Starting phenix.real_space_refine on Tue Mar 19 14:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/03_2024/6bfu_7094.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 129 5.16 5 C 15255 2.51 5 N 3864 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 707": "OD1" <-> "OD2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 725": "OD1" <-> "OD2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 707": "OD1" <-> "OD2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "C" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 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: "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: 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: "M" 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: "N" 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: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: "a" 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 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: "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: 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: "m" 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: "n" 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: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.62, per 1000 atoms: 0.56 Number of scatterers: 24480 At special positions: 0 Unit cell: (122.36, 125.02, 159.6, 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 129 16.00 O 5232 8.00 N 3864 7.00 C 15255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.05 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.01 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.08 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.01 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.05 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.01 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.08 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.01 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.04 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.01 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.08 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.01 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " " BMA i 3 " - " MAN i 5 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1099 " - " ASN A 99 " " NAG A1162 " - " ASN A 162 " " NAG A1169 " - " ASN A 169 " " NAG A1331 " - " ASN A 331 " " NAG A1505 " - " ASN A 505 " " NAG A1531 " - " ASN A 531 " " NAG A1945 " - " ASN A 945 " " NAG A1970 " - " ASN A 970 " " NAG B1099 " - " ASN B 99 " " NAG B1162 " - " ASN B 162 " " NAG B1169 " - " ASN B 169 " " NAG B1331 " - " ASN B 331 " " NAG B1505 " - " ASN B 505 " " NAG B1531 " - " ASN B 531 " " NAG B1945 " - " ASN B 945 " " NAG B1970 " - " ASN B 970 " " NAG C1099 " - " ASN C 99 " " NAG C1162 " - " ASN C 162 " " NAG C1169 " - " ASN C 169 " " NAG C1331 " - " ASN C 331 " " NAG C1505 " - " ASN C 505 " " NAG C1531 " - " ASN C 531 " " NAG C1945 " - " ASN C 945 " " NAG C1970 " - " ASN C 970 " " NAG D 1 " - " ASN A 74 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 311 " " NAG I 1 " - " ASN A 472 " " NAG J 1 " - " ASN A 494 " " NAG K 1 " - " ASN A 526 " " NAG L 1 " - " ASN A 652 " " NAG M 1 " - " ASN A 661 " " NAG N 1 " - " ASN A 788 " " NAG O 1 " - " ASN A 914 " " NAG P 1 " - " ASN A1003 " " NAG Q 1 " - " ASN B 74 " " NAG R 1 " - " ASN B 184 " " NAG S 1 " - " ASN B 241 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 311 " " NAG V 1 " - " ASN B 472 " " NAG W 1 " - " ASN B 494 " " NAG X 1 " - " ASN B 526 " " NAG Y 1 " - " ASN B 652 " " NAG Z 1 " - " ASN B 661 " " NAG a 1 " - " ASN B 788 " " NAG b 1 " - " ASN B 914 " " NAG c 1 " - " ASN B1003 " " NAG d 1 " - " ASN C 74 " " NAG e 1 " - " ASN C 184 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 311 " " NAG i 1 " - " ASN C 472 " " NAG j 1 " - " ASN C 494 " " NAG k 1 " - " ASN C 526 " " NAG l 1 " - " ASN C 652 " " NAG m 1 " - " ASN C 661 " " NAG n 1 " - " ASN C 788 " " NAG o 1 " - " ASN C 914 " " NAG p 1 " - " ASN C1003 " Time building additional restraints: 11.93 Conformation dependent library (CDL) restraints added in 4.1 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 28.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 901 removed outlier: 3.721A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.039A pdb=" N THR B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 706 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 901 removed outlier: 3.719A pdb=" N GLN B 860 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.806A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 695 through 701 Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 901 removed outlier: 3.720A pdb=" N GLN C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1012 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 3.542A pdb=" N LEU A 89 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN A 241 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 91 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 239 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.375A pdb=" N ASP A 244 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR A 259 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 246 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 257 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 248 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 183 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.595A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN A 293 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR A 924 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 930 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET A 932 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 920 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 934 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN A 592 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB8, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 91 removed outlier: 3.543A pdb=" N LEU B 89 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 241 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 91 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 239 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP B 244 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 259 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 246 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 257 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 248 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.532A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 183 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN B 293 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 358 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 587 removed outlier: 6.944A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY B 928 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 924 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 930 " --> pdb=" O THR B 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 922 " --> pdb=" O PHE B 930 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET B 932 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 920 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 934 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 592 through 595 removed outlier: 4.172A pdb=" N GLN B 592 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AD6, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 91 removed outlier: 3.541A pdb=" N LEU C 89 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN C 241 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 91 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 239 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP C 244 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 259 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 246 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 257 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 248 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 183 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 293 through 297 removed outlier: 3.659A pdb=" N GLN C 293 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AE7, first strand: chain 'C' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AE9, first strand: chain 'C' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 928 " --> pdb=" O THR C 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR C 924 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 930 " --> pdb=" O THR C 922 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 922 " --> pdb=" O PHE C 930 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 932 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 920 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 934 " --> pdb=" O ILE C 918 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN C 592 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 991 through 994 Processing sheet with id=AF3, first strand: chain 'C' and resid 964 through 969 1078 hydrogen bonds defined for protein. 2874 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: 10.90 Time building geometry restraints manager: 12.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5199 1.32 - 1.45: 6468 1.45 - 1.58: 12897 1.58 - 1.71: 144 1.71 - 1.83: 180 Bond restraints: 24888 Sorted by residual: bond pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 1.474 1.438 0.036 7.40e-03 1.83e+04 2.31e+01 bond pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.26e+01 bond pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.25e+01 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C2 NAG d 2 " pdb=" N2 NAG d 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 24883 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.67: 493 105.67 - 112.68: 14341 112.68 - 119.70: 6838 119.70 - 126.72: 12164 126.72 - 133.73: 103 Bond angle restraints: 33939 Sorted by residual: angle pdb=" CD1 LEU B 453 " pdb=" CG LEU B 453 " pdb=" CD2 LEU B 453 " ideal model delta sigma weight residual 110.80 132.02 -21.22 2.20e+00 2.07e-01 9.31e+01 angle pdb=" CD1 LEU A 453 " pdb=" CG LEU A 453 " pdb=" CD2 LEU A 453 " ideal model delta sigma weight residual 110.80 131.99 -21.19 2.20e+00 2.07e-01 9.28e+01 angle pdb=" CD1 LEU C 453 " pdb=" CG LEU C 453 " pdb=" CD2 LEU C 453 " ideal model delta sigma weight residual 110.80 131.96 -21.16 2.20e+00 2.07e-01 9.25e+01 angle pdb=" C LYS B 338 " pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta sigma weight residual 119.32 127.75 -8.43 1.14e+00 7.69e-01 5.46e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.32 127.71 -8.39 1.14e+00 7.69e-01 5.42e+01 ... (remaining 33934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 16035 21.43 - 42.87: 624 42.87 - 64.30: 108 64.30 - 85.74: 213 85.74 - 107.17: 138 Dihedral angle restraints: 17118 sinusoidal: 8619 harmonic: 8499 Sorted by residual: dihedral pdb=" CB CYS C 433 " pdb=" SG CYS C 433 " pdb=" SG CYS C 484 " pdb=" CB CYS C 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS A 433 " pdb=" SG CYS A 433 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 433 " pdb=" SG CYS B 433 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.48 78.48 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 17115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 4244 0.153 - 0.306: 151 0.306 - 0.458: 123 0.458 - 0.611: 45 0.611 - 0.764: 3 Chirality restraints: 4566 Sorted by residual: chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4563 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.064 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.064 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR B 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.064 2.00e-02 2.50e+03 3.40e-02 2.32e+01 pdb=" CG TYR C 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " -0.051 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 90 2.58 - 3.16: 22370 3.16 - 3.74: 36760 3.74 - 4.32: 54914 4.32 - 4.90: 87383 Nonbonded interactions: 201517 Sorted by model distance: nonbonded pdb=" O ASN A 169 " pdb=" OD1 ASN A 169 " model vdw 2.005 3.040 nonbonded pdb=" O ASN B 169 " pdb=" OD1 ASN B 169 " model vdw 2.006 3.040 nonbonded pdb=" O ASN C 169 " pdb=" OD1 ASN C 169 " model vdw 2.007 3.040 nonbonded pdb=" O ASN B 914 " pdb=" OD1 ASN B 914 " model vdw 2.060 3.040 nonbonded pdb=" O ASN A 914 " pdb=" OD1 ASN A 914 " model vdw 2.060 3.040 ... (remaining 201512 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'o' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'T' selection = chain 'c' selection = chain 'g' selection = chain 'p' } ncs_group { reference = chain 'I' selection = chain 'V' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.910 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 70.770 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.470 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.018 0.086 24888 Z= 1.155 Angle : 1.391 21.223 33939 Z= 0.814 Chirality : 0.108 0.764 4566 Planarity : 0.006 0.034 4104 Dihedral : 18.523 107.169 11517 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 0.35 % Allowed : 0.94 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2880 helix: 1.17 (0.19), residues: 693 sheet: 0.14 (0.18), residues: 675 loop : 0.18 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP C 396 HIS 0.006 0.001 HIS A 236 PHE 0.024 0.004 PHE A 460 TYR 0.064 0.006 TYR A 114 ARG 0.006 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 529 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.7994 (m-80) cc_final: 0.7721 (m-80) REVERT: A 252 THR cc_start: 0.8447 (p) cc_final: 0.8124 (p) REVERT: A 621 ASN cc_start: 0.8192 (m-40) cc_final: 0.7989 (m110) REVERT: A 886 GLN cc_start: 0.8275 (mt0) cc_final: 0.8069 (mt0) REVERT: B 76 THR cc_start: 0.8874 (p) cc_final: 0.8617 (p) REVERT: B 770 VAL cc_start: 0.9263 (m) cc_final: 0.8898 (p) REVERT: C 76 THR cc_start: 0.9135 (p) cc_final: 0.8915 (p) REVERT: C 770 VAL cc_start: 0.9224 (m) cc_final: 0.8984 (p) outliers start: 9 outliers final: 7 residues processed: 538 average time/residue: 0.3608 time to fit residues: 303.1999 Evaluate side-chains 238 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 231 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 589 GLN A 712 GLN A 772 GLN A 808 ASN A 830 HIS B 168 HIS B 621 ASN B 712 GLN B 808 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS B 988 GLN C 168 HIS ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 712 GLN C 772 GLN C 808 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24888 Z= 0.269 Angle : 0.694 8.352 33939 Z= 0.345 Chirality : 0.047 0.201 4566 Planarity : 0.005 0.084 4104 Dihedral : 14.203 86.499 6527 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.77 % Allowed : 7.71 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.14 (0.16), residues: 2880 helix: 2.69 (0.20), residues: 669 sheet: 0.21 (0.19), residues: 666 loop : 0.23 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 396 HIS 0.011 0.001 HIS C 100 PHE 0.017 0.002 PHE A 930 TYR 0.014 0.001 TYR B 398 ARG 0.007 0.001 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8404 (mpt180) cc_final: 0.8037 (mmt-90) REVERT: A 388 MET cc_start: 0.8102 (mtt) cc_final: 0.7841 (mtt) REVERT: A 884 MET cc_start: 0.8474 (mmt) cc_final: 0.8186 (mmt) REVERT: B 191 LEU cc_start: 0.9034 (tp) cc_final: 0.8656 (mp) REVERT: B 1011 ASN cc_start: 0.7571 (t0) cc_final: 0.7292 (t0) outliers start: 45 outliers final: 26 residues processed: 314 average time/residue: 0.3595 time to fit residues: 176.6272 Evaluate side-chains 220 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 979 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 283 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 923 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24888 Z= 0.251 Angle : 0.647 11.738 33939 Z= 0.317 Chirality : 0.047 0.252 4566 Planarity : 0.004 0.079 4104 Dihedral : 10.942 80.147 6513 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.32 % Allowed : 8.93 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.18 (0.16), residues: 2880 helix: 2.95 (0.20), residues: 672 sheet: 0.15 (0.19), residues: 690 loop : 0.17 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 396 HIS 0.006 0.001 HIS A 100 PHE 0.016 0.002 PHE B 930 TYR 0.014 0.001 TYR A 468 ARG 0.006 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 212 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8382 (mpt180) cc_final: 0.8123 (mmt-90) REVERT: A 703 MET cc_start: 0.8169 (tpp) cc_final: 0.7939 (tpp) REVERT: A 982 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 718 MET cc_start: 0.7335 (ptm) cc_final: 0.7119 (ptp) REVERT: B 780 GLU cc_start: 0.7207 (tp30) cc_final: 0.6923 (tp30) REVERT: C 971 ASN cc_start: 0.7635 (t0) cc_final: 0.7424 (t0) outliers start: 59 outliers final: 29 residues processed: 258 average time/residue: 0.3169 time to fit residues: 135.2514 Evaluate side-chains 211 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 979 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.0970 chunk 196 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.0980 chunk 278 optimal weight: 0.0970 chunk 137 optimal weight: 0.0570 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 HIS A 808 ASN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 HIS B 923 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS C 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 24888 Z= 0.157 Angle : 0.571 9.119 33939 Z= 0.283 Chirality : 0.044 0.261 4566 Planarity : 0.004 0.078 4104 Dihedral : 9.215 73.148 6513 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.22 % Allowed : 10.47 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.08 (0.16), residues: 2880 helix: 2.70 (0.20), residues: 693 sheet: 0.18 (0.20), residues: 651 loop : 0.11 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 396 HIS 0.004 0.001 HIS A 236 PHE 0.014 0.001 PHE C 206 TYR 0.011 0.001 TYR A 696 ARG 0.006 0.000 ARG B 888 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 CYS cc_start: 0.6562 (m) cc_final: 0.6309 (m) REVERT: A 703 MET cc_start: 0.8130 (tpp) cc_final: 0.7829 (tpp) REVERT: A 733 THR cc_start: 0.8456 (p) cc_final: 0.8230 (p) REVERT: A 1011 ASN cc_start: 0.7717 (t0) cc_final: 0.7475 (t0) REVERT: B 780 GLU cc_start: 0.7153 (tp30) cc_final: 0.6910 (tp30) REVERT: C 388 MET cc_start: 0.8286 (mtp) cc_final: 0.8030 (mtp) REVERT: C 434 THR cc_start: 0.8729 (p) cc_final: 0.8514 (p) REVERT: C 971 ASN cc_start: 0.7682 (t0) cc_final: 0.7426 (t0) outliers start: 31 outliers final: 19 residues processed: 244 average time/residue: 0.3243 time to fit residues: 130.3692 Evaluate side-chains 206 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 979 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 142 optimal weight: 0.0670 chunk 249 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN A 808 ASN B 589 GLN B 758 GLN B 772 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN C 639 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 24888 Z= 0.447 Angle : 0.703 8.710 33939 Z= 0.347 Chirality : 0.048 0.275 4566 Planarity : 0.005 0.086 4104 Dihedral : 8.795 66.700 6513 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 11.29 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.71 (0.16), residues: 2880 helix: 2.30 (0.20), residues: 705 sheet: -0.02 (0.20), residues: 651 loop : -0.11 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 973 HIS 0.006 0.001 HIS A 168 PHE 0.025 0.002 PHE A 742 TYR 0.016 0.002 TYR A 259 ARG 0.008 0.001 ARG C 984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9104 (tp) cc_final: 0.8734 (mp) REVERT: A 292 ARG cc_start: 0.8589 (mpt180) cc_final: 0.8327 (mmt-90) REVERT: A 701 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8410 (ppt170) REVERT: A 703 MET cc_start: 0.8252 (tpp) cc_final: 0.7920 (tpp) REVERT: A 727 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8006 (tm-30) outliers start: 62 outliers final: 38 residues processed: 227 average time/residue: 0.3245 time to fit residues: 120.0587 Evaluate side-chains 189 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 979 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 278 optimal weight: 0.5980 chunk 231 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN B 621 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN C 176 ASN C 639 ASN C 917 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24888 Z= 0.207 Angle : 0.577 9.296 33939 Z= 0.286 Chirality : 0.045 0.283 4566 Planarity : 0.004 0.086 4104 Dihedral : 8.090 60.351 6513 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.65 % Allowed : 12.59 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.80 (0.16), residues: 2880 helix: 2.45 (0.20), residues: 708 sheet: 0.08 (0.21), residues: 648 loop : -0.13 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 973 HIS 0.003 0.001 HIS B 100 PHE 0.013 0.001 PHE C 206 TYR 0.011 0.001 TYR A 222 ARG 0.004 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8607 (ttp80) REVERT: A 703 MET cc_start: 0.8228 (tpp) cc_final: 0.7924 (tpp) REVERT: C 703 MET cc_start: 0.8270 (tpp) cc_final: 0.8034 (tpp) REVERT: C 854 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7320 (mt-10) outliers start: 42 outliers final: 34 residues processed: 222 average time/residue: 0.3217 time to fit residues: 117.1195 Evaluate side-chains 195 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 979 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24888 Z= 0.239 Angle : 0.588 10.341 33939 Z= 0.290 Chirality : 0.045 0.278 4566 Planarity : 0.004 0.084 4104 Dihedral : 7.633 59.774 6513 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.09 % Allowed : 12.99 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.76 (0.16), residues: 2880 helix: 2.48 (0.20), residues: 708 sheet: -0.03 (0.21), residues: 642 loop : -0.15 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 PHE 0.012 0.001 PHE B 577 TYR 0.010 0.001 TYR A 222 ARG 0.004 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 703 MET cc_start: 0.8248 (tpp) cc_final: 0.7948 (tpp) REVERT: A 936 LEU cc_start: 0.8831 (tt) cc_final: 0.8473 (mt) REVERT: C 703 MET cc_start: 0.8277 (tpp) cc_final: 0.8043 (tpp) REVERT: C 854 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 971 ASN cc_start: 0.7674 (t0) cc_final: 0.7466 (t0) outliers start: 53 outliers final: 42 residues processed: 212 average time/residue: 0.3310 time to fit residues: 113.5686 Evaluate side-chains 196 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 979 ASN Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.4980 chunk 110 optimal weight: 0.0040 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24888 Z= 0.200 Angle : 0.583 15.827 33939 Z= 0.285 Chirality : 0.044 0.272 4566 Planarity : 0.004 0.076 4104 Dihedral : 7.228 59.716 6513 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.09 % Allowed : 12.87 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.73 (0.16), residues: 2880 helix: 2.50 (0.20), residues: 708 sheet: -0.05 (0.21), residues: 642 loop : -0.19 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 973 HIS 0.003 0.001 HIS C 100 PHE 0.014 0.001 PHE B 577 TYR 0.010 0.001 TYR A 222 ARG 0.006 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 LEU cc_start: 0.8759 (tt) cc_final: 0.8470 (mt) REVERT: B 292 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7956 (mmt180) REVERT: C 703 MET cc_start: 0.8239 (tpp) cc_final: 0.8029 (tpp) REVERT: C 854 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7273 (mt-10) REVERT: C 971 ASN cc_start: 0.7618 (t0) cc_final: 0.7355 (t0) outliers start: 53 outliers final: 38 residues processed: 213 average time/residue: 0.3305 time to fit residues: 114.5155 Evaluate side-chains 195 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 979 ASN Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 233 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN B 715 ASN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24888 Z= 0.243 Angle : 0.598 17.402 33939 Z= 0.292 Chirality : 0.045 0.265 4566 Planarity : 0.004 0.073 4104 Dihedral : 6.950 59.476 6513 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.85 % Allowed : 13.30 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.16), residues: 2880 helix: 2.38 (0.20), residues: 726 sheet: -0.14 (0.21), residues: 612 loop : -0.24 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 973 HIS 0.004 0.001 HIS A 933 PHE 0.012 0.001 PHE A 742 TYR 0.010 0.001 TYR A 222 ARG 0.005 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 160 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.7221 (m-80) cc_final: 0.6969 (m-80) REVERT: A 936 LEU cc_start: 0.8772 (tt) cc_final: 0.8488 (mt) REVERT: B 292 ARG cc_start: 0.8171 (mmt180) cc_final: 0.7890 (mmt180) REVERT: C 854 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7277 (mt-10) outliers start: 47 outliers final: 40 residues processed: 199 average time/residue: 0.3441 time to fit residues: 111.8502 Evaluate side-chains 194 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 979 ASN Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24888 Z= 0.271 Angle : 0.607 13.999 33939 Z= 0.298 Chirality : 0.045 0.257 4566 Planarity : 0.004 0.072 4104 Dihedral : 6.786 58.983 6513 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 13.54 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.58 (0.16), residues: 2880 helix: 2.33 (0.20), residues: 726 sheet: -0.11 (0.21), residues: 642 loop : -0.32 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 PHE 0.018 0.001 PHE C 641 TYR 0.010 0.001 TYR A 222 ARG 0.005 0.000 ARG A 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.7264 (m-80) cc_final: 0.6984 (m-80) REVERT: A 936 LEU cc_start: 0.8796 (tt) cc_final: 0.8474 (mt) REVERT: B 292 ARG cc_start: 0.8344 (mmt180) cc_final: 0.8040 (mmt180) outliers start: 47 outliers final: 44 residues processed: 200 average time/residue: 0.3328 time to fit residues: 108.6932 Evaluate side-chains 192 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 979 ASN Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 69 optimal weight: 0.0670 chunk 210 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079065 restraints weight = 43154.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082567 restraints weight = 21618.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084805 restraints weight = 14459.986| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24888 Z= 0.206 Angle : 0.582 14.286 33939 Z= 0.286 Chirality : 0.044 0.254 4566 Planarity : 0.004 0.069 4104 Dihedral : 6.610 58.588 6513 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.89 % Allowed : 13.62 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.16), residues: 2880 helix: 2.55 (0.20), residues: 708 sheet: -0.10 (0.21), residues: 642 loop : -0.32 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 973 HIS 0.003 0.001 HIS C 100 PHE 0.014 0.001 PHE B 237 TYR 0.010 0.001 TYR A 222 ARG 0.005 0.000 ARG B 943 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.06 seconds wall clock time: 75 minutes 50.00 seconds (4550.00 seconds total)