cc_final: 0.8977 (mtt) REVERT: D 872 GLN cc_start: 0.8209 (mt0) cc_final: 0.7720 (mm-40) REVERT: D 900 MET cc_start: 0.9326 (mmt) cc_final: 0.8744 (mmt) REVERT: D 996 LEU cc_start: 0.9181 (mt) cc_final: 0.8724 (tt) REVERT: D 1037 SER cc_start: 0.8873 (t) cc_final: 0.8131 (m) REVERT: D 1038 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8939 (tptt) REVERT: E 233 ILE cc_start: 0.8488 (pt) cc_final: 0.8286 (mm) REVERT: E 300 LYS cc_start: 0.9094 (mttt) cc_final: 0.8487 (mmtt) REVERT: E 317 ASN cc_start: 0.8656 (m-40) cc_final: 0.8393 (m-40) REVERT: E 326 ILE cc_start: 0.8690 (mt) cc_final: 0.8348 (pt) REVERT: E 360 ASN cc_start: 0.9107 (m-40) cc_final: 0.8391 (p0) REVERT: E 461 LEU cc_start: 0.9515 (mt) cc_final: 0.9312 (mt) REVERT: E 581 THR cc_start: 0.8254 (m) cc_final: 0.7883 (p) REVERT: E 586 ASP cc_start: 0.8749 (t70) cc_final: 0.8501 (t0) REVERT: E 592 PHE cc_start: 0.9157 (t80) cc_final: 0.8845 (t80) REVERT: E 658 ASN cc_start: 0.8568 (m-40) cc_final: 0.7837 (t0) REVERT: E 661 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8808 (mt-10) REVERT: E 737 ASP cc_start: 0.8958 (t0) cc_final: 0.8374 (m-30) REVERT: E 788 ILE cc_start: 0.8419 (tt) cc_final: 0.7956 (pt) REVERT: E 867 ASP cc_start: 0.8550 (m-30) cc_final: 0.8025 (t0) REVERT: E 1031 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: E 1050 MET cc_start: 0.8478 (ptt) cc_final: 0.8165 (ttt) REVERT: F 97 LYS cc_start: 0.8968 (ptpt) cc_final: 0.8584 (ptpt) REVERT: F 111 ASP cc_start: 0.9166 (t0) cc_final: 0.8752 (m-30) REVERT: F 133 PHE cc_start: 0.8670 (m-80) cc_final: 0.8417 (m-80) REVERT: F 153 MET cc_start: 0.8543 (tpp) cc_final: 0.8191 (tpp) REVERT: F 185 ASN cc_start: 0.9137 (m-40) cc_final: 0.8454 (t0) REVERT: F 265 TYR cc_start: 0.7938 (p90) cc_final: 0.7133 (p90) REVERT: F 285 ILE cc_start: 0.9495 (mt) cc_final: 0.9204 (tp) REVERT: F 358 ILE cc_start: 0.9546 (mp) cc_final: 0.9195 (tt) REVERT: F 389 ASP cc_start: 0.9068 (m-30) cc_final: 0.8175 (t70) REVERT: F 513 LEU cc_start: 0.9186 (tp) cc_final: 0.8828 (mp) REVERT: F 867 ASP cc_start: 0.8619 (m-30) cc_final: 0.8301 (t70) REVERT: F 936 ASP cc_start: 0.8666 (m-30) cc_final: 0.8252 (t70) REVERT: F 938 LEU cc_start: 0.9539 (mm) cc_final: 0.9339 (pp) REVERT: F 1028 LYS cc_start: 0.9105 (mttt) cc_final: 0.8639 (tppp) outliers start: 12 outliers final: 2 residues processed: 619 average time/residue: 0.5112 time to fit residues: 548.7803 Evaluate side-chains 367 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 363 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 501 optimal weight: 10.0000 chunk 410 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 604 optimal weight: 6.9990 chunk 652 optimal weight: 9.9990 chunk 537 optimal weight: 7.9990 chunk 599 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 484 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 658 ASN A 872 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1071 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1071 GLN D 66 HIS ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 658 ASN D 872 GLN D 901 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 HIS ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS E1071 GLN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 901 GLN ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1023 ASN F1071 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 55834 Z= 0.471 Angle : 0.882 12.611 76006 Z= 0.456 Chirality : 0.052 0.289 9112 Planarity : 0.006 0.096 9620 Dihedral : 7.259 57.964 10982 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 6642 helix: 0.98 (0.13), residues: 1396 sheet: 0.39 (0.14), residues: 1258 loop : -0.82 (0.09), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 886 HIS 0.010 0.003 HIS B 49 PHE 0.025 0.003 PHE F 192 TYR 0.042 0.003 TYR C 204 ARG 0.010 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 413 time to evaluate : 4.546 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9324 (mt) cc_final: 0.9030 (tt) REVERT: A 523 THR cc_start: 0.9082 (p) cc_final: 0.8569 (t) REVERT: A 731 MET cc_start: 0.8918 (ttm) cc_final: 0.8716 (ttp) REVERT: A 869 MET cc_start: 0.9339 (mtp) cc_final: 0.8865 (mtt) REVERT: A 872 GLN cc_start: 0.8341 (mt0) cc_final: 0.7484 (mm-40) REVERT: A 900 MET cc_start: 0.9201 (mmt) cc_final: 0.8725 (mmt) REVERT: A 975 SER cc_start: 0.9455 (p) cc_final: 0.9038 (m) REVERT: B 53 ASP cc_start: 0.8701 (m-30) cc_final: 0.8101 (m-30) REVERT: B 177 MET cc_start: 0.7476 (mtt) cc_final: 0.6211 (mtt) REVERT: B 300 LYS cc_start: 0.9213 (mttt) cc_final: 0.8692 (mmtm) REVERT: B 360 ASN cc_start: 0.8849 (m-40) cc_final: 0.7740 (p0) REVERT: B 737 ASP cc_start: 0.9114 (t0) cc_final: 0.8453 (t0) REVERT: B 763 LEU cc_start: 0.9259 (mt) cc_final: 0.9054 (mt) REVERT: B 790 LYS cc_start: 0.8875 (mptt) cc_final: 0.8506 (tptt) REVERT: B 867 ASP cc_start: 0.8509 (m-30) cc_final: 0.7778 (t0) REVERT: B 902 MET cc_start: 0.8911 (mmp) cc_final: 0.8676 (mmp) REVERT: B 1050 MET cc_start: 0.8775 (ptt) cc_final: 0.8218 (ttp) REVERT: B 1062 PHE cc_start: 0.8778 (m-80) cc_final: 0.8512 (m-10) REVERT: C 153 MET cc_start: 0.8612 (tpp) cc_final: 0.8194 (tpp) REVERT: C 185 ASN cc_start: 0.9355 (m-40) cc_final: 0.8775 (m-40) REVERT: C 731 MET cc_start: 0.8630 (mtm) cc_final: 0.8301 (mtt) REVERT: C 867 ASP cc_start: 0.8827 (m-30) cc_final: 0.8151 (t70) REVERT: C 900 MET cc_start: 0.9091 (tpp) cc_final: 0.8416 (tpp) REVERT: C 948 LEU cc_start: 0.9270 (mt) cc_final: 0.8921 (mm) REVERT: C 1028 LYS cc_start: 0.9029 (mttt) cc_final: 0.8539 (tppt) REVERT: C 1112 PRO cc_start: 0.7681 (Cg_endo) cc_final: 0.7407 (Cg_exo) REVERT: D 434 ILE cc_start: 0.9321 (mt) cc_final: 0.9032 (tt) REVERT: D 523 THR cc_start: 0.9082 (p) cc_final: 0.8568 (t) REVERT: D 731 MET cc_start: 0.8922 (ttm) cc_final: 0.8717 (ttp) REVERT: D 869 MET cc_start: 0.9337 (mtp) cc_final: 0.8858 (mtt) REVERT: D 872 GLN cc_start: 0.8340 (mt0) cc_final: 0.7476 (mm-40) REVERT: D 900 MET cc_start: 0.9204 (mmt) cc_final: 0.8726 (mmt) REVERT: D 975 SER cc_start: 0.9449 (p) cc_final: 0.9033 (m) REVERT: E 53 ASP cc_start: 0.8700 (m-30) cc_final: 0.8101 (m-30) REVERT: E 177 MET cc_start: 0.7482 (mtt) cc_final: 0.6214 (mtt) REVERT: E 300 LYS cc_start: 0.9212 (mttt) cc_final: 0.8690 (mmtm) REVERT: E 360 ASN cc_start: 0.8853 (m-40) cc_final: 0.7745 (p0) REVERT: E 737 ASP cc_start: 0.9115 (t0) cc_final: 0.8444 (t0) REVERT: E 763 LEU cc_start: 0.9259 (mt) cc_final: 0.9056 (mt) REVERT: E 790 LYS cc_start: 0.8877 (mptt) cc_final: 0.8508 (tptt) REVERT: E 867 ASP cc_start: 0.8512 (m-30) cc_final: 0.7780 (t0) REVERT: E 902 MET cc_start: 0.8912 (mmp) cc_final: 0.8677 (mmp) REVERT: E 1050 MET cc_start: 0.8767 (ptt) cc_final: 0.8211 (ttp) REVERT: E 1062 PHE cc_start: 0.8784 (m-80) cc_final: 0.8503 (m-10) REVERT: F 153 MET cc_start: 0.8605 (tpp) cc_final: 0.8191 (tpp) REVERT: F 185 ASN cc_start: 0.9354 (m-40) cc_final: 0.8777 (m-40) REVERT: F 731 MET cc_start: 0.8634 (mtm) cc_final: 0.8309 (mtt) REVERT: F 867 ASP cc_start: 0.8829 (m-30) cc_final: 0.8162 (t70) REVERT: F 900 MET cc_start: 0.9088 (tpp) cc_final: 0.8412 (tpp) REVERT: F 948 LEU cc_start: 0.9264 (mt) cc_final: 0.8916 (mm) REVERT: F 1028 LYS cc_start: 0.9032 (mttt) cc_final: 0.8557 (tppt) REVERT: F 1112 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.7409 (Cg_exo) outliers start: 6 outliers final: 4 residues processed: 417 average time/residue: 0.5100 time to fit residues: 372.0612 Evaluate side-chains 276 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 272 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 405 optimal weight: 0.9990 chunk 606 optimal weight: 5.9990 chunk 641 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 574 optimal weight: 4.9990 chunk 172 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55834 Z= 0.183 Angle : 0.619 8.368 76006 Z= 0.324 Chirality : 0.047 0.310 9112 Planarity : 0.004 0.049 9620 Dihedral : 6.284 44.472 10982 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6642 helix: 1.56 (0.14), residues: 1396 sheet: 0.35 (0.14), residues: 1274 loop : -0.59 (0.09), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS F 66 PHE 0.029 0.002 PHE C 855 TYR 0.036 0.002 TYR A 37 ARG 0.006 0.000 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 448 time to evaluate : 4.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.9237 (mt0) cc_final: 0.8374 (mt0) REVERT: A 434 ILE cc_start: 0.9298 (mt) cc_final: 0.8967 (tt) REVERT: A 523 THR cc_start: 0.8990 (p) cc_final: 0.8435 (t) REVERT: A 544 ASN cc_start: 0.8926 (m-40) cc_final: 0.8697 (m-40) REVERT: A 582 LEU cc_start: 0.9053 (mt) cc_final: 0.8548 (tt) REVERT: A 806 LEU cc_start: 0.8155 (mt) cc_final: 0.7815 (pp) REVERT: A 869 MET cc_start: 0.9259 (mtp) cc_final: 0.9030 (mtt) REVERT: A 900 MET cc_start: 0.9156 (mmt) cc_final: 0.8606 (mmt) REVERT: A 975 SER cc_start: 0.9351 (p) cc_final: 0.8940 (m) REVERT: A 1037 SER cc_start: 0.8708 (t) cc_final: 0.8411 (m) REVERT: A 1038 LYS cc_start: 0.9293 (mptt) cc_final: 0.8767 (tptp) REVERT: B 42 VAL cc_start: 0.8808 (t) cc_final: 0.8469 (t) REVERT: B 53 ASP cc_start: 0.8632 (m-30) cc_final: 0.7943 (m-30) REVERT: B 177 MET cc_start: 0.7372 (mtt) cc_final: 0.6072 (mtt) REVERT: B 187 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8545 (mmmt) REVERT: B 300 LYS cc_start: 0.9149 (mttt) cc_final: 0.8663 (mttm) REVERT: B 360 ASN cc_start: 0.8966 (m-40) cc_final: 0.7822 (p0) REVERT: B 658 ASN cc_start: 0.8838 (m-40) cc_final: 0.7973 (t0) REVERT: B 697 MET cc_start: 0.8084 (mpp) cc_final: 0.7855 (mpp) REVERT: B 737 ASP cc_start: 0.8996 (t0) cc_final: 0.8361 (t0) REVERT: B 740 MET cc_start: 0.8970 (ttt) cc_final: 0.8558 (ttm) REVERT: B 790 LYS cc_start: 0.8934 (mptt) cc_final: 0.8594 (tptt) REVERT: B 805 ILE cc_start: 0.9517 (tp) cc_final: 0.9308 (mp) REVERT: B 867 ASP cc_start: 0.8523 (m-30) cc_final: 0.7882 (t0) REVERT: B 1054 GLN cc_start: 0.7280 (tp40) cc_final: 0.6910 (tp-100) REVERT: B 1062 PHE cc_start: 0.8641 (m-80) cc_final: 0.8332 (m-10) REVERT: C 185 ASN cc_start: 0.9265 (m-40) cc_final: 0.8837 (t0) REVERT: C 265 TYR cc_start: 0.8398 (p90) cc_final: 0.7886 (p90) REVERT: C 287 ASP cc_start: 0.8937 (t0) cc_final: 0.8679 (t0) REVERT: C 867 ASP cc_start: 0.8815 (m-30) cc_final: 0.8053 (t70) REVERT: C 900 MET cc_start: 0.8905 (tpp) cc_final: 0.8636 (tpt) REVERT: C 936 ASP cc_start: 0.8785 (m-30) cc_final: 0.8192 (t70) REVERT: C 1028 LYS cc_start: 0.8883 (mttt) cc_final: 0.8169 (tppp) REVERT: D 271 GLN cc_start: 0.9238 (mt0) cc_final: 0.8372 (mt0) REVERT: D 434 ILE cc_start: 0.9310 (mt) cc_final: 0.8986 (tt) REVERT: D 523 THR cc_start: 0.8990 (p) cc_final: 0.8437 (t) REVERT: D 544 ASN cc_start: 0.8921 (m-40) cc_final: 0.8690 (m-40) REVERT: D 582 LEU cc_start: 0.9049 (mt) cc_final: 0.8547 (tt) REVERT: D 806 LEU cc_start: 0.8156 (mt) cc_final: 0.7816 (pp) REVERT: D 869 MET cc_start: 0.9258 (mtp) cc_final: 0.9028 (mtt) REVERT: D 900 MET cc_start: 0.9154 (mmt) cc_final: 0.8600 (mmt) REVERT: D 975 SER cc_start: 0.9347 (p) cc_final: 0.8938 (m) REVERT: D 1037 SER cc_start: 0.8704 (t) cc_final: 0.8405 (m) REVERT: D 1038 LYS cc_start: 0.9294 (mptt) cc_final: 0.8769 (tptp) REVERT: E 42 VAL cc_start: 0.8813 (t) cc_final: 0.8451 (t) REVERT: E 53 ASP cc_start: 0.8628 (m-30) cc_final: 0.7944 (m-30) REVERT: E 177 MET cc_start: 0.7375 (mtt) cc_final: 0.6075 (mtt) REVERT: E 187 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8546 (mmmt) REVERT: E 300 LYS cc_start: 0.9149 (mttt) cc_final: 0.8663 (mttm) REVERT: E 360 ASN cc_start: 0.8971 (m-40) cc_final: 0.7829 (p0) REVERT: E 658 ASN cc_start: 0.8841 (m-40) cc_final: 0.7972 (t0) REVERT: E 697 MET cc_start: 0.8079 (mpp) cc_final: 0.7855 (mpp) REVERT: E 737 ASP cc_start: 0.8999 (t0) cc_final: 0.8360 (t0) REVERT: E 740 MET cc_start: 0.8971 (ttt) cc_final: 0.8560 (ttm) REVERT: E 790 LYS cc_start: 0.8933 (mptt) cc_final: 0.8596 (tptt) REVERT: E 805 ILE cc_start: 0.9514 (tp) cc_final: 0.9307 (mp) REVERT: E 867 ASP cc_start: 0.8525 (m-30) cc_final: 0.7877 (t0) REVERT: E 1054 GLN cc_start: 0.7255 (tp40) cc_final: 0.6907 (tp-100) REVERT: E 1062 PHE cc_start: 0.8652 (m-80) cc_final: 0.8325 (m-10) REVERT: F 185 ASN cc_start: 0.9262 (m-40) cc_final: 0.8836 (t0) REVERT: F 265 TYR cc_start: 0.8394 (p90) cc_final: 0.7879 (p90) REVERT: F 287 ASP cc_start: 0.8925 (t0) cc_final: 0.8666 (t0) REVERT: F 867 ASP cc_start: 0.8828 (m-30) cc_final: 0.8057 (t70) REVERT: F 900 MET cc_start: 0.8911 (tpp) cc_final: 0.8646 (tpt) REVERT: F 936 ASP cc_start: 0.8819 (m-30) cc_final: 0.8229 (t70) REVERT: F 1028 LYS cc_start: 0.8883 (mttt) cc_final: 0.8164 (tppp) outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.4973 time to fit residues: 391.7074 Evaluate side-chains 327 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 6.9990 chunk 364 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 477 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 547 optimal weight: 5.9990 chunk 443 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 327 optimal weight: 0.8980 chunk 576 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1054 GLN ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 55834 Z= 0.235 Angle : 0.617 8.056 76006 Z= 0.321 Chirality : 0.046 0.300 9112 Planarity : 0.004 0.068 9620 Dihedral : 6.143 45.117 10982 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 6642 helix: 1.66 (0.14), residues: 1398 sheet: 0.32 (0.14), residues: 1262 loop : -0.60 (0.09), residues: 3982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 886 HIS 0.006 0.001 HIS E1048 PHE 0.021 0.002 PHE A 898 TYR 0.023 0.002 TYR A 37 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.509 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.9012 (p) cc_final: 0.8466 (t) REVERT: A 544 ASN cc_start: 0.9051 (m-40) cc_final: 0.8764 (m-40) REVERT: A 582 LEU cc_start: 0.9009 (mt) cc_final: 0.8428 (tt) REVERT: A 806 LEU cc_start: 0.8147 (mt) cc_final: 0.7736 (pp) REVERT: A 819 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8670 (mp0) REVERT: A 869 MET cc_start: 0.9281 (mtp) cc_final: 0.9066 (mtt) REVERT: A 900 MET cc_start: 0.9181 (mmt) cc_final: 0.8635 (mmt) REVERT: A 975 SER cc_start: 0.9363 (p) cc_final: 0.8994 (m) REVERT: A 1037 SER cc_start: 0.8754 (t) cc_final: 0.8511 (m) REVERT: A 1038 LYS cc_start: 0.9314 (mptt) cc_final: 0.8740 (tptt) REVERT: A 1054 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8508 (mm-40) REVERT: B 53 ASP cc_start: 0.8690 (m-30) cc_final: 0.7953 (m-30) REVERT: B 177 MET cc_start: 0.7459 (mtt) cc_final: 0.5979 (mtt) REVERT: B 187 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8553 (mmmt) REVERT: B 300 LYS cc_start: 0.9144 (mttt) cc_final: 0.8564 (mmtm) REVERT: B 737 ASP cc_start: 0.8979 (t0) cc_final: 0.8418 (t0) REVERT: B 790 LYS cc_start: 0.8942 (mptt) cc_final: 0.8713 (mmtm) REVERT: B 805 ILE cc_start: 0.9525 (tp) cc_final: 0.9290 (mp) REVERT: B 819 GLU cc_start: 0.8162 (tt0) cc_final: 0.7581 (tt0) REVERT: B 867 ASP cc_start: 0.8548 (m-30) cc_final: 0.7914 (t0) REVERT: B 1062 PHE cc_start: 0.8628 (m-80) cc_final: 0.8349 (m-10) REVERT: C 185 ASN cc_start: 0.9338 (m-40) cc_final: 0.8783 (t0) REVERT: C 265 TYR cc_start: 0.8415 (p90) cc_final: 0.7841 (p90) REVERT: C 287 ASP cc_start: 0.8961 (t0) cc_final: 0.8708 (t0) REVERT: C 589 PRO cc_start: 0.8034 (Cg_exo) cc_final: 0.7799 (Cg_endo) REVERT: C 867 ASP cc_start: 0.8836 (m-30) cc_final: 0.8447 (p0) REVERT: C 900 MET cc_start: 0.8961 (tpp) cc_final: 0.8687 (tpt) REVERT: C 936 ASP cc_start: 0.8727 (m-30) cc_final: 0.8137 (t70) REVERT: C 1028 LYS cc_start: 0.8915 (mttt) cc_final: 0.8205 (tppt) REVERT: D 523 THR cc_start: 0.9013 (p) cc_final: 0.8469 (t) REVERT: D 544 ASN cc_start: 0.9037 (m-40) cc_final: 0.8753 (m-40) REVERT: D 582 LEU cc_start: 0.9008 (mt) cc_final: 0.8427 (tt) REVERT: D 806 LEU cc_start: 0.8150 (mt) cc_final: 0.7738 (pp) REVERT: D 819 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8668 (mp0) REVERT: D 869 MET cc_start: 0.9281 (mtp) cc_final: 0.9061 (mtt) REVERT: D 900 MET cc_start: 0.9180 (mmt) cc_final: 0.8632 (mmt) REVERT: D 975 SER cc_start: 0.9361 (p) cc_final: 0.8995 (m) REVERT: D 1037 SER cc_start: 0.8749 (t) cc_final: 0.8505 (m) REVERT: D 1038 LYS cc_start: 0.9315 (mptt) cc_final: 0.8740 (tptt) REVERT: D 1054 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8508 (mm-40) REVERT: E 53 ASP cc_start: 0.8685 (m-30) cc_final: 0.7947 (m-30) REVERT: E 177 MET cc_start: 0.7458 (mtt) cc_final: 0.5973 (mtt) REVERT: E 187 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8555 (mmmt) REVERT: E 300 LYS cc_start: 0.9143 (mttt) cc_final: 0.8562 (mmtm) REVERT: E 737 ASP cc_start: 0.8977 (t0) cc_final: 0.8414 (t0) REVERT: E 790 LYS cc_start: 0.8940 (mptt) cc_final: 0.8710 (mmtm) REVERT: E 805 ILE cc_start: 0.9524 (tp) cc_final: 0.9290 (mp) REVERT: E 819 GLU cc_start: 0.8162 (tt0) cc_final: 0.7580 (tt0) REVERT: E 867 ASP cc_start: 0.8550 (m-30) cc_final: 0.7911 (t0) REVERT: E 1062 PHE cc_start: 0.8635 (m-80) cc_final: 0.8339 (m-10) REVERT: F 185 ASN cc_start: 0.9333 (m-40) cc_final: 0.8780 (t0) REVERT: F 265 TYR cc_start: 0.8413 (p90) cc_final: 0.7840 (p90) REVERT: F 287 ASP cc_start: 0.8951 (t0) cc_final: 0.8694 (t0) REVERT: F 589 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7791 (Cg_endo) REVERT: F 867 ASP cc_start: 0.8850 (m-30) cc_final: 0.8454 (p0) REVERT: F 936 ASP cc_start: 0.8777 (m-30) cc_final: 0.8182 (t70) REVERT: F 1028 LYS cc_start: 0.8905 (mttt) cc_final: 0.8189 (tppt) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.5247 time to fit residues: 366.9249 Evaluate side-chains 282 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 5.9990 chunk 577 optimal weight: 0.0570 chunk 126 optimal weight: 10.0000 chunk 376 optimal weight: 0.5980 chunk 158 optimal weight: 20.0000 chunk 642 optimal weight: 9.9990 chunk 533 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 337 optimal weight: 1.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1010 GLN F1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 55834 Z= 0.231 Angle : 0.610 10.168 76006 Z= 0.318 Chirality : 0.046 0.276 9112 Planarity : 0.004 0.066 9620 Dihedral : 6.152 46.060 10982 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 6642 helix: 1.67 (0.14), residues: 1400 sheet: 0.36 (0.14), residues: 1258 loop : -0.63 (0.09), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 64 HIS 0.005 0.001 HIS E1048 PHE 0.018 0.002 PHE A 898 TYR 0.020 0.002 TYR A 37 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 4.541 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.9016 (p) cc_final: 0.8473 (t) REVERT: A 544 ASN cc_start: 0.9060 (m-40) cc_final: 0.8740 (m-40) REVERT: A 582 LEU cc_start: 0.8978 (mt) cc_final: 0.8316 (tt) REVERT: A 806 LEU cc_start: 0.8111 (mt) cc_final: 0.7658 (pp) REVERT: A 819 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8781 (mp0) REVERT: A 869 MET cc_start: 0.9234 (mtp) cc_final: 0.9019 (mtt) REVERT: A 900 MET cc_start: 0.9119 (mmt) cc_final: 0.8665 (mmt) REVERT: A 975 SER cc_start: 0.9356 (p) cc_final: 0.9012 (m) REVERT: A 1038 LYS cc_start: 0.9302 (mptt) cc_final: 0.8934 (tptt) REVERT: B 53 ASP cc_start: 0.8568 (m-30) cc_final: 0.7953 (m-30) REVERT: B 177 MET cc_start: 0.7307 (mtt) cc_final: 0.6406 (mtp) REVERT: B 187 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8617 (mmmt) REVERT: B 300 LYS cc_start: 0.9152 (mttt) cc_final: 0.8581 (mmtm) REVERT: B 737 ASP cc_start: 0.8995 (t0) cc_final: 0.8089 (m-30) REVERT: B 759 PHE cc_start: 0.8227 (t80) cc_final: 0.7997 (t80) REVERT: B 790 LYS cc_start: 0.8967 (mptt) cc_final: 0.8731 (mmtm) REVERT: B 805 ILE cc_start: 0.9518 (tp) cc_final: 0.9291 (mp) REVERT: B 867 ASP cc_start: 0.8543 (m-30) cc_final: 0.7907 (t0) REVERT: B 1054 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6680 (tp-100) REVERT: B 1062 PHE cc_start: 0.8658 (m-80) cc_final: 0.8401 (m-10) REVERT: C 185 ASN cc_start: 0.9335 (m-40) cc_final: 0.9106 (t0) REVERT: C 233 ILE cc_start: 0.9286 (pt) cc_final: 0.8701 (pt) REVERT: C 265 TYR cc_start: 0.8272 (p90) cc_final: 0.7820 (p90) REVERT: C 867 ASP cc_start: 0.8814 (m-30) cc_final: 0.8425 (p0) REVERT: C 900 MET cc_start: 0.8950 (tpp) cc_final: 0.8627 (tpt) REVERT: C 936 ASP cc_start: 0.8752 (m-30) cc_final: 0.8116 (t70) REVERT: C 948 LEU cc_start: 0.9199 (mp) cc_final: 0.8804 (mm) REVERT: C 1028 LYS cc_start: 0.8852 (mttt) cc_final: 0.8073 (tppt) REVERT: D 523 THR cc_start: 0.9016 (p) cc_final: 0.8473 (t) REVERT: D 544 ASN cc_start: 0.9049 (m-40) cc_final: 0.8729 (m-40) REVERT: D 582 LEU cc_start: 0.8979 (mt) cc_final: 0.8319 (tt) REVERT: D 806 LEU cc_start: 0.8112 (mt) cc_final: 0.7657 (pp) REVERT: D 819 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8780 (mp0) REVERT: D 869 MET cc_start: 0.9233 (mtp) cc_final: 0.9012 (mtt) REVERT: D 900 MET cc_start: 0.9117 (mmt) cc_final: 0.8661 (mmt) REVERT: D 975 SER cc_start: 0.9354 (p) cc_final: 0.9013 (m) REVERT: D 1038 LYS cc_start: 0.9297 (mptt) cc_final: 0.8932 (tptt) REVERT: E 53 ASP cc_start: 0.8562 (m-30) cc_final: 0.7950 (m-30) REVERT: E 177 MET cc_start: 0.7310 (mtt) cc_final: 0.6404 (mtp) REVERT: E 187 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8614 (mmmt) REVERT: E 300 LYS cc_start: 0.9152 (mttt) cc_final: 0.8578 (mmtm) REVERT: E 737 ASP cc_start: 0.8996 (t0) cc_final: 0.8084 (m-30) REVERT: E 759 PHE cc_start: 0.8228 (t80) cc_final: 0.7998 (t80) REVERT: E 790 LYS cc_start: 0.8966 (mptt) cc_final: 0.8730 (mmtm) REVERT: E 805 ILE cc_start: 0.9518 (tp) cc_final: 0.9292 (mp) REVERT: E 867 ASP cc_start: 0.8544 (m-30) cc_final: 0.7902 (t0) REVERT: E 1054 GLN cc_start: 0.7005 (tp-100) cc_final: 0.6683 (tp-100) REVERT: E 1062 PHE cc_start: 0.8659 (m-80) cc_final: 0.8389 (m-10) REVERT: F 185 ASN cc_start: 0.9330 (m-40) cc_final: 0.9104 (t0) REVERT: F 233 ILE cc_start: 0.9282 (pt) cc_final: 0.8697 (pt) REVERT: F 265 TYR cc_start: 0.8269 (p90) cc_final: 0.7815 (p90) REVERT: F 287 ASP cc_start: 0.8858 (t0) cc_final: 0.8652 (t0) REVERT: F 867 ASP cc_start: 0.8830 (m-30) cc_final: 0.8426 (p0) REVERT: F 936 ASP cc_start: 0.8798 (m-30) cc_final: 0.8221 (t70) REVERT: F 948 LEU cc_start: 0.9200 (mp) cc_final: 0.8809 (mm) REVERT: F 1028 LYS cc_start: 0.8886 (mttt) cc_final: 0.8147 (tppt) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.4822 time to fit residues: 343.0727 Evaluate side-chains 285 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 366 optimal weight: 0.0170 chunk 469 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 chunk 540 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 639 optimal weight: 9.9990 chunk 400 optimal weight: 5.9990 chunk 390 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 55834 Z= 0.302 Angle : 0.666 10.287 76006 Z= 0.343 Chirality : 0.047 0.291 9112 Planarity : 0.004 0.065 9620 Dihedral : 6.420 46.329 10982 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 6642 helix: 1.49 (0.14), residues: 1406 sheet: 0.22 (0.14), residues: 1288 loop : -0.76 (0.09), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 64 HIS 0.006 0.001 HIS B1048 PHE 0.018 0.002 PHE D 898 TYR 0.042 0.002 TYR A 37 ARG 0.014 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 4.475 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: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9323 (mt) cc_final: 0.9094 (tt) REVERT: A 465 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 523 THR cc_start: 0.9026 (p) cc_final: 0.8493 (t) REVERT: A 544 ASN cc_start: 0.9061 (m-40) cc_final: 0.8798 (m-40) REVERT: A 582 LEU cc_start: 0.9005 (mt) cc_final: 0.8299 (tt) REVERT: A 819 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8560 (mp0) REVERT: A 869 MET cc_start: 0.9242 (mtp) cc_final: 0.8813 (mtt) REVERT: A 872 GLN cc_start: 0.8400 (mt0) cc_final: 0.7388 (mm-40) REVERT: A 900 MET cc_start: 0.9126 (mmt) cc_final: 0.8674 (mmt) REVERT: A 975 SER cc_start: 0.9391 (p) cc_final: 0.9125 (m) REVERT: A 1038 LYS cc_start: 0.9288 (mptt) cc_final: 0.9027 (tptp) REVERT: A 1054 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8490 (mm-40) REVERT: B 177 MET cc_start: 0.7501 (mtt) cc_final: 0.6176 (mtt) REVERT: B 187 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8640 (mmmt) REVERT: B 300 LYS cc_start: 0.9173 (mttt) cc_final: 0.8625 (mmtm) REVERT: B 790 LYS cc_start: 0.9037 (mptt) cc_final: 0.8779 (mmtm) REVERT: B 867 ASP cc_start: 0.8633 (m-30) cc_final: 0.7941 (t0) REVERT: B 1054 GLN cc_start: 0.7035 (tp-100) cc_final: 0.6732 (tp-100) REVERT: C 185 ASN cc_start: 0.9433 (m-40) cc_final: 0.9134 (m-40) REVERT: C 867 ASP cc_start: 0.8823 (m-30) cc_final: 0.8375 (p0) REVERT: C 900 MET cc_start: 0.8992 (tpp) cc_final: 0.8720 (tpp) REVERT: C 936 ASP cc_start: 0.8802 (m-30) cc_final: 0.8162 (t70) REVERT: C 948 LEU cc_start: 0.9311 (mp) cc_final: 0.9000 (mm) REVERT: C 1028 LYS cc_start: 0.8833 (mttt) cc_final: 0.8075 (tppt) REVERT: D 434 ILE cc_start: 0.9328 (mt) cc_final: 0.9095 (tt) REVERT: D 523 THR cc_start: 0.9025 (p) cc_final: 0.8496 (t) REVERT: D 544 ASN cc_start: 0.9054 (m-40) cc_final: 0.8793 (m-40) REVERT: D 582 LEU cc_start: 0.9005 (mt) cc_final: 0.8301 (tt) REVERT: D 819 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8566 (mp0) REVERT: D 869 MET cc_start: 0.9244 (mtp) cc_final: 0.8808 (mtt) REVERT: D 872 GLN cc_start: 0.8395 (mt0) cc_final: 0.7379 (mm-40) REVERT: D 900 MET cc_start: 0.9124 (mmt) cc_final: 0.8670 (mmt) REVERT: D 975 SER cc_start: 0.9389 (p) cc_final: 0.9115 (m) REVERT: D 1038 LYS cc_start: 0.9262 (mptt) cc_final: 0.9024 (tptp) REVERT: D 1054 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8490 (mm-40) REVERT: E 177 MET cc_start: 0.7502 (mtt) cc_final: 0.6170 (mtt) REVERT: E 187 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8641 (mmmt) REVERT: E 300 LYS cc_start: 0.9174 (mttt) cc_final: 0.8624 (mmtm) REVERT: E 790 LYS cc_start: 0.9035 (mptt) cc_final: 0.8779 (mmtm) REVERT: E 867 ASP cc_start: 0.8635 (m-30) cc_final: 0.7934 (t0) REVERT: E 1054 GLN cc_start: 0.7033 (tp-100) cc_final: 0.6732 (tp-100) REVERT: F 185 ASN cc_start: 0.9428 (m-40) cc_final: 0.9132 (m-40) REVERT: F 233 ILE cc_start: 0.9279 (pt) cc_final: 0.8856 (pt) REVERT: F 867 ASP cc_start: 0.8831 (m-30) cc_final: 0.8375 (p0) REVERT: F 936 ASP cc_start: 0.8826 (m-30) cc_final: 0.8191 (t70) REVERT: F 948 LEU cc_start: 0.9313 (mp) cc_final: 0.8979 (mm) REVERT: F 1028 LYS cc_start: 0.8935 (mttt) cc_final: 0.8165 (tppt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.4827 time to fit residues: 321.6965 Evaluate side-chains 276 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 382 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 406 optimal weight: 8.9990 chunk 436 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 503 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55834 Z= 0.164 Angle : 0.574 8.430 76006 Z= 0.299 Chirality : 0.045 0.270 9112 Planarity : 0.004 0.065 9620 Dihedral : 5.954 44.925 10982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 6642 helix: 1.72 (0.14), residues: 1400 sheet: 0.35 (0.15), residues: 1260 loop : -0.62 (0.09), residues: 3982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 64 HIS 0.005 0.001 HIS C 69 PHE 0.027 0.001 PHE C 888 TYR 0.027 0.001 TYR C 266 ARG 0.018 0.000 ARG D1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 6.268 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: A 434 ILE cc_start: 0.9316 (mt) cc_final: 0.9036 (tt) REVERT: A 523 THR cc_start: 0.8962 (p) cc_final: 0.8410 (t) REVERT: A 544 ASN cc_start: 0.9029 (m-40) cc_final: 0.8761 (m-40) REVERT: A 740 MET cc_start: 0.9108 (tpp) cc_final: 0.8901 (ttt) REVERT: A 819 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8521 (mp0) REVERT: A 869 MET cc_start: 0.9201 (mtp) cc_final: 0.8793 (mtt) REVERT: A 872 GLN cc_start: 0.8294 (mt0) cc_final: 0.7489 (mm-40) REVERT: A 900 MET cc_start: 0.9033 (mmt) cc_final: 0.8563 (mmt) REVERT: A 975 SER cc_start: 0.9367 (p) cc_final: 0.9145 (m) REVERT: A 1038 LYS cc_start: 0.9278 (mptt) cc_final: 0.9003 (tptt) REVERT: A 1054 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8476 (mm-40) REVERT: B 177 MET cc_start: 0.7510 (mtt) cc_final: 0.6182 (mtt) REVERT: B 187 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8664 (mmmt) REVERT: B 300 LYS cc_start: 0.9141 (mttt) cc_final: 0.8609 (mmtt) REVERT: B 697 MET cc_start: 0.8186 (mpp) cc_final: 0.7672 (mpp) REVERT: B 790 LYS cc_start: 0.9023 (mptt) cc_final: 0.8806 (mmtm) REVERT: B 867 ASP cc_start: 0.8639 (m-30) cc_final: 0.7947 (t0) REVERT: B 1054 GLN cc_start: 0.7125 (tp-100) cc_final: 0.6726 (tp-100) REVERT: C 185 ASN cc_start: 0.9406 (m-40) cc_final: 0.9106 (t0) REVERT: C 233 ILE cc_start: 0.9270 (pt) cc_final: 0.8865 (pt) REVERT: C 867 ASP cc_start: 0.8830 (m-30) cc_final: 0.8386 (p0) REVERT: C 900 MET cc_start: 0.8915 (tpp) cc_final: 0.8671 (tpp) REVERT: C 936 ASP cc_start: 0.8751 (m-30) cc_final: 0.8308 (t70) REVERT: C 1000 ARG cc_start: 0.9040 (mtt180) cc_final: 0.8773 (mtt180) REVERT: C 1028 LYS cc_start: 0.8705 (mttt) cc_final: 0.7945 (tppt) REVERT: C 1034 LEU cc_start: 0.8796 (mp) cc_final: 0.8475 (mp) REVERT: D 434 ILE cc_start: 0.9321 (mt) cc_final: 0.9044 (tt) REVERT: D 523 THR cc_start: 0.8961 (p) cc_final: 0.8413 (t) REVERT: D 544 ASN cc_start: 0.9028 (m-40) cc_final: 0.8760 (m-40) REVERT: D 740 MET cc_start: 0.9084 (tpp) cc_final: 0.8878 (ttt) REVERT: D 819 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8519 (mp0) REVERT: D 869 MET cc_start: 0.9202 (mtp) cc_final: 0.8789 (mtt) REVERT: D 872 GLN cc_start: 0.8289 (mt0) cc_final: 0.7483 (mm-40) REVERT: D 900 MET cc_start: 0.9029 (mmt) cc_final: 0.8559 (mmt) REVERT: D 975 SER cc_start: 0.9366 (p) cc_final: 0.9148 (m) REVERT: D 1038 LYS cc_start: 0.9273 (mptt) cc_final: 0.8995 (tptt) REVERT: D 1054 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8473 (mm-40) REVERT: E 177 MET cc_start: 0.7507 (mtt) cc_final: 0.6169 (mtt) REVERT: E 187 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8664 (mmmt) REVERT: E 300 LYS cc_start: 0.9139 (mttt) cc_final: 0.8608 (mmtt) REVERT: E 697 MET cc_start: 0.8191 (mpp) cc_final: 0.7677 (mpp) REVERT: E 790 LYS cc_start: 0.9022 (mptt) cc_final: 0.8804 (mmtm) REVERT: E 867 ASP cc_start: 0.8638 (m-30) cc_final: 0.7943 (t0) REVERT: E 1054 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6732 (tp-100) REVERT: F 185 ASN cc_start: 0.9398 (m-40) cc_final: 0.9106 (t0) REVERT: F 867 ASP cc_start: 0.8806 (m-30) cc_final: 0.8357 (p0) REVERT: F 900 MET cc_start: 0.8767 (tpp) cc_final: 0.8499 (tpp) REVERT: F 936 ASP cc_start: 0.8758 (m-30) cc_final: 0.8310 (t70) REVERT: F 1000 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8770 (mtt180) REVERT: F 1028 LYS cc_start: 0.8835 (mttt) cc_final: 0.8044 (tppt) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.4942 time to fit residues: 360.2755 Evaluate side-chains 285 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 0.8980 chunk 613 optimal weight: 6.9990 chunk 559 optimal weight: 9.9990 chunk 596 optimal weight: 0.0870 chunk 612 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 468 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 538 optimal weight: 3.9990 chunk 564 optimal weight: 8.9990 overall best weight: 2.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 55834 Z= 0.204 Angle : 0.586 8.587 76006 Z= 0.304 Chirality : 0.046 0.267 9112 Planarity : 0.004 0.064 9620 Dihedral : 5.905 44.916 10982 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6642 helix: 1.71 (0.14), residues: 1408 sheet: 0.28 (0.14), residues: 1306 loop : -0.64 (0.10), residues: 3928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 64 HIS 0.004 0.001 HIS E1048 PHE 0.018 0.001 PHE B 718 TYR 0.039 0.001 TYR C 904 ARG 0.012 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 4.517 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.8986 (p) cc_final: 0.8451 (t) REVERT: A 544 ASN cc_start: 0.9034 (m-40) cc_final: 0.8747 (m-40) REVERT: A 819 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8855 (mp0) REVERT: A 900 MET cc_start: 0.9050 (mmt) cc_final: 0.8591 (mmt) REVERT: A 975 SER cc_start: 0.9374 (p) cc_final: 0.9007 (m) REVERT: A 1038 LYS cc_start: 0.9257 (mptt) cc_final: 0.8988 (tptt) REVERT: B 177 MET cc_start: 0.7721 (mtt) cc_final: 0.6709 (mtp) REVERT: B 187 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8633 (mmmt) REVERT: B 300 LYS cc_start: 0.9150 (mttt) cc_final: 0.8596 (mmtm) REVERT: B 697 MET cc_start: 0.8195 (mpp) cc_final: 0.7553 (mpp) REVERT: B 759 PHE cc_start: 0.8157 (t80) cc_final: 0.7930 (t80) REVERT: B 790 LYS cc_start: 0.9019 (mptt) cc_final: 0.8813 (mmtm) REVERT: B 867 ASP cc_start: 0.8637 (m-30) cc_final: 0.7975 (t0) REVERT: B 1054 GLN cc_start: 0.6992 (tp-100) cc_final: 0.6685 (tp-100) REVERT: C 185 ASN cc_start: 0.9417 (m-40) cc_final: 0.9114 (t0) REVERT: C 731 MET cc_start: 0.8259 (mtm) cc_final: 0.8035 (mtt) REVERT: C 867 ASP cc_start: 0.8844 (m-30) cc_final: 0.8395 (p0) REVERT: C 936 ASP cc_start: 0.8761 (m-30) cc_final: 0.8328 (t70) REVERT: C 1028 LYS cc_start: 0.8679 (mttt) cc_final: 0.7880 (tppt) REVERT: D 523 THR cc_start: 0.8986 (p) cc_final: 0.8451 (t) REVERT: D 544 ASN cc_start: 0.9034 (m-40) cc_final: 0.8746 (m-40) REVERT: D 819 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8864 (mp0) REVERT: D 900 MET cc_start: 0.9047 (mmt) cc_final: 0.8585 (mmt) REVERT: D 975 SER cc_start: 0.9376 (p) cc_final: 0.9004 (m) REVERT: D 1038 LYS cc_start: 0.9256 (mptt) cc_final: 0.9010 (tptt) REVERT: E 177 MET cc_start: 0.7718 (mtt) cc_final: 0.6700 (mtp) REVERT: E 187 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8633 (mmmt) REVERT: E 300 LYS cc_start: 0.9150 (mttt) cc_final: 0.8595 (mmtm) REVERT: E 697 MET cc_start: 0.8198 (mpp) cc_final: 0.7557 (mpp) REVERT: E 759 PHE cc_start: 0.8163 (t80) cc_final: 0.7937 (t80) REVERT: E 790 LYS cc_start: 0.9015 (mptt) cc_final: 0.8810 (mmtm) REVERT: E 867 ASP cc_start: 0.8639 (m-30) cc_final: 0.7971 (t0) REVERT: E 1054 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6682 (tp-100) REVERT: F 185 ASN cc_start: 0.9408 (m-40) cc_final: 0.9114 (t0) REVERT: F 731 MET cc_start: 0.8257 (mtm) cc_final: 0.8033 (mtt) REVERT: F 867 ASP cc_start: 0.8849 (m-30) cc_final: 0.8393 (p0) REVERT: F 900 MET cc_start: 0.8766 (tpp) cc_final: 0.8483 (tpp) REVERT: F 936 ASP cc_start: 0.8770 (m-30) cc_final: 0.8331 (t70) REVERT: F 1028 LYS cc_start: 0.8847 (mttt) cc_final: 0.8040 (tppt) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.4748 time to fit residues: 315.4218 Evaluate side-chains 267 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 7.9990 chunk 391 optimal weight: 6.9990 chunk 630 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 438 optimal weight: 0.0770 chunk 661 optimal weight: 4.9990 chunk 608 optimal weight: 10.0000 chunk 526 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 406 optimal weight: 1.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 55834 Z= 0.221 Angle : 0.594 8.877 76006 Z= 0.307 Chirality : 0.046 0.259 9112 Planarity : 0.004 0.063 9620 Dihedral : 5.955 43.357 10982 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 6642 helix: 1.70 (0.14), residues: 1410 sheet: 0.25 (0.14), residues: 1300 loop : -0.69 (0.10), residues: 3932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.005 0.001 HIS E1048 PHE 0.019 0.002 PHE E 888 TYR 0.026 0.002 TYR C 266 ARG 0.004 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 4.489 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9331 (mt) cc_final: 0.9108 (tt) REVERT: A 523 THR cc_start: 0.9042 (p) cc_final: 0.8491 (t) REVERT: A 819 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8839 (mp0) REVERT: A 900 MET cc_start: 0.9074 (mmt) cc_final: 0.8630 (mmt) REVERT: A 975 SER cc_start: 0.9436 (p) cc_final: 0.9047 (m) REVERT: A 1038 LYS cc_start: 0.9258 (mptt) cc_final: 0.9000 (tptt) REVERT: B 177 MET cc_start: 0.7642 (mtt) cc_final: 0.6596 (mtp) REVERT: B 187 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8664 (mmmt) REVERT: B 300 LYS cc_start: 0.9150 (mttt) cc_final: 0.8592 (mmtm) REVERT: B 718 PHE cc_start: 0.9052 (p90) cc_final: 0.8776 (p90) REVERT: B 759 PHE cc_start: 0.8170 (t80) cc_final: 0.7948 (t80) REVERT: B 790 LYS cc_start: 0.9082 (mptt) cc_final: 0.8871 (mmtm) REVERT: B 867 ASP cc_start: 0.8675 (m-30) cc_final: 0.8001 (t0) REVERT: B 902 MET cc_start: 0.8858 (mmp) cc_final: 0.8656 (mmp) REVERT: B 1054 GLN cc_start: 0.7054 (tp-100) cc_final: 0.6715 (tp-100) REVERT: C 185 ASN cc_start: 0.9434 (m-40) cc_final: 0.9004 (p0) REVERT: C 867 ASP cc_start: 0.8855 (m-30) cc_final: 0.8378 (p0) REVERT: C 936 ASP cc_start: 0.8774 (m-30) cc_final: 0.8325 (t70) REVERT: D 523 THR cc_start: 0.9043 (p) cc_final: 0.8493 (t) REVERT: D 819 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8847 (mp0) REVERT: D 869 MET cc_start: 0.9185 (mtp) cc_final: 0.8980 (mtt) REVERT: D 900 MET cc_start: 0.9070 (mmt) cc_final: 0.8626 (mmt) REVERT: D 975 SER cc_start: 0.9437 (p) cc_final: 0.9051 (m) REVERT: D 1038 LYS cc_start: 0.9258 (mptt) cc_final: 0.9001 (tptt) REVERT: E 177 MET cc_start: 0.7637 (mtt) cc_final: 0.6588 (mtp) REVERT: E 187 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8664 (mmmt) REVERT: E 300 LYS cc_start: 0.9148 (mttt) cc_final: 0.8587 (mmtm) REVERT: E 718 PHE cc_start: 0.9055 (p90) cc_final: 0.8782 (p90) REVERT: E 759 PHE cc_start: 0.8177 (t80) cc_final: 0.7953 (t80) REVERT: E 790 LYS cc_start: 0.9076 (mptt) cc_final: 0.8867 (mmtm) REVERT: E 867 ASP cc_start: 0.8676 (m-30) cc_final: 0.7992 (t0) REVERT: E 902 MET cc_start: 0.8862 (mmp) cc_final: 0.8657 (mmp) REVERT: E 1054 GLN cc_start: 0.7054 (tp-100) cc_final: 0.6714 (tp-100) REVERT: F 185 ASN cc_start: 0.9430 (m-40) cc_final: 0.9001 (p0) REVERT: F 867 ASP cc_start: 0.8859 (m-30) cc_final: 0.8377 (p0) REVERT: F 900 MET cc_start: 0.8815 (tpp) cc_final: 0.8481 (tpp) REVERT: F 904 TYR cc_start: 0.8319 (m-80) cc_final: 0.8054 (m-80) REVERT: F 936 ASP cc_start: 0.8720 (m-30) cc_final: 0.8289 (t70) REVERT: F 1028 LYS cc_start: 0.8850 (mttt) cc_final: 0.8053 (tppt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.4694 time to fit residues: 301.6775 Evaluate side-chains 275 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 9.9990 chunk 418 optimal weight: 7.9990 chunk 561 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 485 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 527 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 541 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 957 GLN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 ASN ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.052117 restraints weight = 256225.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053460 restraints weight = 150645.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054392 restraints weight = 101332.954| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 55834 Z= 0.218 Angle : 0.588 8.978 76006 Z= 0.305 Chirality : 0.046 0.257 9112 Planarity : 0.004 0.063 9620 Dihedral : 5.948 43.968 10982 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.03 % Allowed : 0.14 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 6642 helix: 1.72 (0.14), residues: 1410 sheet: 0.21 (0.14), residues: 1292 loop : -0.67 (0.10), residues: 3940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 64 HIS 0.015 0.001 HIS F 69 PHE 0.024 0.001 PHE B 888 TYR 0.022 0.002 TYR A 37 ARG 0.004 0.000 ARG F 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8727.98 seconds wall clock time: 154 minutes 29.47 seconds (9269.47 seconds total)