Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 12 10:03:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/05_2023/6q05_20543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/05_2023/6q05_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_20543/05_2023/6q05_20543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/05_2023/6q05_20543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/05_2023/6q05_20543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q05_20543/05_2023/6q05_20543_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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 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 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 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 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 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 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 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: 14.57, per 1000 atoms: 0.50 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 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 " ALPHA2-3 " GAL N 2 " - " SIA N 3 " " GAL Y 2 " - " SIA Y 3 " " GAL j 2 " - " SIA j 3 " 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: 14.46 Conformation dependent library (CDL) restraints added in 4.2 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: 4.96 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: 13.89 Time building geometry restraints manager: 15.17 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: 16060 26.83 - 53.66: 269 53.66 - 80.50: 78 80.50 - 107.33: 18 107.33 - 134.16: 3 Dihedral angle restraints: 16428 sinusoidal: 6312 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 16425 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.400 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 77.640 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.380 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: 0.000 Load rotamer database and sin/cos tables:16.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.010 ------------------------------------------------------------------------------- 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 : 11.499 134.160 9819 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 % 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 *********************** 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 : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 4 residues processed: 600 average time/residue: 1.3308 time to fit residues: 943.1278 Evaluate side-chains 337 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 333 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.3865 time to fit residues: 5.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 164 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 313 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 708 GLN B 766 HIS B 812 ASN B 833 GLN B 974 GLN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN B1208 GLN C 261 GLN C 280 GLN C 436 ASN C 466 GLN C 766 HIS C 815 GLN C 833 GLN C1056 GLN C1063 GLN C1169 ASN C1208 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 29421 Z= 0.273 Angle : 0.701 8.897 40047 Z= 0.359 Chirality : 0.046 0.223 4890 Planarity : 0.004 0.033 4974 Dihedral : 6.344 114.439 3789 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.52 % 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: 0.68 (0.14), residues: 3447 helix: 0.97 (0.20), residues: 693 sheet: 0.53 (0.17), residues: 843 loop : 0.35 (0.13), residues: 1911 *********************** 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 491 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 416 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 23 residues processed: 467 average time/residue: 1.2753 time to fit residues: 710.3925 Evaluate side-chains 338 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 315 time to evaluate : 3.092 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.2701 time to fit residues: 7.4935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 260 optimal weight: 0.0270 chunk 213 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 311 optimal weight: 0.0570 chunk 107 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 194 HIS A 261 GLN A 681 HIS A 708 GLN A 792 GLN A 819 GLN A 833 GLN A1145 ASN A1160 ASN B 36 GLN B 599 GLN B 708 GLN B 815 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN B 974 GLN B1097 GLN 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 29421 Z= 0.205 Angle : 0.590 8.591 40047 Z= 0.302 Chirality : 0.043 0.180 4890 Planarity : 0.004 0.040 4974 Dihedral : 5.589 92.194 3789 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 3.46 % 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: 0.56 (0.14), residues: 3447 helix: 1.22 (0.20), residues: 702 sheet: 0.28 (0.16), residues: 873 loop : 0.21 (0.14), residues: 1872 *********************** 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 460 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 357 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 43 residues processed: 423 average time/residue: 1.2180 time to fit residues: 620.0369 Evaluate side-chains 350 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 307 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 35 residues processed: 9 average time/residue: 0.5957 time to fit residues: 11.9063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 149 optimal weight: 1.9990 chunk 210 optimal weight: 0.0040 chunk 314 optimal weight: 0.0980 chunk 333 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 A1084 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN B1169 ASN C 261 GLN C 708 GLN C 842 GLN C 927 GLN C1063 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 29421 Z= 0.283 Angle : 0.621 10.240 40047 Z= 0.317 Chirality : 0.044 0.250 4890 Planarity : 0.004 0.046 4974 Dihedral : 5.623 76.817 3789 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 3.70 % 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: 0.36 (0.14), residues: 3447 helix: 1.14 (0.20), residues: 720 sheet: 0.23 (0.16), residues: 867 loop : -0.02 (0.14), residues: 1860 *********************** 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 447 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 337 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 61 residues processed: 417 average time/residue: 1.1489 time to fit residues: 585.2957 Evaluate side-chains 379 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 318 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 46 residues processed: 15 average time/residue: 0.5888 time to fit residues: 16.7961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 4 optimal weight: 0.2980 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 GLN A 819 GLN A1119 GLN B 708 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN B1169 ASN C 261 GLN C 708 GLN C 765 ASN C1072 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3357 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= 0.203 Angle : 0.568 8.585 40047 Z= 0.288 Chirality : 0.043 0.213 4890 Planarity : 0.004 0.045 4974 Dihedral : 5.311 65.808 3789 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 3.12 % 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: 0.34 (0.14), residues: 3447 helix: 1.27 (0.20), residues: 720 sheet: 0.17 (0.17), residues: 873 loop : -0.07 (0.14), residues: 1854 *********************** 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 423 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 330 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 52 residues processed: 405 average time/residue: 1.1630 time to fit residues: 574.7668 Evaluate side-chains 362 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 310 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 6 average time/residue: 0.4316 time to fit residues: 8.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3543 > 50: distance: 50 - 72: 9.914 distance: 56 - 83: 9.191 distance: 60 - 88: 5.242 distance: 66 - 72: 7.808 distance: 67 - 94: 5.097 distance: 72 - 73: 15.101 distance: 73 - 74: 17.992 distance: 73 - 76: 25.690 distance: 74 - 75: 27.946 distance: 74 - 83: 12.676 distance: 76 - 77: 18.516 distance: 77 - 78: 5.984 distance: 77 - 79: 4.787 distance: 78 - 80: 6.027 distance: 79 - 81: 3.761 distance: 80 - 82: 5.077 distance: 81 - 82: 4.247 distance: 83 - 84: 19.591 distance: 84 - 85: 7.047 distance: 84 - 87: 9.283 distance: 85 - 86: 4.675 distance: 85 - 88: 9.267 distance: 88 - 89: 10.816 distance: 89 - 90: 10.763 distance: 89 - 92: 3.132 distance: 90 - 91: 10.858 distance: 90 - 94: 5.945 distance: 94 - 95: 17.194 distance: 95 - 96: 16.762 distance: 95 - 98: 30.278 distance: 96 - 97: 12.436 distance: 96 - 101: 8.683 distance: 98 - 99: 8.675 distance: 98 - 100: 8.897 distance: 101 - 102: 7.488 distance: 102 - 103: 9.253 distance: 102 - 105: 4.727 distance: 103 - 104: 31.093 distance: 103 - 110: 16.917 distance: 105 - 106: 8.782 distance: 106 - 107: 6.256 distance: 108 - 109: 3.170 distance: 110 - 111: 11.724 distance: 111 - 112: 11.447 distance: 111 - 114: 9.599 distance: 112 - 113: 29.504 distance: 112 - 116: 23.490 distance: 114 - 115: 5.988 distance: 116 - 117: 12.609 distance: 117 - 118: 13.000 distance: 117 - 120: 13.578 distance: 118 - 119: 47.862 distance: 118 - 122: 16.015 distance: 120 - 121: 5.146 distance: 122 - 123: 23.485 distance: 123 - 124: 11.316 distance: 123 - 126: 36.483 distance: 124 - 125: 24.242 distance: 124 - 131: 22.369 distance: 126 - 127: 14.722 distance: 127 - 128: 24.275 distance: 128 - 129: 4.052 distance: 128 - 130: 8.737 distance: 131 - 132: 21.149 distance: 132 - 133: 35.960 distance: 132 - 135: 26.518 distance: 133 - 134: 42.102 distance: 133 - 137: 15.398 distance: 135 - 136: 44.349 distance: 137 - 138: 24.585 distance: 138 - 139: 28.849 distance: 138 - 141: 45.479 distance: 139 - 140: 40.989 distance: 139 - 143: 23.277 distance: 141 - 142: 25.615