Starting phenix.real_space_refine on Sun Feb 25 11:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7h_31771/02_2024/7v7h_31771.pdb" } resolution = 3.2 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= 0.057 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 32364 2.51 5 N 8252 2.21 5 O 10111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 950": "OD1" <-> "OD2" Residue "D TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 571": "OD1" <-> "OD2" Residue "F PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50949 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: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "E" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8070 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 53, 'TRANS': 978} Chain breaks: 7 Chain: "F" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8070 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 53, 'TRANS': 978} 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: 25.97, per 1000 atoms: 0.51 Number of scatterers: 50949 At special positions: 0 Unit cell: (167.2, 155.1, 328.9, 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 10111 8.00 N 8252 7.00 C 32364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=74, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " NAG-ASN " NAG 0 1 " - " ASN D1098 " " NAG 1 1 " - " ASN D1134 " " NAG 2 1 " - " ASN E 122 " " NAG 3 1 " - " ASN E 165 " " NAG 4 1 " - " ASN E 234 " " NAG 5 1 " - " ASN E 282 " " NAG 6 1 " - " ASN E 343 " " NAG 7 1 " - " ASN E 616 " " NAG 8 1 " - " ASN E 709 " " NAG 9 1 " - " ASN E 717 " " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 331 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 331 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 331 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D2001 " - " ASN D 61 " " NAG D2002 " - " ASN D 331 " " NAG D2003 " - " ASN D 603 " " NAG D2004 " - " ASN D 657 " " NAG E2001 " - " ASN E 61 " " NAG E2002 " - " ASN E 331 " " NAG E2003 " - " ASN E 603 " " NAG 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: 21.32 Conformation dependent library (CDL) restraints added in 8.2 seconds 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11638 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 92 sheets defined 25.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.89 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 387 removed outlier: 3.624A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.735A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.628A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.066A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (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: 3.552A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.514A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.954A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.893A 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 371 removed outlier: 3.667A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.630A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.752A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.534A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.579A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.578A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.506A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 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: 3.709A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.690A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.416A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.587A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (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 737 through 742 removed outlier: 3.526A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.031A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.928A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.550A 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: 3.573A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.283A 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 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: 3.703A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.103A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.618A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.830A pdb=" N SER D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.681A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.951A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.886A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.518A pdb=" N THR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.536A 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 909 removed outlier: 3.546A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.301A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.654A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.470A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.612A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.603A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.856A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.535A pdb=" N ALA E 766 " --> pdb=" O GLN E 762 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU E 767 " --> pdb=" O LEU E 763 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR E 768 " --> pdb=" O ASN E 764 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY E 769 " --> pdb=" O ARG E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.753A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 913 through 919 removed outlier: 3.605A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.791A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 984 " --> pdb=" O ILE E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E1033 " --> pdb=" O MET E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1146 removed outlier: 3.637A 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 365 through 371 removed outlier: 3.652A pdb=" N SER F 371 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.309A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 738 through 743 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.887A pdb=" N GLN F 762 " --> pdb=" O SER F 758 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 766 " --> pdb=" O GLN F 762 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 767 " --> pdb=" O LEU F 763 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR F 768 " --> pdb=" O ASN F 764 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY F 769 " --> pdb=" O ARG F 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.540A 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: 3.506A pdb=" N ILE F 909 " --> pdb=" O ARG F 905 " (cutoff:3.500A) Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.208A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 removed outlier: 3.578A pdb=" N ILE F 980 " --> pdb=" O VAL F 976 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 984 " --> pdb=" O ILE F 980 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.628A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1146 removed outlier: 3.505A pdb=" N ASP F1146 " --> pdb=" O GLN F1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.879A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.964A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.179A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.819A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.193A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.959A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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 573 through 576 removed outlier: 3.616A pdb=" N PHE B 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.337A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.508A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.007A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.269A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.138A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.721A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.718A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.828A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.658A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.730A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.515A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.515A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.338A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.110A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.073A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.669A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 143 through 144 removed outlier: 5.292A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.168A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.447A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.607A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.133A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.403A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.760A pdb=" N PHE D 43 " --> pdb=" O ARG F 567 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.107A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.793A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 130 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.567A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 325 through 326 removed outlier: 5.822A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 354 through 358 removed outlier: 7.356A pdb=" N ASN D 437 " --> pdb=" O PHE D 374 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE D 374 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AG3, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AG4, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.018A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AG6, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.736A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 787 through 789 removed outlier: 5.745A pdb=" N ILE D 788 " --> pdb=" O ASN F 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AH1, first strand: chain 'D' and resid 1094 through 1096 Processing sheet with id=AH2, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.212A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.129A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.668A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN E 165 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLN E 134 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA E 163 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.549A pdb=" N THR E 315 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 325 through 326 removed outlier: 3.634A pdb=" N VAL E 576 " --> pdb=" O LEU E 585 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE E 565 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.545A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AI1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AI2, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.759A pdb=" N THR E 696 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN E 658 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 701 through 702 removed outlier: 6.580A pdb=" N ALA E 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.702A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.702A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AI8, first strand: chain 'F' and resid 27 through 30 removed outlier: 8.322A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AI9, 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=AJ1, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.690A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN F 165 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLN F 134 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA F 163 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.202A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AJ4, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AJ5, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AJ6, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AJ7, first strand: chain 'F' and resid 664 through 667 removed outlier: 6.043A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.654A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 5.097A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) 2022 hydrogen bonds defined for protein. 5466 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: 24.36 Time building geometry restraints manager: 22.77 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: 16023 1.34 - 1.47: 13248 1.47 - 1.59: 22512 1.59 - 1.71: 0 1.71 - 1.83: 276 Bond restraints: 52059 Sorted by residual: bond pdb=" C1 NAG 6 1 " pdb=" O5 NAG 6 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C PRO F 986 " pdb=" N PRO F 987 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.51e+00 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.29e+00 ... (remaining 52054 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.62: 1082 105.62 - 112.72: 28201 112.72 - 119.81: 15963 119.81 - 126.90: 25136 126.90 - 134.00: 467 Bond angle restraints: 70849 Sorted by residual: angle pdb=" C LEU F 984 " pdb=" N ASP F 985 " pdb=" CA ASP F 985 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C LEU E 984 " pdb=" N ASP E 985 " pdb=" CA ASP E 985 " ideal model delta sigma weight residual 120.49 127.79 -7.30 1.42e+00 4.96e-01 2.64e+01 angle pdb=" N THR F 618 " pdb=" CA THR F 618 " pdb=" C THR F 618 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" N LEU D 984 " pdb=" CA LEU D 984 " pdb=" C LEU D 984 " ideal model delta sigma weight residual 108.34 113.55 -5.21 1.31e+00 5.83e-01 1.58e+01 angle pdb=" CA LEU D 560 " pdb=" CB LEU D 560 " pdb=" CG LEU D 560 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 ... (remaining 70844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 30901 22.02 - 44.05: 1898 44.05 - 66.07: 300 66.07 - 88.09: 101 88.09 - 110.12: 51 Dihedral angle restraints: 33251 sinusoidal: 15170 harmonic: 18081 Sorted by residual: dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -169.93 83.93 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.41 82.41 1 1.00e+01 1.00e-02 8.33e+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 -165.16 79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 33248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 8505 0.168 - 0.335: 41 0.335 - 0.503: 3 0.503 - 0.670: 6 0.670 - 0.838: 2 Chirality restraints: 8557 Sorted by residual: chirality pdb=" C1 NAGBA 1 " pdb=" ND2 ASN E1074 " pdb=" C2 NAGBA 1 " pdb=" O5 NAGBA 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 8554 not shown) Planarity restraints: 9031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 985 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.85e+00 pdb=" N PRO F 986 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO F 986 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 986 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 985 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO E 986 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 986 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 986 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO A 987 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.033 5.00e-02 4.00e+02 ... (remaining 9028 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1743 2.71 - 3.26: 49863 3.26 - 3.80: 78086 3.80 - 4.35: 92818 4.35 - 4.90: 161383 Nonbonded interactions: 383893 Sorted by model distance: nonbonded pdb=" OG SER D 349 " pdb=" O ARG D 452 " model vdw 2.162 2.440 nonbonded pdb=" OG1 THR C 716 " pdb=" O HIS C1071 " model vdw 2.180 2.440 nonbonded pdb=" OG SER B 116 " pdb=" O CYS B 131 " model vdw 2.191 2.440 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.191 2.440 nonbonded pdb=" OG SER E 349 " pdb=" O ARG E 452 " model vdw 2.192 2.440 ... (remaining 383888 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' and (resid 14 through 246 or resid 263 through 1146 or resid 2001 thr \ ough 2004)) selection = (chain 'B' and (resid 14 through 246 or resid 263 through 1146 or resid 2001 thr \ ough 2004)) selection = (chain 'C' and (resid 14 through 246 or resid 263 through 1146 or resid 2001 thr \ ough 2004)) selection = chain 'D' selection = (chain 'E' and (resid 14 through 246 or resid 263 through 1146 or resid 2001 thr \ ough 2004)) selection = (chain 'F' and (resid 14 through 246 or resid 263 through 1146 or resid 2001 thr \ ough 2004)) } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.090 Check model and map are aligned: 0.840 Set scattering table: 0.510 Process input model: 130.460 Find NCS groups from input model: 4.580 Set up NCS constraints: 1.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 52059 Z= 0.239 Angle : 0.624 13.592 70849 Z= 0.307 Chirality : 0.052 0.838 8557 Planarity : 0.004 0.065 8936 Dihedral : 14.686 110.117 21391 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.75 % 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: -0.31 (0.11), residues: 6113 helix: 1.98 (0.15), residues: 1312 sheet: 0.53 (0.14), residues: 1380 loop : -1.49 (0.10), residues: 3421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.000 HIS C 655 PHE 0.016 0.001 PHE F 377 TYR 0.013 0.001 TYR B1067 ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 6.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8948 (ptm) cc_final: 0.8742 (ptm) REVERT: A 779 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8704 (tm-30) REVERT: B 102 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.7099 (mmp80) REVERT: C 779 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 153 MET cc_start: 0.3084 (ptt) cc_final: 0.2731 (ptt) REVERT: D 170 TYR cc_start: 0.8434 (t80) cc_final: 0.7969 (t80) REVERT: D 754 LEU cc_start: 0.9450 (mt) cc_final: 0.9100 (mt) REVERT: E 933 LYS cc_start: 0.9478 (tptp) cc_final: 0.9270 (tppt) REVERT: F 153 MET cc_start: 0.3749 (ppp) cc_final: 0.3145 (ppp) REVERT: F 1002 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 1029 MET cc_start: 0.8552 (tmm) cc_final: 0.8136 (ttm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.5924 time to fit residues: 230.7618 Evaluate side-chains 141 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 6.374 ------------------------------------------------------------------------------- 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: 10.0000 chunk 468 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 315 optimal weight: 0.0870 chunk 250 optimal weight: 0.0870 chunk 484 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 360 optimal weight: 9.9990 chunk 561 optimal weight: 0.9980 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN A 953 ASN D 955 ASN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN E 641 ASN ** F 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 52059 Z= 0.153 Angle : 0.538 10.503 70849 Z= 0.268 Chirality : 0.047 0.550 8557 Planarity : 0.004 0.061 8936 Dihedral : 9.840 124.860 10301 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 0.33 % Allowed : 4.88 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6113 helix: 1.92 (0.15), residues: 1351 sheet: 0.65 (0.14), residues: 1390 loop : -1.44 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.002 0.000 HIS C1088 PHE 0.018 0.001 PHE B 168 TYR 0.034 0.001 TYR E 369 ARG 0.005 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 5.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8709 (tm-30) REVERT: B 102 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7053 (mmp80) REVERT: B 153 MET cc_start: 0.4127 (tmm) cc_final: 0.3700 (tmm) REVERT: C 779 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 153 MET cc_start: 0.3098 (ptt) cc_final: 0.2692 (ptt) REVERT: D 170 TYR cc_start: 0.8444 (t80) cc_final: 0.8044 (t80) REVERT: D 754 LEU cc_start: 0.9409 (mt) cc_final: 0.9016 (mt) REVERT: E 118 LEU cc_start: 0.9161 (tt) cc_final: 0.8958 (tt) REVERT: F 153 MET cc_start: 0.3515 (ppp) cc_final: 0.2949 (ppp) REVERT: F 820 ASP cc_start: 0.7417 (m-30) cc_final: 0.7031 (m-30) REVERT: F 1002 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7938 (tm-30) REVERT: F 1029 MET cc_start: 0.8665 (tmm) cc_final: 0.8096 (ttm) outliers start: 18 outliers final: 11 residues processed: 163 average time/residue: 0.5645 time to fit residues: 167.2858 Evaluate side-chains 146 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain E residue 88 ASP 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: 8.9990 chunk 174 optimal weight: 7.9990 chunk 467 optimal weight: 6.9990 chunk 382 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 562 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 0.9980 chunk 557 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 451 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 953 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1011 GLN D 953 ASN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS F 658 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 52059 Z= 0.466 Angle : 0.680 9.391 70849 Z= 0.343 Chirality : 0.050 0.571 8557 Planarity : 0.004 0.059 8936 Dihedral : 8.853 121.639 10301 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 0.68 % Allowed : 10.19 % Favored : 89.13 % 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: -0.64 (0.11), residues: 6113 helix: 1.44 (0.15), residues: 1349 sheet: 0.44 (0.14), residues: 1413 loop : -1.68 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1102 HIS 0.008 0.001 HIS C1058 PHE 0.027 0.002 PHE A 906 TYR 0.024 0.002 TYR F 453 ARG 0.006 0.001 ARG F1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4906 (tmm) cc_final: 0.4695 (tmm) REVERT: C 779 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8549 (tm-30) REVERT: F 153 MET cc_start: 0.4702 (ppp) cc_final: 0.4377 (tmm) REVERT: F 563 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: F 902 MET cc_start: 0.9233 (mmm) cc_final: 0.9000 (tpt) REVERT: F 1029 MET cc_start: 0.8635 (tmm) cc_final: 0.8239 (ttm) outliers start: 37 outliers final: 21 residues processed: 158 average time/residue: 0.5710 time to fit residues: 165.2319 Evaluate side-chains 142 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 5.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 990 GLU Chi-restraints excluded: chain F residue 563 GLN Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 867 ASP 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: 0.8980 chunk 422 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 377 optimal weight: 0.8980 chunk 564 optimal weight: 10.0000 chunk 597 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 534 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN F 658 ASN F 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 52059 Z= 0.150 Angle : 0.535 10.404 70849 Z= 0.268 Chirality : 0.047 0.556 8557 Planarity : 0.004 0.063 8936 Dihedral : 7.926 118.767 10301 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 0.90 % Allowed : 11.98 % Favored : 87.12 % 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: -0.31 (0.11), residues: 6113 helix: 1.70 (0.15), residues: 1366 sheet: 0.69 (0.14), residues: 1393 loop : -1.50 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.002 0.000 HIS D1083 PHE 0.024 0.001 PHE B 168 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 5.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 153 MET cc_start: 0.4862 (tmm) cc_final: 0.4591 (tmm) REVERT: C 114 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 779 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 754 LEU cc_start: 0.9405 (mt) cc_final: 0.8984 (mt) REVERT: E 118 LEU cc_start: 0.9223 (tt) cc_final: 0.8807 (mt) REVERT: E 318 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8199 (p90) REVERT: E 985 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: F 820 ASP cc_start: 0.7352 (m-30) cc_final: 0.7078 (m-30) REVERT: F 984 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (pp) REVERT: F 1002 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8008 (tm-30) REVERT: F 1029 MET cc_start: 0.8588 (tmm) cc_final: 0.8195 (ttm) outliers start: 49 outliers final: 20 residues processed: 187 average time/residue: 0.5323 time to fit residues: 181.9965 Evaluate side-chains 159 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 444 optimal weight: 5.9990 chunk 246 optimal weight: 0.5980 chunk 509 optimal weight: 9.9990 chunk 412 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 305 optimal weight: 1.9990 chunk 536 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 658 ASN F 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 52059 Z= 0.366 Angle : 0.606 11.582 70849 Z= 0.304 Chirality : 0.048 0.567 8557 Planarity : 0.004 0.063 8936 Dihedral : 7.806 115.110 10301 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 1.49 % Allowed : 13.43 % Favored : 85.08 % 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: -0.49 (0.11), residues: 6113 helix: 1.66 (0.15), residues: 1338 sheet: 0.48 (0.14), residues: 1417 loop : -1.60 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1102 HIS 0.005 0.001 HIS C1058 PHE 0.030 0.001 PHE A 157 TYR 0.017 0.001 TYR B 904 ARG 0.003 0.000 ARG F1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 130 time to evaluate : 5.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8439 (p0) REVERT: B 153 MET cc_start: 0.4877 (tmm) cc_final: 0.4557 (tmm) REVERT: C 114 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8069 (p) REVERT: C 779 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8514 (tm-30) REVERT: E 318 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8312 (p90) REVERT: E 434 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8607 (mm) REVERT: E 1116 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8506 (p) REVERT: F 153 MET cc_start: 0.5288 (ppp) cc_final: 0.3666 (ppp) REVERT: F 563 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: F 820 ASP cc_start: 0.7413 (m-30) cc_final: 0.7096 (m-30) REVERT: F 1029 MET cc_start: 0.8698 (tmm) cc_final: 0.8265 (ttm) outliers start: 81 outliers final: 43 residues processed: 203 average time/residue: 0.5283 time to fit residues: 196.2541 Evaluate side-chains 175 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 990 GLU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 563 GLN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 6.9990 chunk 537 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 147 optimal weight: 0.0970 chunk 597 optimal weight: 9.9990 chunk 496 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN F 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 52059 Z= 0.245 Angle : 0.561 10.745 70849 Z= 0.281 Chirality : 0.047 0.560 8557 Planarity : 0.004 0.063 8936 Dihedral : 7.593 114.186 10301 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 1.45 % Allowed : 14.35 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6113 helix: 1.72 (0.15), residues: 1337 sheet: 0.51 (0.14), residues: 1408 loop : -1.54 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 886 HIS 0.003 0.001 HIS C1058 PHE 0.026 0.001 PHE B 168 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 139 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8413 (p0) REVERT: B 153 MET cc_start: 0.4946 (tmm) cc_final: 0.4603 (tmm) REVERT: C 114 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 779 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8451 (tm-30) REVERT: D 754 LEU cc_start: 0.9438 (mt) cc_final: 0.9047 (mt) REVERT: E 318 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8175 (p90) REVERT: E 434 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8628 (mm) REVERT: E 985 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: E 1116 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (p) REVERT: F 563 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: F 820 ASP cc_start: 0.7422 (m-30) cc_final: 0.7139 (m-30) REVERT: F 1029 MET cc_start: 0.8632 (tmm) cc_final: 0.8245 (ttm) outliers start: 79 outliers final: 47 residues processed: 210 average time/residue: 0.5302 time to fit residues: 202.8627 Evaluate side-chains 184 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 563 GLN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 436 optimal weight: 0.5980 chunk 338 optimal weight: 0.9980 chunk 503 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 595 optimal weight: 0.1980 chunk 372 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 HIS B 239 GLN D 949 GLN D1005 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 52059 Z= 0.138 Angle : 0.529 11.126 70849 Z= 0.262 Chirality : 0.046 0.547 8557 Planarity : 0.004 0.063 8936 Dihedral : 7.109 112.573 10301 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 1.32 % Allowed : 14.85 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6113 helix: 1.89 (0.15), residues: 1343 sheet: 0.65 (0.14), residues: 1399 loop : -1.41 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.002 0.000 HIS C 655 PHE 0.018 0.001 PHE C 157 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 146 time to evaluate : 6.878 Fit side-chains revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8324 (p0) REVERT: B 102 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.7066 (mmp80) REVERT: B 153 MET cc_start: 0.4921 (tmm) cc_final: 0.4608 (tmm) REVERT: C 114 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8201 (p) REVERT: C 779 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8403 (tm-30) REVERT: D 754 LEU cc_start: 0.9387 (mt) cc_final: 0.8975 (mt) REVERT: E 118 LEU cc_start: 0.9268 (tt) cc_final: 0.8859 (mt) REVERT: E 933 LYS cc_start: 0.9437 (tppt) cc_final: 0.9232 (pttt) REVERT: E 985 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: E 1116 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8692 (p) REVERT: F 820 ASP cc_start: 0.7425 (m-30) cc_final: 0.7131 (m-30) REVERT: F 1002 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8009 (tm-30) REVERT: F 1029 MET cc_start: 0.8660 (tmm) cc_final: 0.8134 (ttm) outliers start: 72 outliers final: 43 residues processed: 205 average time/residue: 0.5458 time to fit residues: 205.4407 Evaluate side-chains 182 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 5.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 317 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 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 926 GLN Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 chunk 355 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 378 optimal weight: 0.9990 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 468 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 52059 Z= 0.204 Angle : 0.540 10.757 70849 Z= 0.269 Chirality : 0.046 0.563 8557 Planarity : 0.004 0.061 8936 Dihedral : 7.007 111.239 10301 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 1.25 % Allowed : 15.34 % Favored : 83.40 % 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: 6113 helix: 1.86 (0.15), residues: 1353 sheet: 0.58 (0.14), residues: 1421 loop : -1.42 (0.10), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS C1058 PHE 0.026 0.001 PHE C 429 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG D1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 137 time to evaluate : 7.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8388 (p0) REVERT: B 153 MET cc_start: 0.5035 (tmm) cc_final: 0.4710 (tmm) REVERT: C 114 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 779 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8417 (tm-30) REVERT: D 754 LEU cc_start: 0.9412 (mt) cc_final: 0.8985 (mt) REVERT: E 118 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8853 (mt) REVERT: E 318 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8136 (p90) REVERT: E 387 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9263 (mm) REVERT: E 985 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: E 1116 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8706 (p) REVERT: F 820 ASP cc_start: 0.7448 (m-30) cc_final: 0.7147 (m-30) REVERT: F 1002 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8116 (tm-30) REVERT: F 1029 MET cc_start: 0.8694 (tmm) cc_final: 0.8111 (ttm) outliers start: 68 outliers final: 47 residues processed: 195 average time/residue: 0.5503 time to fit residues: 197.1135 Evaluate side-chains 187 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 133 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE 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 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 979 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 6.9990 chunk 570 optimal weight: 7.9990 chunk 520 optimal weight: 9.9990 chunk 555 optimal weight: 4.9990 chunk 334 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 435 optimal weight: 0.0770 chunk 170 optimal weight: 2.9990 chunk 501 optimal weight: 0.3980 chunk 524 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 907 ASN D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 52059 Z= 0.152 Angle : 0.529 11.330 70849 Z= 0.263 Chirality : 0.046 0.548 8557 Planarity : 0.004 0.062 8936 Dihedral : 6.811 110.927 10301 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.31 % Rotamer: Outliers : 1.23 % Allowed : 15.44 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 6113 helix: 1.91 (0.15), residues: 1351 sheet: 0.65 (0.14), residues: 1422 loop : -1.38 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS C 519 PHE 0.023 0.001 PHE B 168 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 147 time to evaluate : 5.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8347 (p0) REVERT: B 102 ARG cc_start: 0.7734 (mmt-90) cc_final: 0.7133 (mmp80) REVERT: B 153 MET cc_start: 0.5070 (tmm) cc_final: 0.4740 (tmm) REVERT: C 114 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 779 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 754 LEU cc_start: 0.9401 (mt) cc_final: 0.8990 (mt) REVERT: E 118 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8851 (mt) REVERT: E 387 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9248 (mm) REVERT: E 985 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: F 820 ASP cc_start: 0.7460 (m-30) cc_final: 0.7154 (m-30) REVERT: F 1002 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8042 (tm-30) REVERT: F 1029 MET cc_start: 0.8664 (tmm) cc_final: 0.8062 (ttm) outliers start: 67 outliers final: 53 residues processed: 205 average time/residue: 0.5572 time to fit residues: 207.7552 Evaluate side-chains 197 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 139 time to evaluate : 6.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE 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 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 4.9990 chunk 586 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 408 optimal weight: 0.8980 chunk 615 optimal weight: 10.0000 chunk 566 optimal weight: 6.9990 chunk 490 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 378 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.794 52059 Z= 0.299 Angle : 0.625 65.536 70849 Z= 0.301 Chirality : 0.046 0.548 8557 Planarity : 0.004 0.062 8936 Dihedral : 6.812 110.918 10301 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.12 % Allowed : 15.79 % Favored : 83.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.17 (0.11), residues: 6113 helix: 1.91 (0.15), residues: 1351 sheet: 0.64 (0.14), residues: 1424 loop : -1.38 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS F1064 PHE 0.022 0.001 PHE B 168 TYR 0.015 0.001 TYR C1067 ARG 0.001 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12226 Ramachandran restraints generated. 6113 Oldfield, 0 Emsley, 6113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 140 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8349 (p0) REVERT: B 102 ARG cc_start: 0.7734 (mmt-90) cc_final: 0.7135 (mmp80) REVERT: B 153 MET cc_start: 0.5071 (tmm) cc_final: 0.4737 (tmm) REVERT: C 114 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 779 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 754 LEU cc_start: 0.9401 (mt) cc_final: 0.8983 (mt) REVERT: E 118 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8852 (mt) REVERT: E 318 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8111 (p90) REVERT: E 387 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9249 (mm) REVERT: E 985 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: F 820 ASP cc_start: 0.7463 (m-30) cc_final: 0.7157 (m-30) REVERT: F 1002 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8044 (tm-30) REVERT: F 1029 MET cc_start: 0.8670 (tmm) cc_final: 0.8066 (ttm) outliers start: 61 outliers final: 53 residues processed: 193 average time/residue: 0.5379 time to fit residues: 189.0350 Evaluate side-chains 199 residues out of total 5435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 140 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE 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 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 8.9990 chunk 522 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 452 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 491 optimal weight: 9.9990 chunk 205 optimal weight: 0.5980 chunk 504 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN D 949 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052729 restraints weight = 180120.757| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.79 r_work: 0.2819 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.792 52059 Z= 0.298 Angle : 0.625 65.600 70849 Z= 0.301 Chirality : 0.046 0.548 8557 Planarity : 0.004 0.062 8936 Dihedral : 6.811 110.918 10301 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.09 % Allowed : 15.82 % Favored : 83.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.17 (0.11), residues: 6113 helix: 1.91 (0.15), residues: 1351 sheet: 0.64 (0.14), residues: 1424 loop : -1.38 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS F1064 PHE 0.022 0.001 PHE B 168 TYR 0.015 0.001 TYR C1067 ARG 0.001 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8771.94 seconds wall clock time: 162 minutes 48.09 seconds (9768.09 seconds total)