Starting phenix.real_space_refine on Tue Feb 20 22:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/02_2024/6q05_20543_updated.pdb" } resolution = 2.8 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= 0.003 sd= 0.116 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 147 5.16 5 C 18168 2.51 5 N 4536 2.21 5 O 6126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 740": "OD1" <-> "OD2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 922": "OD1" <-> "OD2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1039": "OE1" <-> "OE2" Residue "B GLU 1090": "OE1" <-> "OE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1148": "OE1" <-> "OE2" Residue "B TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 216": "OD1" <-> "OD2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 664": "OD1" <-> "OD2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 740": "OD1" <-> "OD2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 922": "OD1" <-> "OD2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1039": "OE1" <-> "OE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28977 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "B" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "C" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" 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: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Time building chain proxies: 15.76, per 1000 atoms: 0.54 Number of scatterers: 28977 At special positions: 0 Unit cell: (151.2, 158.55, 160.65, 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 147 16.00 O 6126 8.00 N 4536 7.00 C 18168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.08 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.09 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.06 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.12 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.09 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.05 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.08 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.01 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.17 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.09 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.02 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.06 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.12 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.09 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.05 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.08 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.09 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.02 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.06 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.12 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.09 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " 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 ?2-3 " GAL N 2 " - " SIA N 3 " " GAL Y 2 " - " SIA Y 3 " " GAL j 2 " - " SIA j 3 " ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 6 " - " MAN Q 7 " " MAN b 4 " - " MAN b 5 " " MAN b 6 " - " MAN b 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 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 W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 6 " " BMA g 3 " - " MAN g 5 " " BMA h 3 " - " MAN h 5 " BETA1-3 " NAG N 1 " - " FUC N 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Y 1 " - " FUC Y 4 " " NAG j 1 " - " FUC j 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " GAL N 2 " " 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 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 Y 1 " - " GAL Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " GAL j 2 " NAG-ASN " NAG A1414 " - " ASN A 487 " " NAG A1415 " - " ASN A 592 " " NAG A1416 " - " ASN A 619 " " NAG A1417 " - " ASN A 719 " " NAG A1418 " - " ASN A 774 " " NAG A1419 " - " ASN A 785 " " NAG A1436 " - " ASN A 155 " " NAG B1414 " - " ASN B 487 " " NAG B1415 " - " ASN B 592 " " NAG B1416 " - " ASN B 619 " " NAG B1417 " - " ASN B 719 " " NAG B1418 " - " ASN B 774 " " NAG B1419 " - " ASN B 785 " " NAG B1436 " - " ASN B 155 " " NAG C1414 " - " ASN C 487 " " NAG C1415 " - " ASN C 592 " " NAG C1416 " - " ASN C 619 " " NAG C1417 " - " ASN C 719 " " NAG C1418 " - " ASN C 774 " " NAG C1419 " - " ASN C 785 " " NAG C1436 " - " ASN C 155 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 236 " " NAG F 1 " - " ASN A 410 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN A 66 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN A 125 " " NAG L 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 244 " " NAG O 1 " - " ASN B 222 " " NAG P 1 " - " ASN B 236 " " NAG Q 1 " - " ASN B 410 " " NAG R 1 " - " ASN B 870 " " NAG S 1 " - " ASN B1213 " " NAG T 1 " - " ASN B 66 " " NAG U 1 " - " ASN B 104 " " NAG V 1 " - " ASN B 125 " " NAG W 1 " - " ASN B 166 " " NAG X 1 " - " ASN B 244 " " NAG Z 1 " - " ASN C 222 " " NAG a 1 " - " ASN C 236 " " NAG b 1 " - " ASN C 410 " " NAG c 1 " - " ASN C 870 " " NAG d 1 " - " ASN C1213 " " NAG e 1 " - " ASN C 66 " " NAG f 1 " - " ASN C 104 " " NAG g 1 " - " ASN C 125 " " NAG h 1 " - " ASN C 166 " " NAG i 1 " - " ASN C 244 " Time building additional restraints: 14.18 Conformation dependent library (CDL) restraints added in 6.0 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB FOL A1444 " pdb=" CB FOL B1444 " pdb=" CB FOL C1444 " Number of C-beta restraints generated: 6456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 60 sheets defined 23.4% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 210 through 213 No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.854A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 343 through 350 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.471A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 450 through 456 removed outlier: 5.380A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 525 through 528 removed outlier: 3.918A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 525 through 528' Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 806 through 811 Processing helix chain 'A' and resid 815 through 824 removed outlier: 4.329A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 853 removed outlier: 3.792A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.679A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.844A pdb=" N ALA A 930 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 958 removed outlier: 4.916A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.632A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.921A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1041 removed outlier: 4.173A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1060 through 1106 removed outlier: 4.318A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 210 through 213 No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.854A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 411 through 417 removed outlier: 4.471A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 450 through 456 removed outlier: 5.380A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 525 through 528 removed outlier: 3.918A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 525 through 528' Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 815 through 824 removed outlier: 4.329A pdb=" N GLU B 823 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 853 removed outlier: 3.792A pdb=" N GLN B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 896 Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.680A pdb=" N MET B 913 " --> pdb=" O TYR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.844A pdb=" N ALA B 930 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 958 removed outlier: 4.916A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 983 removed outlier: 3.631A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 992 Processing helix chain 'B' and resid 994 through 1008 removed outlier: 3.921A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1041 removed outlier: 4.173A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1057 Processing helix chain 'B' and resid 1060 through 1106 removed outlier: 4.318A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 210 through 213 No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.855A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 411 through 417 removed outlier: 4.470A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 450 through 456 removed outlier: 5.380A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 525 through 528 removed outlier: 3.918A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 525 through 528' Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 815 through 824 removed outlier: 4.329A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 853 removed outlier: 3.792A pdb=" N GLN C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 896 Processing helix chain 'C' and resid 908 through 914 removed outlier: 3.680A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.844A pdb=" N ALA C 930 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 958 removed outlier: 4.916A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 983 removed outlier: 3.632A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 994 through 1008 removed outlier: 3.921A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1041 removed outlier: 4.174A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1057 Processing helix chain 'C' and resid 1060 through 1106 removed outlier: 4.318A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.347A pdb=" N LEU A 100 " --> pdb=" O ASP A 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.040A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.006A pdb=" N PHE A 239 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 186 through 189 Processing sheet with id= F, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.836A pdb=" N HIS A 208 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 359 through 363 removed outlier: 4.571A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 373 through 376 removed outlier: 7.747A pdb=" N VAL A 374 " --> pdb=" O CYS A 603 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU A 605 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLU A 376 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 607 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 407 through 409 Processing sheet with id= K, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.192A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 735 through 738 removed outlier: 7.774A pdb=" N SER A 761 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 722 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 777 through 782 Processing sheet with id= N, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 6.012A pdb=" N GLN A1212 " --> pdb=" O CYS A1156 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'A' and resid 1164 through 1167 removed outlier: 4.072A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id= S, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 153 through 155 Processing sheet with id= U, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.347A pdb=" N LEU B 100 " --> pdb=" O ASP B 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 292 through 295 removed outlier: 4.006A pdb=" N PHE B 239 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 186 through 189 Processing sheet with id= Z, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.835A pdb=" N HIS B 208 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 359 through 363 removed outlier: 4.571A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 373 through 376 removed outlier: 7.748A pdb=" N VAL B 374 " --> pdb=" O CYS B 603 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU B 605 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLU B 376 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER B 607 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 407 through 409 Processing sheet with id= AE, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.192A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 735 through 738 removed outlier: 7.774A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 777 through 782 Processing sheet with id= AH, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 1155 through 1157 removed outlier: 6.012A pdb=" N GLN B1212 " --> pdb=" O CYS B1156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 4.072A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 1170 through 1173 Processing sheet with id= AM, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= AO, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.346A pdb=" N LEU C 100 " --> pdb=" O ASP C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.040A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 292 through 295 removed outlier: 4.006A pdb=" N PHE C 239 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 186 through 189 Processing sheet with id= AT, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.837A pdb=" N HIS C 208 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 359 through 363 removed outlier: 4.571A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 373 through 376 removed outlier: 7.747A pdb=" N VAL C 374 " --> pdb=" O CYS C 603 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU C 605 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLU C 376 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER C 607 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= AY, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.192A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'C' and resid 735 through 738 removed outlier: 7.773A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 777 through 782 Processing sheet with id= BB, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.925A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'C' and resid 1155 through 1157 removed outlier: 6.012A pdb=" N GLN C1212 " --> pdb=" O CYS C1156 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'C' and resid 1164 through 1167 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'C' and resid 1170 through 1173 Processing sheet with id= BG, first strand: chain 'C' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'C' and resid 153 through 155 987 hydrogen bonds defined for protein. 2709 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: 14.39 Time building geometry restraints manager: 14.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 3 1.06 - 1.26: 4512 1.26 - 1.46: 12164 1.46 - 1.66: 12526 1.66 - 1.85: 216 Bond restraints: 29421 Sorted by residual: bond pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 1.234 0.866 0.368 1.22e-02 6.72e+03 9.12e+02 bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.866 0.368 1.22e-02 6.72e+03 9.11e+02 bond pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.09e+02 bond pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 1.331 1.558 -0.227 1.43e-02 4.89e+03 2.53e+02 bond pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 1.331 1.558 -0.227 1.43e-02 4.89e+03 2.52e+02 ... (remaining 29416 not shown) Histogram of bond angle deviations from ideal: 94.04 - 105.16: 920 105.16 - 116.28: 19383 116.28 - 127.40: 19551 127.40 - 138.53: 187 138.53 - 149.65: 6 Bond angle restraints: 40047 Sorted by residual: angle pdb=" N ASN B 199 " pdb=" CA ASN B 199 " pdb=" C ASN B 199 " ideal model delta sigma weight residual 111.07 149.65 -38.58 1.07e+00 8.73e-01 1.30e+03 angle pdb=" N ASN A 199 " pdb=" CA ASN A 199 " pdb=" C ASN A 199 " ideal model delta sigma weight residual 111.07 149.63 -38.56 1.07e+00 8.73e-01 1.30e+03 angle pdb=" N ASN C 199 " pdb=" CA ASN C 199 " pdb=" C ASN C 199 " ideal model delta sigma weight residual 111.07 149.59 -38.52 1.07e+00 8.73e-01 1.30e+03 angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.33 -21.41 1.15e+00 7.56e-01 3.46e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.30 -21.38 1.15e+00 7.56e-01 3.46e+02 ... (remaining 40042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 18607 26.83 - 53.66: 419 53.66 - 80.50: 138 80.50 - 107.33: 120 107.33 - 134.16: 33 Dihedral angle restraints: 19317 sinusoidal: 9201 harmonic: 10116 Sorted by residual: dihedral pdb=" N ASN A 199 " pdb=" C ASN A 199 " pdb=" CA ASN A 199 " pdb=" CB ASN A 199 " ideal model delta harmonic sigma weight residual 122.80 153.67 -30.87 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CA ASN B 199 " pdb=" CB ASN B 199 " ideal model delta harmonic sigma weight residual 122.80 153.67 -30.87 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N ASN C 199 " pdb=" C ASN C 199 " pdb=" CA ASN C 199 " pdb=" CB ASN C 199 " ideal model delta harmonic sigma weight residual 122.80 153.61 -30.81 0 2.50e+00 1.60e-01 1.52e+02 ... (remaining 19314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4810 0.390 - 0.780: 68 0.780 - 1.170: 6 1.170 - 1.560: 0 1.560 - 1.950: 6 Chirality restraints: 4890 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 3.01 -0.61 2.00e-02 2.50e+03 9.34e+02 chirality pdb=" C1 MAN g 4 " pdb=" O3 BMA g 3 " pdb=" C2 MAN g 4 " pdb=" O5 MAN g 4 " both_signs ideal model delta sigma weight residual False 2.40 2.80 -0.40 2.00e-02 2.50e+03 4.00e+02 chirality pdb=" C1 MAN V 5 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 5 " pdb=" O5 MAN V 5 " both_signs ideal model delta sigma weight residual False 2.40 2.78 -0.38 2.00e-02 2.50e+03 3.57e+02 ... (remaining 4887 not shown) Planarity restraints: 5025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR B 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR A 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 777 " 0.078 2.00e-02 2.50e+03 4.32e-02 3.73e+01 pdb=" CG TYR C 777 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 777 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 777 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5022 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7459 2.78 - 3.31: 26420 3.31 - 3.84: 52014 3.84 - 4.37: 63750 4.37 - 4.90: 101928 Nonbonded interactions: 251571 Sorted by model distance: nonbonded pdb=" O5 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.255 2.432 nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.255 2.432 nonbonded pdb=" O5 BMA g 3 " pdb=" O6 BMA g 3 " model vdw 2.255 2.432 nonbonded pdb=" NE2 GLN B 304 " pdb=" O6 NAG Y 1 " model vdw 2.277 2.520 nonbonded pdb=" NE2 GLN C 304 " pdb=" O6 NAG j 1 " model vdw 2.277 2.520 ... (remaining 251566 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' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'N' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'O' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'Y' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'Z' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'j' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'i' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'c' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'V' selection = chain 'W' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.770 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: 0.000 Extract box with map and model: 12.620 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 84.580 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.400 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:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.025 0.368 29421 Z= 1.645 Angle : 2.064 38.578 40047 Z= 1.327 Chirality : 0.156 1.950 4890 Planarity : 0.009 0.048 4974 Dihedral : 15.796 134.160 12708 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.91 % Allowed : 1.41 % Favored : 97.68 % Cbeta Deviations : 0.84 % 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: 0.58 (0.13), residues: 3447 helix: -0.49 (0.17), residues: 678 sheet: 0.67 (0.17), residues: 846 loop : 0.78 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A1184 HIS 0.009 0.003 HIS B 264 PHE 0.050 0.006 PHE B 473 TYR 0.079 0.011 TYR A 184 ARG 0.012 0.002 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 585 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 GLN cc_start: 0.7783 (mt0) cc_final: 0.7531 (mt0) REVERT: A 849 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8775 (tp) REVERT: B 427 GLN cc_start: 0.7639 (mt0) cc_final: 0.7326 (mt0) REVERT: B 521 ASN cc_start: 0.8383 (m-40) cc_final: 0.8059 (m110) REVERT: B 766 HIS cc_start: 0.7671 (m90) cc_final: 0.7463 (m170) REVERT: B 994 GLN cc_start: 0.7398 (mt0) cc_final: 0.7195 (mt0) REVERT: C 505 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7815 (mtm180) REVERT: C 539 ASP cc_start: 0.8332 (m-30) cc_final: 0.7960 (m-30) REVERT: C 576 GLN cc_start: 0.7654 (mt0) cc_final: 0.7425 (mp10) REVERT: C 849 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8673 (tp) outliers start: 27 outliers final: 4 residues processed: 600 average time/residue: 1.2948 time to fit residues: 916.0679 Evaluate side-chains 342 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1097 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 313 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 466 GLN A 812 ASN A 815 GLN A 819 GLN A1063 GLN A1163 ASN A1169 ASN A1208 GLN B 261 GLN B 280 GLN B 466 GLN B 521 ASN B 708 GLN B 812 ASN B 833 GLN B 974 GLN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 GLN B1169 ASN B1208 GLN C 261 GLN C 280 GLN C 436 ASN C 466 GLN C 766 HIS C 812 ASN C 815 GLN C 833 GLN C1056 GLN C1063 GLN C1208 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29421 Z= 0.278 Angle : 0.714 9.101 40047 Z= 0.363 Chirality : 0.048 0.233 4890 Planarity : 0.004 0.033 4974 Dihedral : 12.969 112.642 6689 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.76 % Allowed : 8.13 % Favored : 89.11 % Cbeta Deviations : 0.09 % 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: 0.63 (0.13), residues: 3447 helix: 0.91 (0.20), residues: 693 sheet: 0.51 (0.17), residues: 843 loop : 0.32 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 960 HIS 0.004 0.001 HIS C 167 PHE 0.023 0.002 PHE B 473 TYR 0.027 0.002 TYR A 909 ARG 0.007 0.001 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 419 time to evaluate : 3.343 Fit side-chains revert: symmetry clash REVERT: A 158 ASP cc_start: 0.7009 (p0) cc_final: 0.6794 (m-30) REVERT: A 193 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: A 652 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6901 (mtt-85) REVERT: A 719 ASN cc_start: 0.7012 (t0) cc_final: 0.6741 (t0) REVERT: A 1039 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: A 1112 LYS cc_start: 0.7860 (mttp) cc_final: 0.7405 (mppt) REVERT: B 413 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7958 (mttm) REVERT: B 427 GLN cc_start: 0.7655 (mt0) cc_final: 0.7409 (mt0) REVERT: B 849 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8735 (tt) REVERT: B 1105 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: B 1112 LYS cc_start: 0.7542 (mttp) cc_final: 0.7237 (mptt) REVERT: C 536 GLU cc_start: 0.7158 (pt0) cc_final: 0.6855 (pt0) REVERT: C 539 ASP cc_start: 0.8425 (m-30) cc_final: 0.8141 (m-30) REVERT: C 576 GLN cc_start: 0.7522 (mt0) cc_final: 0.7181 (mp10) REVERT: C 605 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 618 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: C 738 LEU cc_start: 0.8094 (tp) cc_final: 0.7728 (mm) REVERT: C 1039 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: C 1056 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7345 (tt0) outliers start: 82 outliers final: 25 residues processed: 476 average time/residue: 1.2671 time to fit residues: 718.2671 Evaluate side-chains 343 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 310 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 1039 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 260 optimal weight: 0.0070 chunk 213 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 311 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 681 HIS A 792 GLN A 819 GLN A1145 ASN A1160 ASN B 599 GLN B 708 GLN B 815 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 36 GLN C 408 ASN C 708 GLN C 766 HIS C 812 ASN C1145 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29421 Z= 0.187 Angle : 0.598 8.955 40047 Z= 0.301 Chirality : 0.044 0.187 4890 Planarity : 0.004 0.039 4974 Dihedral : 10.732 93.522 6680 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 10.01 % Favored : 86.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.57 (0.14), residues: 3447 helix: 1.20 (0.20), residues: 702 sheet: 0.35 (0.16), residues: 843 loop : 0.19 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.003 0.001 HIS B 681 PHE 0.015 0.001 PHE B 473 TYR 0.020 0.001 TYR B 909 ARG 0.003 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 355 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 ASN cc_start: 0.6975 (t0) cc_final: 0.6697 (t0) REVERT: A 892 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: A 1039 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 1069 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7413 (ttp80) REVERT: A 1105 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: A 1112 LYS cc_start: 0.7830 (mttp) cc_final: 0.7418 (mppt) REVERT: B 161 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6695 (mmt) REVERT: B 193 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7531 (m-40) REVERT: B 207 TYR cc_start: 0.8384 (p90) cc_final: 0.8067 (p90) REVERT: B 413 LYS cc_start: 0.8308 (ttmm) cc_final: 0.8092 (mttm) REVERT: B 427 GLN cc_start: 0.7902 (mt0) cc_final: 0.7670 (mt0) REVERT: B 849 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8737 (tt) REVERT: B 1112 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7202 (mppt) REVERT: C 288 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: C 605 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 618 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: C 848 ASN cc_start: 0.7992 (t0) cc_final: 0.7717 (t0) REVERT: C 892 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: C 912 CYS cc_start: 0.5412 (m) cc_final: 0.5022 (t) outliers start: 91 outliers final: 34 residues processed: 419 average time/residue: 1.2504 time to fit residues: 625.4896 Evaluate side-chains 351 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 306 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1039 GLU Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN A 819 GLN A1132 ASN B 708 GLN B 815 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN B1169 ASN C 111 GLN C 261 GLN C 708 GLN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 GLN C1063 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 29421 Z= 0.488 Angle : 0.759 10.682 40047 Z= 0.386 Chirality : 0.051 0.268 4890 Planarity : 0.005 0.053 4974 Dihedral : 9.919 89.159 6680 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.23 % Allowed : 9.85 % Favored : 85.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.06 (0.13), residues: 3447 helix: 0.90 (0.19), residues: 708 sheet: 0.13 (0.17), residues: 816 loop : -0.25 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 535 HIS 0.008 0.002 HIS C1138 PHE 0.021 0.003 PHE B 116 TYR 0.017 0.003 TYR A 909 ARG 0.006 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 334 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7803 (mttt) REVERT: A 60 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: A 108 ASP cc_start: 0.6606 (t0) cc_final: 0.6300 (t70) REVERT: A 193 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7454 (m-40) REVERT: A 719 ASN cc_start: 0.7051 (t0) cc_final: 0.6838 (t0) REVERT: A 849 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 892 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6907 (m-30) REVERT: A 1105 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: A 1112 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7455 (mppt) REVERT: B 60 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: B 193 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7769 (m-40) REVERT: B 427 GLN cc_start: 0.8126 (mt0) cc_final: 0.7848 (mt0) REVERT: B 450 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 849 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8811 (tt) REVERT: B 887 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7704 (mtm180) REVERT: B 892 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6968 (m-30) REVERT: B 1105 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7144 (tp30) REVERT: B 1112 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7510 (mptt) REVERT: C 60 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: C 652 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7136 (mtt-85) REVERT: C 849 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8883 (tp) REVERT: C 892 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6820 (m-30) outliers start: 126 outliers final: 58 residues processed: 423 average time/residue: 1.1642 time to fit residues: 597.2206 Evaluate side-chains 389 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 991 SER Chi-restraints excluded: chain C residue 992 GLU Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 84 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 GLN A 993 ASN A1119 GLN B 708 GLN B 819 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 261 GLN C 599 GLN C 708 GLN C 765 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29421 Z= 0.214 Angle : 0.603 8.901 40047 Z= 0.302 Chirality : 0.045 0.237 4890 Planarity : 0.004 0.045 4974 Dihedral : 8.644 85.332 6678 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.49 % Allowed : 11.29 % Favored : 85.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3447 helix: 1.22 (0.20), residues: 711 sheet: 0.11 (0.17), residues: 831 loop : -0.19 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 535 HIS 0.002 0.001 HIS B 348 PHE 0.021 0.001 PHE A 786 TYR 0.017 0.001 TYR C 909 ARG 0.003 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 329 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7750 (mttt) REVERT: A 161 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6898 (mmt) REVERT: A 193 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (m-40) REVERT: A 542 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7594 (mtt-85) REVERT: A 719 ASN cc_start: 0.7007 (t0) cc_final: 0.6807 (t0) REVERT: A 1019 PHE cc_start: 0.8437 (t80) cc_final: 0.8231 (t80) REVERT: A 1105 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: A 1112 LYS cc_start: 0.7826 (mttp) cc_final: 0.7441 (mppt) REVERT: B 193 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7619 (m-40) REVERT: B 207 TYR cc_start: 0.8259 (p90) cc_final: 0.7813 (p90) REVERT: B 450 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 757 MET cc_start: 0.7965 (mtt) cc_final: 0.7706 (mtt) REVERT: B 841 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7030 (tpt170) REVERT: B 849 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (tt) REVERT: B 1112 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7396 (mptt) REVERT: C 179 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8975 (pt) REVERT: C 533 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 618 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7381 (mt0) outliers start: 104 outliers final: 45 residues processed: 411 average time/residue: 1.1937 time to fit residues: 601.7363 Evaluate side-chains 364 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 307 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 991 SER Chi-restraints excluded: chain C residue 992 GLU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 195 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 277 optimal weight: 0.0060 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 175 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 GLN A 993 ASN A1119 GLN B 819 GLN B 842 GLN B1169 ASN C 261 GLN C 637 ASN C 708 GLN C 765 ASN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1056 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29421 Z= 0.177 Angle : 0.569 8.285 40047 Z= 0.282 Chirality : 0.044 0.230 4890 Planarity : 0.004 0.043 4974 Dihedral : 7.778 82.688 6678 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.23 % Allowed : 12.13 % Favored : 84.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.27 (0.14), residues: 3447 helix: 1.36 (0.20), residues: 717 sheet: 0.10 (0.17), residues: 843 loop : -0.16 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.002 0.001 HIS B 167 PHE 0.027 0.001 PHE A 786 TYR 0.013 0.001 TYR C 909 ARG 0.004 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 333 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: A 161 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6892 (mmt) REVERT: A 193 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: A 261 GLN cc_start: 0.8276 (mt0) cc_final: 0.8032 (mt0) REVERT: A 352 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: A 542 ARG cc_start: 0.7884 (ptp90) cc_final: 0.7608 (mtt-85) REVERT: A 849 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 892 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: A 1105 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7107 (tp30) REVERT: A 1112 LYS cc_start: 0.7818 (mttp) cc_final: 0.7461 (mptt) REVERT: B 193 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7579 (m-40) REVERT: B 450 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8183 (mm) REVERT: B 722 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6737 (mt) REVERT: B 841 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6952 (tpt170) REVERT: B 849 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 1112 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7432 (mptt) REVERT: C 104 ASN cc_start: 0.7539 (p0) cc_final: 0.7291 (p0) REVERT: C 179 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8954 (pt) REVERT: C 533 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 618 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: C 652 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7109 (mtt-85) REVERT: C 892 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: C 1056 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7426 (tt0) outliers start: 96 outliers final: 32 residues processed: 398 average time/residue: 1.1326 time to fit residues: 547.0393 Evaluate side-chains 364 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 313 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 992 GLU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 0.0970 chunk 186 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 521 ASN A 819 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1119 GLN B 348 HIS B 576 GLN B1042 ASN B1169 ASN B1208 GLN C 348 HIS C 708 GLN C 765 ASN C 833 GLN C 842 GLN C1056 GLN C1072 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29421 Z= 0.301 Angle : 0.628 9.385 40047 Z= 0.314 Chirality : 0.046 0.262 4890 Planarity : 0.004 0.045 4974 Dihedral : 7.802 84.666 6678 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.63 % Allowed : 11.86 % Favored : 84.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3447 helix: 1.32 (0.20), residues: 711 sheet: 0.11 (0.17), residues: 810 loop : -0.29 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS C1138 PHE 0.030 0.002 PHE A 786 TYR 0.028 0.002 TYR B 909 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 309 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7846 (mttt) REVERT: A 193 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: A 542 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7521 (mtt-85) REVERT: A 849 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8644 (tp) REVERT: A 892 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: A 1105 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: A 1112 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7434 (mptt) REVERT: B 60 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5969 (mp10) REVERT: B 450 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8199 (mm) REVERT: B 722 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6850 (mt) REVERT: B 841 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6911 (tpt170) REVERT: B 849 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 892 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: B 1062 GLU cc_start: 0.7423 (tp30) cc_final: 0.7218 (mm-30) REVERT: B 1084 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7631 (mm-40) REVERT: B 1105 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: C 60 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6280 (mp-120) REVERT: C 104 ASN cc_start: 0.7473 (p0) cc_final: 0.7261 (p0) REVERT: C 179 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8990 (pt) REVERT: C 193 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7462 (m-40) REVERT: C 533 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8005 (p) REVERT: C 618 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: C 652 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6977 (mtt-85) REVERT: C 892 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: C 1105 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7221 (tp30) outliers start: 108 outliers final: 57 residues processed: 390 average time/residue: 1.1785 time to fit residues: 557.7302 Evaluate side-chains 377 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 298 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 164 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 819 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN B 708 GLN B 819 GLN B1042 ASN B1169 ASN C 708 GLN C 765 ASN C 993 ASN C1072 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29421 Z= 0.218 Angle : 0.591 10.730 40047 Z= 0.293 Chirality : 0.045 0.598 4890 Planarity : 0.004 0.044 4974 Dihedral : 7.439 83.812 6678 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.23 % Allowed : 12.80 % Favored : 83.97 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.10 (0.14), residues: 3447 helix: 1.19 (0.20), residues: 735 sheet: 0.06 (0.17), residues: 810 loop : -0.31 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.004 0.001 HIS A 348 PHE 0.033 0.001 PHE A 786 TYR 0.025 0.001 TYR B 909 ARG 0.002 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 315 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6367 (mp10) REVERT: A 161 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6901 (mmt) REVERT: A 193 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: A 542 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7521 (mtt-85) REVERT: A 849 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 892 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: A 1105 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: A 1112 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7443 (mptt) REVERT: B 207 TYR cc_start: 0.8271 (p90) cc_final: 0.7847 (p90) REVERT: B 450 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 722 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6823 (mt) REVERT: B 841 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6917 (tpt170) REVERT: B 849 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 1084 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: B 1105 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: C 37 GLN cc_start: 0.7954 (tp40) cc_final: 0.7637 (tp-100) REVERT: C 179 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8971 (pt) REVERT: C 533 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 618 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7275 (mt0) REVERT: C 652 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7063 (mtt-85) REVERT: C 892 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: C 1105 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7173 (tp30) outliers start: 96 outliers final: 49 residues processed: 391 average time/residue: 1.1526 time to fit residues: 546.5994 Evaluate side-chains 374 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 306 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 290 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 280 optimal weight: 0.0770 chunk 293 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 GLN A 842 GLN A 993 ASN B 708 GLN B 819 GLN B1169 ASN C 708 GLN C 765 ASN C 993 ASN C1072 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29421 Z= 0.206 Angle : 0.582 11.583 40047 Z= 0.289 Chirality : 0.044 0.403 4890 Planarity : 0.004 0.044 4974 Dihedral : 7.230 83.108 6678 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.79 % Allowed : 13.47 % Favored : 83.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3447 helix: 1.34 (0.20), residues: 729 sheet: 0.07 (0.18), residues: 786 loop : -0.30 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.003 0.001 HIS B 348 PHE 0.033 0.001 PHE A 786 TYR 0.021 0.001 TYR B 909 ARG 0.002 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 316 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: A 161 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6907 (mmt) REVERT: A 193 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: A 849 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 892 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: A 1105 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: A 1112 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7439 (mptt) REVERT: B 207 TYR cc_start: 0.8303 (p90) cc_final: 0.7865 (p90) REVERT: B 450 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 722 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6782 (mt) REVERT: B 841 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6955 (tpt170) REVERT: B 849 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8762 (tt) REVERT: B 1084 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7618 (mm-40) REVERT: B 1105 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: C 37 GLN cc_start: 0.7936 (tp40) cc_final: 0.7695 (tp-100) REVERT: C 179 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8966 (pt) REVERT: C 193 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: C 533 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8003 (p) REVERT: C 618 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: C 652 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7216 (mmt-90) REVERT: C 892 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: C 1105 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7158 (tp30) outliers start: 83 outliers final: 50 residues processed: 382 average time/residue: 1.1969 time to fit residues: 555.9672 Evaluate side-chains 373 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 303 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 343 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 273 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 211 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 708 GLN A 819 GLN A 993 ASN A1208 GLN B 708 GLN B 819 GLN B1042 ASN B1169 ASN C 708 GLN C 765 ASN C1072 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29421 Z= 0.229 Angle : 0.595 13.592 40047 Z= 0.298 Chirality : 0.047 1.096 4890 Planarity : 0.004 0.044 4974 Dihedral : 7.159 83.355 6678 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.72 % Allowed : 13.74 % Favored : 83.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.15 (0.14), residues: 3447 helix: 1.34 (0.20), residues: 729 sheet: 0.06 (0.18), residues: 786 loop : -0.31 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.004 0.001 HIS A 348 PHE 0.034 0.002 PHE A 786 TYR 0.019 0.001 TYR B 909 ARG 0.002 0.000 ARG B 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 311 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: A 161 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6912 (mmt) REVERT: A 193 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (m-40) REVERT: A 849 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 892 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 1105 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: A 1112 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7442 (mptt) REVERT: B 207 TYR cc_start: 0.8316 (p90) cc_final: 0.7898 (p90) REVERT: B 450 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8188 (mm) REVERT: B 841 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6892 (tpt170) REVERT: B 849 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8762 (tt) REVERT: B 1084 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7623 (mm-40) REVERT: B 1105 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: C 37 GLN cc_start: 0.7924 (tp40) cc_final: 0.7671 (tp-100) REVERT: C 179 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8976 (pt) REVERT: C 193 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: C 533 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8007 (p) REVERT: C 548 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7675 (tt) REVERT: C 618 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: C 652 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7029 (mtt-85) REVERT: C 892 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: C 1105 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7171 (tp30) outliers start: 81 outliers final: 54 residues processed: 375 average time/residue: 1.1765 time to fit residues: 542.1336 Evaluate side-chains 382 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 GLN A 819 GLN A 993 ASN B 708 GLN B 819 GLN B1097 GLN B1169 ASN C 708 GLN C 765 ASN C1042 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.141323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.116088 restraints weight = 31135.270| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.61 r_work: 0.2977 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 29421 Z= 0.426 Angle : 0.704 11.954 40047 Z= 0.356 Chirality : 0.050 0.703 4890 Planarity : 0.005 0.047 4974 Dihedral : 7.941 88.542 6678 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.89 % Allowed : 13.78 % Favored : 83.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.07 (0.13), residues: 3447 helix: 1.10 (0.19), residues: 711 sheet: 0.09 (0.18), residues: 771 loop : -0.49 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 253 HIS 0.008 0.001 HIS A 348 PHE 0.036 0.003 PHE A 786 TYR 0.016 0.002 TYR B 909 ARG 0.005 0.001 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10115.70 seconds wall clock time: 182 minutes 8.85 seconds (10928.85 seconds total)