Starting phenix.real_space_refine on Mon Mar 25 20:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7i_31772/03_2024/7v7i_31772.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. Process input model Symmetric amino acids flipped Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 950": "OD1" <-> "OD2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "F PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "IA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "KA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "LA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "MA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "NA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "OA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "PA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 26.00, per 1000 atoms: 0.51 Number of scatterers: 51072 At special positions: 0 Unit cell: (169.4, 155.1, 324.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 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=76, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " 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=2.03 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=2.03 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=2.03 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=2.04 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 291 " - pdb=" SG CYS F 301 " 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=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 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 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: 21.34 Conformation dependent library (CDL) restraints added in 9.0 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: 127 helices and 89 sheets defined 25.2% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 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 390 removed outlier: 3.504A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.695A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.232A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 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: 6.813A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.876A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.731A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.775A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.816A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) 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 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.685A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.633A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.146A 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 737 through 743 removed outlier: 3.525A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.243A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.253A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.508A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.558A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.702A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.745A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 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 343 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: 4.822A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.676A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.002A 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 438 through 443 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.944A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.223A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) 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 909 removed outlier: 3.506A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.157A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.550A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) 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: 3.771A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.507A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 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 370 Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.829A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 3.752A 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 438 through 443 removed outlier: 3.591A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 removed outlier: 4.002A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 4.330A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.631A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 912 through 941 removed outlier: 4.096A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) 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: 3.531A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1084 No H-bonds generated for 'chain 'D' and resid 1082 through 1084' Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 removed outlier: 4.207A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.733A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.861A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.810A 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 removed outlier: 3.551A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 743 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.838A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.867A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU E 767 " --> pdb=" O LEU E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.279A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 965 removed outlier: 4.319A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) 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: 3.703A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.994A pdb=" N GLU E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1146 removed outlier: 3.603A pdb=" N ASP E1146 " --> pdb=" O GLN E1142 " (cutoff:3.500A) 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 371 removed outlier: 4.490A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.621A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 3.779A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.582A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 755 removed outlier: 4.100A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.528A 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 removed outlier: 3.538A pdb=" N ILE F 909 " --> pdb=" O ARG F 905 " (cutoff:3.500A) Processing helix chain 'F' and resid 913 through 919 removed outlier: 3.575A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 945 through 966 removed outlier: 4.069A pdb=" N LEU F 966 " --> pdb=" O LEU F 962 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN F1002 " --> pdb=" O THR F 998 " (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: 7.984A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.968A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.836A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.139A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.532A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.252A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.972A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.330A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.157A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.752A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.188A 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: 4.072A 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: 3.583A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 9.091A 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: 3.592A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.751A 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 removed outlier: 5.670A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) 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: 6.737A 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 654 through 660 removed outlier: 6.120A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.860A 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: 6.640A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.560A 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: 4.656A 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 1125 removed outlier: 4.941A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.530A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.085A 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: 4.138A 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: 3.932A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 135 through 140 removed outlier: 9.920A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (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: 6.951A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.515A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.224A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.791A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.588A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE9, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.538A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.578A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG F 328 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.007A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.832A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 130 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.202A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 325 through 326 removed outlier: 5.597A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 354 through 358 removed outlier: 6.071A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 516 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.588A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.405A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.487A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.483A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 787 through 789 removed outlier: 5.875A pdb=" N ILE D 788 " --> pdb=" O ASN F 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 1086 through 1090 removed outlier: 5.157A pdb=" N GLY D1124 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE D1089 " --> pdb=" O VAL D1122 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL D1122 " --> pdb=" O PHE D1089 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 1094 through 1095 Processing sheet with id=AG7, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.434A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.798A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN E 165 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLN E 134 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA E 163 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N CYS E 136 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N SER E 161 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP E 138 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL E 159 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.092A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AH3, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH5, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AH6, first strand: chain 'E' and resid 565 through 567 removed outlier: 3.868A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.156A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 701 through 703 Processing sheet with id=AH9, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.790A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AI2, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AI3, first strand: chain 'E' and resid 1094 through 1095 Processing sheet with id=AI4, first strand: chain 'F' and resid 27 through 30 removed outlier: 8.435A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 36 through 37 removed outlier: 7.154A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'F' and resid 47 through 55 removed outlier: 4.071A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.797A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE F 105 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASN F 165 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLN F 134 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA F 163 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.215A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AJ1, first strand: chain 'F' and resid 361 through 362 removed outlier: 3.700A pdb=" N CYS F 525 " --> pdb=" O CYS F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AJ3, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AJ4, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.739A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 734 through 736 Processing sheet with id=AJ7, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 5.031A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 1094 through 1096 1997 hydrogen bonds defined for protein. 5388 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: 26.47 Time building geometry restraints manager: 23.01 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: 16069 1.34 - 1.46: 13284 1.46 - 1.59: 22559 1.59 - 1.71: 0 1.71 - 1.83: 276 Bond restraints: 52188 Sorted by residual: bond pdb=" C1 NAGFA 1 " pdb=" O5 NAGFA 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 BMAIA 3 " pdb=" C2 BMAIA 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG r 1 " pdb=" O5 NAG r 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG z 1 " pdb=" O5 NAG z 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 ... (remaining 52183 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.18: 983 105.18 - 112.39: 27813 112.39 - 119.59: 15965 119.59 - 126.79: 25769 126.79 - 134.00: 498 Bond angle restraints: 71028 Sorted by residual: angle pdb=" C GLU F 516 " pdb=" N LEU F 517 " pdb=" CA LEU F 517 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA LEU F 517 " pdb=" CB LEU F 517 " pdb=" CG LEU F 517 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.20 109.71 3.49 9.60e-01 1.09e+00 1.32e+01 angle pdb=" C VAL C 781 " pdb=" N PHE C 782 " pdb=" CA PHE C 782 " ideal model delta sigma weight residual 122.60 116.16 6.44 1.88e+00 2.83e-01 1.18e+01 angle pdb=" C VAL D 781 " pdb=" N PHE D 782 " pdb=" CA PHE D 782 " ideal model delta sigma weight residual 122.79 117.00 5.79 1.70e+00 3.46e-01 1.16e+01 ... (remaining 71023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.78: 31114 22.78 - 45.56: 1795 45.56 - 68.34: 265 68.34 - 91.12: 97 91.12 - 113.90: 41 Dihedral angle restraints: 33312 sinusoidal: 15186 harmonic: 18126 Sorted by residual: dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual -86.00 -172.43 86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.81 81.81 1 1.00e+01 1.00e-02 8.23e+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 -167.33 81.33 1 1.00e+01 1.00e-02 8.15e+01 ... (remaining 33309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 8117 0.097 - 0.195: 427 0.195 - 0.292: 21 0.292 - 0.390: 2 0.390 - 0.487: 6 Chirality restraints: 8573 Sorted by residual: chirality pdb=" C1 NAG F2001 " pdb=" ND2 ASN F 61 " pdb=" C2 NAG F2001 " pdb=" O5 NAG F2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C1 NAG C2001 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C2001 " pdb=" O5 NAG C2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG E2001 " pdb=" ND2 ASN E 61 " pdb=" C2 NAG E2001 " pdb=" O5 NAG E2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 8570 not shown) Planarity restraints: 9053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 985 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO E 986 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 986 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 986 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 986 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 897 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " -0.027 5.00e-02 4.00e+02 ... (remaining 9050 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1263 2.68 - 3.24: 50269 3.24 - 3.79: 76964 3.79 - 4.35: 95998 4.35 - 4.90: 162972 Nonbonded interactions: 387466 Sorted by model distance: nonbonded pdb=" OD1 ASP E 568 " pdb=" OG1 THR E 572 " model vdw 2.128 2.440 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.130 2.440 nonbonded pdb=" OH TYR D 91 " pdb=" OE2 GLU D 191 " model vdw 2.149 2.440 nonbonded pdb=" OD1 ASP F 568 " pdb=" OG1 THR F 572 " model vdw 2.154 2.440 nonbonded pdb=" OD1 ASP D 568 " pdb=" OG1 THR D 572 " model vdw 2.165 2.440 ... (remaining 387461 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 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.360 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 139.200 Find NCS groups from input model: 4.070 Set up NCS constraints: 1.740 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.005 0.081 52188 Z= 0.347 Angle : 0.666 12.853 71028 Z= 0.332 Chirality : 0.049 0.487 8573 Planarity : 0.004 0.063 8958 Dihedral : 14.453 113.898 21420 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.23 (0.11), residues: 6132 helix: 2.11 (0.15), residues: 1258 sheet: 0.57 (0.13), residues: 1438 loop : -1.42 (0.10), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.005 0.001 HIS E1064 PHE 0.023 0.001 PHE D 906 TYR 0.030 0.001 TYR D 873 ARG 0.005 0.000 ARG E1019 *********************** 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 174 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 5.766 Fit side-chains REVERT: D 869 MET cc_start: 0.8818 (mpp) cc_final: 0.8586 (mtm) REVERT: E 1029 MET cc_start: 0.8936 (tmm) cc_final: 0.8698 (ttm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.5500 time to fit residues: 171.2024 Evaluate side-chains 116 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 5.568 ------------------------------------------------------------------------------- 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: 1.9990 chunk 468 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 484 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 561 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN D 245 HIS D 394 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 52188 Z= 0.245 Angle : 0.563 9.566 71028 Z= 0.285 Chirality : 0.046 0.528 8573 Planarity : 0.004 0.064 8958 Dihedral : 9.069 101.934 10320 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 0.33 % Allowed : 5.97 % Favored : 93.70 % 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: -0.24 (0.11), residues: 6132 helix: 1.99 (0.15), residues: 1310 sheet: 0.67 (0.13), residues: 1434 loop : -1.49 (0.10), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS E 66 PHE 0.018 0.001 PHE F 135 TYR 0.017 0.001 TYR A1067 ARG 0.008 0.000 ARG B1107 *********************** 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 141 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 6.088 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7631 (tmm) cc_final: 0.7292 (tmm) REVERT: A 1017 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 1029 MET cc_start: 0.8373 (ttm) cc_final: 0.7995 (ttm) REVERT: D 153 MET cc_start: 0.4764 (mpp) cc_final: 0.3493 (mpp) REVERT: D 869 MET cc_start: 0.9026 (mpp) cc_final: 0.8515 (mtm) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.5470 time to fit residues: 133.6746 Evaluate side-chains 126 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 900 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 7.9990 chunk 174 optimal weight: 0.1980 chunk 467 optimal weight: 3.9990 chunk 382 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 562 optimal weight: 4.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 3.9990 chunk 557 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 451 optimal weight: 0.0060 overall best weight: 2.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1083 HIS ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D 907 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 52188 Z= 0.246 Angle : 0.544 11.589 71028 Z= 0.275 Chirality : 0.045 0.528 8573 Planarity : 0.004 0.067 8958 Dihedral : 7.844 101.729 10320 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 0.64 % Allowed : 9.06 % Favored : 90.30 % 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: -0.24 (0.11), residues: 6132 helix: 1.94 (0.15), residues: 1316 sheet: 0.66 (0.13), residues: 1438 loop : -1.47 (0.10), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS B1088 PHE 0.019 0.001 PHE E 898 TYR 0.017 0.001 TYR B1067 ARG 0.015 0.000 ARG F1107 *********************** 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 153 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 6.376 Fit side-chains REVERT: A 153 MET cc_start: 0.7741 (tmm) cc_final: 0.7382 (tmm) REVERT: A 1017 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 153 MET cc_start: 0.5122 (mpp) cc_final: 0.3955 (mpp) REVERT: D 869 MET cc_start: 0.9096 (mpp) cc_final: 0.8455 (mtm) outliers start: 35 outliers final: 17 residues processed: 141 average time/residue: 0.5630 time to fit residues: 148.8204 Evaluate side-chains 127 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 900 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 0.9990 chunk 422 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 564 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 245 HIS ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 658 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 52188 Z= 0.349 Angle : 0.597 9.255 71028 Z= 0.302 Chirality : 0.046 0.526 8573 Planarity : 0.004 0.068 8958 Dihedral : 7.305 101.789 10320 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 1.36 % Allowed : 11.63 % Favored : 87.01 % 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: -0.37 (0.11), residues: 6132 helix: 1.78 (0.15), residues: 1308 sheet: 0.54 (0.13), residues: 1442 loop : -1.51 (0.10), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS B 519 PHE 0.018 0.001 PHE A 559 TYR 0.017 0.001 TYR B1067 ARG 0.012 0.001 ARG B1107 *********************** 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 181 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 107 time to evaluate : 5.703 Fit side-chains REVERT: A 153 MET cc_start: 0.7790 (tmm) cc_final: 0.7446 (tmm) REVERT: A 1017 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 900 MET cc_start: 0.8977 (mtp) cc_final: 0.8708 (mtm) REVERT: E 985 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8443 (t0) outliers start: 74 outliers final: 35 residues processed: 172 average time/residue: 0.5002 time to fit residues: 161.9745 Evaluate side-chains 143 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 0.9990 chunk 339 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 444 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 509 optimal weight: 0.9990 chunk 412 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 305 optimal weight: 0.5980 chunk 536 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 52188 Z= 0.174 Angle : 0.516 9.567 71028 Z= 0.261 Chirality : 0.044 0.519 8573 Planarity : 0.004 0.069 8958 Dihedral : 6.887 102.035 10320 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 1.25 % Allowed : 12.79 % Favored : 85.96 % 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: -0.20 (0.11), residues: 6132 helix: 2.02 (0.15), residues: 1302 sheet: 0.62 (0.13), residues: 1456 loop : -1.42 (0.11), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS A1064 PHE 0.017 0.001 PHE A1052 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG F 214 *********************** 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 188 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 120 time to evaluate : 6.032 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 900 MET cc_start: 0.8937 (mtp) cc_final: 0.8634 (mtm) REVERT: D 153 MET cc_start: 0.5179 (mpp) cc_final: 0.3776 (mpp) REVERT: E 586 ASP cc_start: 0.8310 (t0) cc_final: 0.8055 (t0) REVERT: E 740 MET cc_start: 0.8854 (mmm) cc_final: 0.8598 (mmm) REVERT: E 985 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (t0) outliers start: 68 outliers final: 35 residues processed: 179 average time/residue: 0.5195 time to fit residues: 175.5181 Evaluate side-chains 151 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 5.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 9.9990 chunk 537 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 147 optimal weight: 0.0570 chunk 597 optimal weight: 4.9990 chunk 496 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 313 optimal weight: 6.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 52188 Z= 0.167 Angle : 0.508 11.636 71028 Z= 0.256 Chirality : 0.044 0.500 8573 Planarity : 0.004 0.069 8958 Dihedral : 6.599 100.963 10320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 1.19 % Allowed : 13.71 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6132 helix: 2.03 (0.15), residues: 1314 sheet: 0.72 (0.13), residues: 1444 loop : -1.37 (0.11), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1102 HIS 0.002 0.000 HIS B1083 PHE 0.011 0.001 PHE B1103 TYR 0.021 0.001 TYR F 369 ARG 0.003 0.000 ARG B1107 *********************** 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 196 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 131 time to evaluate : 5.938 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 900 MET cc_start: 0.8927 (mtp) cc_final: 0.8602 (mtm) REVERT: D 153 MET cc_start: 0.5282 (mpp) cc_final: 0.3952 (mpp) REVERT: E 586 ASP cc_start: 0.8304 (t0) cc_final: 0.8081 (t0) REVERT: E 985 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8398 (t0) REVERT: F 1050 MET cc_start: 0.8645 (ptp) cc_final: 0.8396 (mtp) outliers start: 65 outliers final: 44 residues processed: 186 average time/residue: 0.5328 time to fit residues: 184.2907 Evaluate side-chains 161 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 436 optimal weight: 0.7980 chunk 338 optimal weight: 0.3980 chunk 503 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 595 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 52188 Z= 0.262 Angle : 0.542 9.331 71028 Z= 0.273 Chirality : 0.044 0.484 8573 Planarity : 0.004 0.069 8958 Dihedral : 6.598 100.805 10320 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 1.49 % Allowed : 14.20 % Favored : 84.31 % 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: -0.14 (0.11), residues: 6132 helix: 2.09 (0.15), residues: 1294 sheet: 0.67 (0.13), residues: 1442 loop : -1.39 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1102 HIS 0.003 0.001 HIS A1064 PHE 0.013 0.001 PHE E 377 TYR 0.019 0.001 TYR C 904 ARG 0.007 0.000 ARG B1107 *********************** 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 192 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 111 time to evaluate : 5.922 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 551 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8963 (m) REVERT: B 900 MET cc_start: 0.8947 (mtp) cc_final: 0.8649 (mtm) REVERT: D 153 MET cc_start: 0.5467 (mpp) cc_final: 0.4129 (mpp) REVERT: E 586 ASP cc_start: 0.8326 (t0) cc_final: 0.8054 (t0) REVERT: E 985 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (t0) outliers start: 81 outliers final: 57 residues processed: 183 average time/residue: 0.5299 time to fit residues: 181.2384 Evaluate side-chains 168 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 109 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 468 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 52188 Z= 0.254 Angle : 0.541 9.336 71028 Z= 0.273 Chirality : 0.044 0.468 8573 Planarity : 0.004 0.068 8958 Dihedral : 6.538 101.263 10320 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 1.49 % Allowed : 14.63 % Favored : 83.88 % 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: -0.19 (0.11), residues: 6132 helix: 2.02 (0.15), residues: 1304 sheet: 0.65 (0.13), residues: 1442 loop : -1.43 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS C1058 PHE 0.015 0.001 PHE E 377 TYR 0.023 0.001 TYR F 369 ARG 0.005 0.000 ARG B1107 *********************** 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 195 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 114 time to evaluate : 6.210 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 551 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8965 (m) REVERT: B 900 MET cc_start: 0.8950 (mtp) cc_final: 0.8671 (mtm) REVERT: C 101 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (mm) REVERT: D 153 MET cc_start: 0.5392 (mpp) cc_final: 0.4149 (mpp) REVERT: E 586 ASP cc_start: 0.8345 (t0) cc_final: 0.8059 (t0) REVERT: E 985 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8381 (t0) outliers start: 81 outliers final: 66 residues processed: 184 average time/residue: 0.5373 time to fit residues: 183.1482 Evaluate side-chains 179 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 110 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 0.8980 chunk 570 optimal weight: 7.9990 chunk 520 optimal weight: 0.0010 chunk 555 optimal weight: 0.0060 chunk 334 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 435 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 501 optimal weight: 1.9990 chunk 524 optimal weight: 5.9990 chunk 553 optimal weight: 5.9990 overall best weight: 1.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 52188 Z= 0.152 Angle : 0.505 9.441 71028 Z= 0.254 Chirality : 0.044 0.453 8573 Planarity : 0.004 0.069 8958 Dihedral : 6.205 100.033 10320 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.71 % Rotamer: Outliers : 1.29 % Allowed : 14.96 % Favored : 83.76 % 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: -0.02 (0.11), residues: 6132 helix: 2.20 (0.15), residues: 1294 sheet: 0.74 (0.14), residues: 1442 loop : -1.32 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS B1083 PHE 0.013 0.001 PHE E 377 TYR 0.020 0.001 TYR F 369 ARG 0.005 0.000 ARG B1107 *********************** 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 203 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 133 time to evaluate : 5.376 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 551 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8918 (m) REVERT: B 900 MET cc_start: 0.8892 (mtp) cc_final: 0.8562 (mtm) REVERT: C 153 MET cc_start: 0.4902 (ptm) cc_final: 0.3105 (pmm) REVERT: D 153 MET cc_start: 0.5261 (mpp) cc_final: 0.3991 (mpp) REVERT: E 586 ASP cc_start: 0.8285 (t0) cc_final: 0.8047 (t0) REVERT: E 985 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8328 (t0) outliers start: 70 outliers final: 54 residues processed: 192 average time/residue: 0.5264 time to fit residues: 185.3864 Evaluate side-chains 175 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 6.9990 chunk 586 optimal weight: 0.0050 chunk 358 optimal weight: 2.9990 chunk 278 optimal weight: 0.0870 chunk 408 optimal weight: 9.9990 chunk 615 optimal weight: 6.9990 chunk 566 optimal weight: 5.9990 chunk 490 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 378 optimal weight: 4.9990 chunk 300 optimal weight: 0.9990 overall best weight: 1.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN D 955 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 52188 Z= 0.193 Angle : 0.516 9.384 71028 Z= 0.259 Chirality : 0.044 0.440 8573 Planarity : 0.004 0.066 8958 Dihedral : 6.161 99.338 10320 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 1.23 % Allowed : 15.12 % Favored : 83.65 % 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: -0.02 (0.11), residues: 6132 helix: 2.24 (0.15), residues: 1284 sheet: 0.75 (0.14), residues: 1432 loop : -1.32 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1102 HIS 0.002 0.001 HIS F1083 PHE 0.013 0.001 PHE E 377 TYR 0.036 0.001 TYR C 904 ARG 0.015 0.000 ARG B 319 ********************** 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 183 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 116 time to evaluate : 5.897 Fit side-chains REVERT: A 1017 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 551 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8924 (m) REVERT: B 900 MET cc_start: 0.8922 (mtp) cc_final: 0.8604 (mtm) REVERT: C 153 MET cc_start: 0.4917 (ptm) cc_final: 0.3122 (pmm) REVERT: D 153 MET cc_start: 0.5298 (mpp) cc_final: 0.4041 (mpp) REVERT: E 586 ASP cc_start: 0.8302 (t0) cc_final: 0.8057 (t0) REVERT: E 985 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8346 (t0) outliers start: 67 outliers final: 59 residues processed: 173 average time/residue: 0.5037 time to fit residues: 163.3341 Evaluate side-chains 176 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 115 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 540 ASN Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 860 VAL Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 977 LEU 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: 8.9990 chunk 150 optimal weight: 2.9990 chunk 452 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 491 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 504 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.071696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050303 restraints weight = 188162.740| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.42 r_work: 0.2816 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52188 Z= 0.185 Angle : 0.513 9.391 71028 Z= 0.257 Chirality : 0.044 0.429 8573 Planarity : 0.004 0.067 8958 Dihedral : 6.082 98.614 10320 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 1.27 % Allowed : 15.18 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6132 helix: 2.23 (0.15), residues: 1284 sheet: 0.69 (0.13), residues: 1456 loop : -1.33 (0.11), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1102 HIS 0.002 0.000 HIS F1083 PHE 0.012 0.001 PHE E 377 TYR 0.027 0.001 TYR C 904 ARG 0.013 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8016.11 seconds wall clock time: 148 minutes 43.39 seconds (8923.39 seconds total)