Starting phenix.real_space_refine (version: dev) on Thu Dec 22 19:46:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7j_31773/12_2022/7v7j_31773.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.054 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51072 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "E" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "F" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 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 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 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 chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "IA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 27.59, per 1000 atoms: 0.54 Number of scatterers: 51072 At special positions: 0 Unit cell: (171.6, 155.1, 326.7, 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 222 16.00 O 10134 8.00 N 8274 7.00 C 32442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=74, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 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 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 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 E1032 " - pdb=" SG CYS E1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 6 2 " - " BMA 6 3 " " 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 K 2 " - " BMA K 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG 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 i 2 " - " BMA i 3 " " 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 u 2 " - " BMA u 3 " " 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 " " NAGIA 2 " - " BMAIA 3 " " 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 " NAG-ASN " NAG 0 1 " - " ASN D1098 " " NAG 1 1 " - " ASN D1134 " " NAG 2 1 " - " ASN E 122 " " NAG 3 1 " - " ASN E 165 " " NAG 4 1 " - " ASN E 234 " " NAG 5 1 " - " ASN E 282 " " NAG 6 1 " - " ASN E 343 " " NAG 7 1 " - " ASN E 616 " " NAG 8 1 " - " ASN E 709 " " NAG 9 1 " - " ASN E 717 " " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 331 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 331 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 331 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D2001 " - " ASN D 61 " " NAG D2002 " - " ASN D 331 " " NAG D2003 " - " ASN D 603 " " NAG D2004 " - " ASN D 657 " " NAG E2001 " - " ASN E 61 " " NAG E2002 " - " ASN E 331 " " NAG E2003 " - " ASN E 603 " " NAG E2004 " - " ASN E 657 " " NAG F2001 " - " ASN F 61 " " NAG F2002 " - " ASN F 331 " " NAG F2003 " - " ASN F 603 " " NAG F2004 " - " ASN F 657 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 343 " " NAG L 1 " - " ASN A 616 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 165 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B1098 " " NAG d 1 " - " ASN B1134 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 165 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 282 " " NAG i 1 " - " ASN C 343 " " NAG j 1 " - " ASN C 616 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN D 122 " " NAG r 1 " - " ASN D 165 " " NAG s 1 " - " ASN D 234 " " NAG t 1 " - " ASN D 282 " " NAG u 1 " - " ASN D 343 " " NAG v 1 " - " ASN D 616 " " NAG w 1 " - " ASN D 709 " " NAG x 1 " - " ASN D 717 " " NAG y 1 " - " ASN D 801 " " NAG z 1 " - " ASN D1074 " " NAGAA 1 " - " ASN E 801 " " NAGBA 1 " - " ASN E1074 " " NAGCA 1 " - " ASN E1098 " " NAGDA 1 " - " ASN E1134 " " NAGEA 1 " - " ASN F 122 " " NAGFA 1 " - " ASN F 165 " " NAGGA 1 " - " ASN F 234 " " NAGHA 1 " - " ASN F 282 " " NAGIA 1 " - " ASN F 343 " " NAGJA 1 " - " ASN F 616 " " NAGKA 1 " - " ASN F 709 " " NAGLA 1 " - " ASN F 717 " " NAGMA 1 " - " ASN F 801 " " NAGNA 1 " - " ASN F1074 " " NAGOA 1 " - " ASN F1098 " " NAGPA 1 " - " ASN F1134 " Time building additional restraints: 23.31 Conformation dependent library (CDL) restraints added in 7.2 seconds 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 90 sheets defined 25.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.969A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.698A 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 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.112A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.538A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.277A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.526A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.553A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) 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 removed outlier: 3.566A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.629A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.105A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.465A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.785A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.109A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 6.715A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.653A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.851A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.640A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.142A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.759A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 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 removed outlier: 3.675A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.822A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.779A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.849A pdb=" N SER D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.057A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.584A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.757A pdb=" N ALA D 766 " --> pdb=" O GLN D 762 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.617A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.513A pdb=" N GLN D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.359A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 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 removed outlier: 4.027A pdb=" N LEU D 984 " --> pdb=" O ILE D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1034 removed outlier: 4.400A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D1034 " --> pdb=" O SER D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 removed outlier: 3.536A pdb=" N ASP D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.641A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.572A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.661A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.349A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 767 " --> pdb=" O LEU E 763 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 768 " --> pdb=" O ASN E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 884 removed outlier: 3.537A pdb=" N ILE E 870 " --> pdb=" O THR E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.524A pdb=" N GLN E 901 " --> pdb=" O PRO E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.390A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 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 removed outlier: 3.644A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.816A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1146 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.164A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.532A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 3.627A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 755 removed outlier: 3.905A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 removed outlier: 3.550A pdb=" N LEU F 763 " --> pdb=" O PHE F 759 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 767 " --> pdb=" O LEU F 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.500A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 912 through 941 removed outlier: 4.343A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) Processing helix chain 'F' and resid 946 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 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.985A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.881A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.913A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.149A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.378A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.161A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.588A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.094A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.278A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.807A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.592A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.355A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.090A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.818A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.253A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 575 through 576 removed outlier: 7.285A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.561A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.079A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.852A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 11.167A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 143 through 144 removed outlier: 4.979A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.529A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.269A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.810A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.482A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF1, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.727A pdb=" N PHE D 43 " --> pdb=" O ARG F 567 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY F 566 " --> pdb=" O ASP F 574 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.189A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.822A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N VAL D 126 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU D 169 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE D 128 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR D 167 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 130 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN D 165 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU D 132 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA D 163 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN D 134 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS D 136 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N VAL D 159 " --> pdb=" O CYS D 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 143 through 144 removed outlier: 5.516A pdb=" N VAL D 143 " --> pdb=" O ARG D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.486A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 325 through 328 removed outlier: 7.643A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AF9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'D' and resid 573 through 576 removed outlier: 3.693A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 654 through 660 removed outlier: 5.844A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AG5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 735 through 736 Processing sheet with id=AG7, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AG8, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 5.448A pdb=" N VAL D1122 " --> pdb=" O PHE D1089 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE D1089 " --> pdb=" O VAL D1122 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY D1124 " --> pdb=" O ALA D1087 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1094 through 1096 Processing sheet with id=AH1, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.852A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.117A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.801A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN E 165 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN E 134 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA E 163 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 325 through 326 removed outlier: 5.797A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.937A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH9, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AI1, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.213A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 701 through 703 Processing sheet with id=AI3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.498A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E1047 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AI5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 5.470A pdb=" N VAL E1122 " --> pdb=" O PHE E1089 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE E1089 " --> pdb=" O VAL E1122 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY E1124 " --> pdb=" O ALA E1087 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 1094 through 1096 Processing sheet with id=AI7, first strand: chain 'F' and resid 27 through 30 removed outlier: 8.051A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 47 through 55 removed outlier: 4.165A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.812A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE F 105 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN F 165 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN F 134 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 163 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.218A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AJ3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AJ4, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AJ5, first strand: chain 'F' and resid 654 through 659 removed outlier: 5.949A pdb=" N THR F 696 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASN F 658 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.883A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.883A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 5.293A pdb=" N VAL F1122 " --> pdb=" O PHE F1089 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE F1089 " --> pdb=" O VAL F1122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY F1124 " --> pdb=" O ALA F1087 " (cutoff:3.500A) 1981 hydrogen bonds defined for protein. 5364 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: 27.18 Time building geometry restraints manager: 25.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16052 1.34 - 1.46: 12810 1.46 - 1.58: 23050 1.58 - 1.70: 0 1.70 - 1.82: 276 Bond restraints: 52188 Sorted by residual: bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.426 1.381 0.045 3.20e-02 9.77e+02 1.94e+00 bond pdb=" C TYR D 421 " pdb=" N ASN D 422 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.89e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.426 1.465 -0.039 3.20e-02 9.77e+02 1.50e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.46e+00 bond pdb=" CG GLN F1002 " pdb=" CD GLN F1002 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.38e+00 ... (remaining 52183 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 1065 105.66 - 112.74: 28654 112.74 - 119.81: 15815 119.81 - 126.89: 25026 126.89 - 133.97: 468 Bond angle restraints: 71028 Sorted by residual: angle pdb=" C LEU F 518 " pdb=" CA LEU F 518 " pdb=" CB LEU F 518 " ideal model delta sigma weight residual 115.79 108.47 7.32 1.19e+00 7.06e-01 3.78e+01 angle pdb=" C5 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 109.25 117.42 -8.17 2.08e+00 2.31e-01 1.54e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 113.20 109.61 3.59 9.60e-01 1.09e+00 1.40e+01 angle pdb=" N GLN F1002 " pdb=" CA GLN F1002 " pdb=" CB GLN F1002 " ideal model delta sigma weight residual 110.12 115.26 -5.14 1.47e+00 4.63e-01 1.22e+01 ... (remaining 71023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 28642 21.41 - 42.82: 1798 42.82 - 64.23: 209 64.23 - 85.64: 64 85.64 - 107.05: 19 Dihedral angle restraints: 30732 sinusoidal: 12606 harmonic: 18126 Sorted by residual: dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -175.87 89.87 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS F 662 " pdb=" SG CYS F 662 " pdb=" SG CYS F 671 " pdb=" CB CYS F 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.70 88.70 1 1.00e+01 1.00e-02 9.38e+01 ... (remaining 30729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 8539 0.163 - 0.326: 28 0.326 - 0.488: 3 0.488 - 0.651: 3 0.651 - 0.814: 1 Chirality restraints: 8574 Sorted by residual: chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG D2001 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D2001 " pdb=" O5 NAG D2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" C1 NAG 3 1 " pdb=" ND2 ASN E 165 " pdb=" C2 NAG 3 1 " pdb=" O5 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.02e+00 ... (remaining 8571 not shown) Planarity restraints: 9054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B1041 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ASP B1041 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP B1041 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE B1042 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 986 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 61 " 0.019 2.00e-02 2.50e+03 1.78e-02 3.95e+00 pdb=" CG ASN E 61 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN E 61 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN E 61 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG E2001 " 0.018 2.00e-02 2.50e+03 ... (remaining 9051 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1582 2.70 - 3.25: 51295 3.25 - 3.80: 79089 3.80 - 4.35: 95455 4.35 - 4.90: 162445 Nonbonded interactions: 389866 Sorted by model distance: nonbonded pdb=" O GLU E 661 " pdb=" OH TYR E 695 " model vdw 2.144 2.440 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.151 2.440 nonbonded pdb=" OG SER E 116 " pdb=" O CYS E 131 " model vdw 2.158 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O ARG A 452 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASP D 568 " pdb=" OG1 THR D 572 " model vdw 2.161 2.440 ... (remaining 389861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'J' selection = chain 'JA' 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' 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 '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 't' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '6' selection = chain 'IA' selection = chain 'K' selection = chain 'W' selection = chain 'i' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 222 5.16 5 C 32442 2.51 5 N 8274 2.21 5 O 10134 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 17.190 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.460 Process input model: 136.650 Find NCS groups from input model: 5.070 Set up NCS constraints: 1.730 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.004 0.051 52188 Z= 0.241 Angle : 0.564 11.047 71028 Z= 0.306 Chirality : 0.046 0.814 8574 Planarity : 0.004 0.053 8958 Dihedral : 13.546 107.050 18846 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer Outliers : 0.00 % 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: -0.39 (0.11), residues: 6132 helix: 1.78 (0.15), residues: 1316 sheet: 0.54 (0.14), residues: 1382 loop : -1.50 (0.10), residues: 3434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 6.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.5703 time to fit residues: 182.9833 Evaluate side-chains 123 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 5.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 8.9990 chunk 468 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 315 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 484 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 294 optimal weight: 8.9990 chunk 360 optimal weight: 5.9990 chunk 561 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1011 GLN A1106 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 GLN E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1106 GLN F 188 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 949 GLN F 953 ASN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.089 52188 Z= 0.441 Angle : 0.632 8.769 71028 Z= 0.333 Chirality : 0.048 0.781 8574 Planarity : 0.004 0.053 8958 Dihedral : 6.203 107.783 7746 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer Outliers : 0.31 % 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: -0.69 (0.11), residues: 6132 helix: 1.32 (0.15), residues: 1342 sheet: 0.32 (0.13), residues: 1446 loop : -1.63 (0.10), residues: 3344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 140 average time/residue: 0.5678 time to fit residues: 144.6769 Evaluate side-chains 127 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 5.409 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4086 time to fit residues: 15.9051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 10.0000 chunk 174 optimal weight: 0.0030 chunk 467 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 562 optimal weight: 5.9990 chunk 607 optimal weight: 0.9980 chunk 500 optimal weight: 7.9990 chunk 557 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 451 optimal weight: 0.3980 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 474 GLN C 606 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 926 GLN ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 52188 Z= 0.163 Angle : 0.495 7.954 71028 Z= 0.263 Chirality : 0.045 0.776 8574 Planarity : 0.004 0.058 8958 Dihedral : 5.945 106.503 7746 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.94 % Rotamer Outliers : 0.50 % 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: -0.43 (0.11), residues: 6132 helix: 1.54 (0.15), residues: 1374 sheet: 0.54 (0.14), residues: 1408 loop : -1.52 (0.11), residues: 3350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 167 average time/residue: 0.5955 time to fit residues: 180.4584 Evaluate side-chains 132 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 6.080 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4533 time to fit residues: 16.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 564 optimal weight: 4.9990 chunk 597 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 534 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 52188 Z= 0.415 Angle : 0.600 8.695 71028 Z= 0.315 Chirality : 0.047 0.782 8574 Planarity : 0.004 0.056 8958 Dihedral : 6.126 107.838 7746 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.26 % Favored : 92.68 % Rotamer Outliers : 1.01 % 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 (0.11), residues: 6132 helix: 1.34 (0.15), residues: 1355 sheet: 0.16 (0.13), residues: 1476 loop : -1.60 (0.11), residues: 3301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 120 time to evaluate : 5.901 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 26 residues processed: 168 average time/residue: 0.5403 time to fit residues: 168.4549 Evaluate side-chains 142 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 6.101 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4399 time to fit residues: 30.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 3.9990 chunk 339 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 444 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 509 optimal weight: 9.9990 chunk 412 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 305 optimal weight: 0.8980 chunk 536 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 52188 Z= 0.240 Angle : 0.518 8.437 71028 Z= 0.274 Chirality : 0.045 0.772 8574 Planarity : 0.004 0.057 8958 Dihedral : 6.009 107.075 7746 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer Outliers : 0.97 % 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: -0.56 (0.11), residues: 6132 helix: 1.45 (0.15), residues: 1367 sheet: 0.33 (0.14), residues: 1432 loop : -1.54 (0.11), residues: 3333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 6.020 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 21 residues processed: 177 average time/residue: 0.5581 time to fit residues: 179.8173 Evaluate side-chains 138 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 5.631 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4192 time to fit residues: 24.4462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 6.9990 chunk 537 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 597 optimal weight: 1.9990 chunk 496 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 774 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 52188 Z= 0.175 Angle : 0.492 8.461 71028 Z= 0.260 Chirality : 0.045 0.769 8574 Planarity : 0.004 0.058 8958 Dihedral : 5.872 107.035 7746 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.62 % Rotamer Outliers : 0.90 % 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: -0.39 (0.11), residues: 6132 helix: 1.69 (0.15), residues: 1347 sheet: 0.51 (0.13), residues: 1431 loop : -1.50 (0.11), residues: 3354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 6.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 17 residues processed: 181 average time/residue: 0.5720 time to fit residues: 188.4268 Evaluate side-chains 137 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 5.822 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4338 time to fit residues: 21.8694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 436 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 503 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 595 optimal weight: 0.8980 chunk 372 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 52188 Z= 0.215 Angle : 0.508 10.952 71028 Z= 0.266 Chirality : 0.045 0.766 8574 Planarity : 0.004 0.058 8958 Dihedral : 5.872 107.344 7746 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer Outliers : 0.83 % 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: -0.42 (0.11), residues: 6132 helix: 1.65 (0.15), residues: 1354 sheet: 0.44 (0.14), residues: 1429 loop : -1.50 (0.11), residues: 3349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 6.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 161 average time/residue: 0.5510 time to fit residues: 165.0712 Evaluate side-chains 138 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 6.005 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4353 time to fit residues: 22.4090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 378 optimal weight: 0.9980 chunk 405 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 468 optimal weight: 0.2980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 52188 Z= 0.165 Angle : 0.494 8.553 71028 Z= 0.258 Chirality : 0.044 0.758 8574 Planarity : 0.004 0.059 8958 Dihedral : 5.812 107.084 7746 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.94 % Favored : 94.99 % Rotamer Outliers : 0.28 % 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: -0.32 (0.11), residues: 6132 helix: 1.75 (0.15), residues: 1342 sheet: 0.49 (0.14), residues: 1453 loop : -1.43 (0.11), residues: 3337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.5566 time to fit residues: 147.8533 Evaluate side-chains 130 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 6.066 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4653 time to fit residues: 14.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 520 optimal weight: 3.9990 chunk 555 optimal weight: 0.9980 chunk 334 optimal weight: 3.9990 chunk 241 optimal weight: 0.1980 chunk 435 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 501 optimal weight: 5.9990 chunk 524 optimal weight: 9.9990 chunk 553 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 52188 Z= 0.204 Angle : 0.504 8.990 71028 Z= 0.263 Chirality : 0.044 0.758 8574 Planarity : 0.004 0.059 8958 Dihedral : 5.820 107.335 7746 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.36 % Rotamer Outliers : 0.26 % 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: -0.39 (0.11), residues: 6132 helix: 1.72 (0.15), residues: 1342 sheet: 0.38 (0.14), residues: 1461 loop : -1.46 (0.11), residues: 3329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 6.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 136 average time/residue: 0.5581 time to fit residues: 141.0063 Evaluate side-chains 125 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 5.880 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4512 time to fit residues: 10.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 9.9990 chunk 586 optimal weight: 0.0570 chunk 358 optimal weight: 1.9990 chunk 278 optimal weight: 0.4980 chunk 408 optimal weight: 0.0670 chunk 615 optimal weight: 1.9990 chunk 566 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 378 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN F 188 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 52188 Z= 0.132 Angle : 0.489 12.826 71028 Z= 0.255 Chirality : 0.044 0.746 8574 Planarity : 0.004 0.060 8958 Dihedral : 5.722 106.868 7746 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer Outliers : 0.09 % 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: -0.26 (0.11), residues: 6132 helix: 1.80 (0.15), residues: 1340 sheet: 0.51 (0.14), residues: 1462 loop : -1.40 (0.11), residues: 3330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 8.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 143 average time/residue: 0.5848 time to fit residues: 156.5794 Evaluate side-chains 130 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 6.166 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4341 time to fit residues: 9.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 9.9990 chunk 522 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 452 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 491 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 504 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN F 188 ASN F 394 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.065772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046190 restraints weight = 218181.030| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.61 r_work: 0.2778 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 52188 Z= 0.267 Angle : 0.534 8.986 71028 Z= 0.278 Chirality : 0.045 0.754 8574 Planarity : 0.004 0.060 8958 Dihedral : 5.832 107.655 7746 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.06 % Rotamer Outliers : 0.18 % 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: -0.39 (0.11), residues: 6132 helix: 1.73 (0.15), residues: 1332 sheet: 0.36 (0.14), residues: 1454 loop : -1.44 (0.11), residues: 3346 =============================================================================== Job complete usr+sys time: 7550.75 seconds wall clock time: 140 minutes 35.87 seconds (8435.87 seconds total)