Starting phenix.real_space_refine on Tue Feb 20 21:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q04_20542/02_2024/6q04_20542_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.101 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 18108 2.51 5 N 4533 2.21 5 O 6123 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28911 Number of models: 1 Model: "" Number of chains: 39 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: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Time building chain proxies: 15.31, per 1000 atoms: 0.53 Number of scatterers: 28911 At special positions: 0 Unit cell: (141.75, 150.15, 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 6123 8.00 N 4533 7.00 C 18108 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=2.02 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 P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 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 N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 5 " 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 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-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 N 1 " - " ASN B 222 " " NAG O 1 " - " ASN B 236 " " NAG P 1 " - " ASN B 410 " " NAG Q 1 " - " ASN B 870 " " NAG R 1 " - " ASN B1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 166 " " NAG W 1 " - " ASN B 244 " " NAG X 1 " - " ASN C 222 " " NAG Y 1 " - " ASN C 236 " " NAG Z 1 " - " ASN C 410 " " NAG a 1 " - " ASN C 870 " " NAG b 1 " - " ASN C1213 " " NAG c 1 " - " ASN C 66 " " NAG d 1 " - " ASN C 104 " " NAG e 1 " - " ASN C 125 " " NAG f 1 " - " ASN C 166 " " NAG g 1 " - " ASN C 244 " Time building additional restraints: 12.88 Conformation dependent library (CDL) restraints added in 4.8 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: 8.09 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: 3.917A 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: 3.920A 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: 3.853A 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: 4.472A 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: 3.679A 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: 3.632A 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: 3.854A 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: 4.471A 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: 3.633A 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: 5.175A 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: 4.319A 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: 4.165A 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: 6.039A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.244A 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: 6.324A 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: 4.249A 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: 7.773A 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: 5.826A 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: 4.610A 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: 6.348A 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: 4.166A 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: 5.243A 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: 3.836A 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: 7.747A 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: 8.216A pdb=" N GLU B 376 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 6.359A 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: 6.613A 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: 3.525A 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: 4.248A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.407A 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: 7.773A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.387A 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: 4.610A 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: 5.425A 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: 6.347A 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: 4.165A 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: 6.039A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.244A 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: 3.835A 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: 7.748A 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: 6.359A pdb=" N SER C 607 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.277A 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: 6.360A 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: 7.774A 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: 5.926A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.825A 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: 6.011A 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: 13.21 Time building geometry restraints manager: 13.80 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: 4510 1.26 - 1.46: 12119 1.46 - 1.66: 12468 1.66 - 1.85: 216 Bond restraints: 29316 Sorted by residual: bond pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.08e+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 9.08e+02 bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.05e+02 bond pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 bond pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 ... (remaining 29311 not shown) Histogram of bond angle deviations from ideal: 94.04 - 103.68: 516 103.68 - 113.32: 15713 113.32 - 122.97: 20716 122.97 - 132.61: 2925 132.61 - 142.25: 36 Bond angle restraints: 39906 Sorted by residual: angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.20 -21.28 1.15e+00 7.56e-01 3.42e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 115.86 94.48 21.38 1.24e+00 6.50e-01 2.97e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 115.86 94.49 21.37 1.24e+00 6.50e-01 2.97e+02 ... (remaining 39901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18444 26.84 - 53.67: 405 53.67 - 80.51: 138 80.51 - 107.34: 131 107.34 - 134.18: 31 Dihedral angle restraints: 19149 sinusoidal: 9033 harmonic: 10116 Sorted by residual: dihedral pdb=" N CYS A 383 " pdb=" C CYS A 383 " pdb=" CA CYS A 383 " pdb=" CB CYS A 383 " ideal model delta harmonic sigma weight residual 122.80 96.18 26.62 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS C 383 " pdb=" C CYS C 383 " pdb=" CA CYS C 383 " pdb=" CB CYS C 383 " ideal model delta harmonic sigma weight residual 122.80 96.19 26.61 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS B 383 " pdb=" C CYS B 383 " pdb=" CA CYS B 383 " pdb=" CB CYS B 383 " ideal model delta harmonic sigma weight residual 122.80 96.19 26.61 0 2.50e+00 1.60e-01 1.13e+02 ... (remaining 19146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4771 0.390 - 0.781: 68 0.781 - 1.171: 6 1.171 - 1.561: 0 1.561 - 1.952: 3 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 MAN U 5 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 5 " pdb=" O5 MAN U 5 " both_signs ideal model delta sigma weight residual False 2.40 2.85 -0.45 2.00e-02 2.50e+03 4.96e+02 chirality pdb=" C1 MAN e 4 " pdb=" O3 BMA e 3 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 2.84 -0.44 2.00e-02 2.50e+03 4.80e+02 chirality pdb=" C1 MAN K 5 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 5 " pdb=" O5 MAN K 5 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-02 2.50e+03 4.72e+02 ... (remaining 4845 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " -0.078 2.00e-02 2.50e+03 4.34e-02 3.76e+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 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.009 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 B 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.73e+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 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.009 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 C 777 " 0.078 2.00e-02 2.50e+03 4.31e-02 3.72e+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 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7513 2.78 - 3.31: 26278 3.31 - 3.84: 51990 3.84 - 4.37: 63688 4.37 - 4.90: 101827 Nonbonded interactions: 251296 Sorted by model distance: nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA U 3 " pdb=" O6 BMA U 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA e 3 " pdb=" O6 BMA e 3 " model vdw 2.256 2.432 nonbonded pdb=" N ASP B 343 " pdb=" OD1 ASP B 343 " model vdw 2.345 2.520 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.346 2.520 ... (remaining 251291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' selection = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'U' selection = chain 'V' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 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: 0.030 Extract box with map and model: 16.470 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 82.740 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.490 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 29316 Z= 1.648 Angle : 2.020 21.848 39906 Z= 1.281 Chirality : 0.148 1.952 4848 Planarity : 0.009 0.048 4971 Dihedral : 15.995 134.180 12540 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.91 % Allowed : 1.31 % Favored : 97.78 % Cbeta Deviations : 0.62 % 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 C 264 PHE 0.050 0.006 PHE B 473 TYR 0.079 0.011 TYR A 184 ARG 0.012 0.002 ARG C 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 617 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 590 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8324 (pt) cc_final: 0.8104 (pt) outliers start: 27 outliers final: 4 residues processed: 605 average time/residue: 1.3403 time to fit residues: 954.9403 Evaluate side-chains 326 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 107 GLN A 280 GLN A 466 GLN A 521 ASN A 576 GLN A 582 ASN A 681 HIS A 832 ASN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN A1072 ASN A1163 ASN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 280 GLN B 582 ASN B 681 HIS B 819 GLN B 832 ASN B 987 GLN B 988 GLN B 994 GLN B1063 GLN B1072 ASN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 280 GLN C 304 GLN C 521 ASN C 582 ASN C 812 ASN C 907 GLN C 987 GLN C1072 ASN C1145 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29316 Z= 0.264 Angle : 0.691 17.127 39906 Z= 0.353 Chirality : 0.050 0.421 4848 Planarity : 0.004 0.037 4971 Dihedral : 12.940 114.246 6518 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.52 % Allowed : 10.11 % Favored : 87.37 % 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: 0.78 (0.20), residues: 699 sheet: 0.52 (0.16), residues: 870 loop : 0.37 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 310 HIS 0.007 0.001 HIS C1122 PHE 0.019 0.002 PHE A 850 TYR 0.022 0.002 TYR B 77 ARG 0.007 0.001 ARG C 141 *********************** 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 507 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 432 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6917 (t70) REVERT: A 1137 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7314 (mtm) REVERT: B 812 ASN cc_start: 0.7992 (t0) cc_final: 0.7601 (t0) REVERT: B 1148 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: C 406 ASN cc_start: 0.7154 (m-40) cc_final: 0.6914 (m-40) REVERT: C 1056 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: C 1137 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7425 (mtm) outliers start: 75 outliers final: 19 residues processed: 474 average time/residue: 1.2064 time to fit residues: 684.5052 Evaluate side-chains 335 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 313 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 311 optimal weight: 0.0270 chunk 107 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 832 ASN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 466 GLN B 681 HIS ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B 927 GLN B 987 GLN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 346 GLN C 466 GLN C 812 ASN C 987 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29316 Z= 0.347 Angle : 0.692 16.798 39906 Z= 0.353 Chirality : 0.049 0.280 4848 Planarity : 0.005 0.040 4971 Dihedral : 10.906 92.238 6516 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.70 % Allowed : 11.49 % Favored : 84.81 % 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: 0.38 (0.14), residues: 3447 helix: 0.85 (0.20), residues: 711 sheet: 0.34 (0.17), residues: 882 loop : 0.09 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.007 0.002 HIS C 208 PHE 0.022 0.002 PHE C 473 TYR 0.019 0.002 TYR C 928 ARG 0.008 0.001 ARG C 887 *********************** 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 450 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 340 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7863 (mmmm) REVERT: A 548 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7003 (mt) REVERT: A 1068 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6931 (t70) REVERT: A 1137 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7406 (mtm) REVERT: A 1148 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: B 796 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: B 818 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: B 1137 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7268 (mtp) REVERT: B 1148 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: C 252 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6322 (pt0) REVERT: C 406 ASN cc_start: 0.7146 (m-40) cc_final: 0.6837 (m-40) REVERT: C 818 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: C 842 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: C 1056 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: C 1084 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7262 (tp-100) outliers start: 110 outliers final: 53 residues processed: 411 average time/residue: 1.1840 time to fit residues: 586.0067 Evaluate side-chains 365 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 832 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 582 ASN B 681 HIS B 812 ASN B 832 ASN B 927 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 346 GLN C 812 ASN C 987 GLN C1042 ASN C1169 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 29316 Z= 0.425 Angle : 0.728 21.262 39906 Z= 0.369 Chirality : 0.051 0.322 4848 Planarity : 0.005 0.043 4971 Dihedral : 9.453 76.104 6516 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.40 % Allowed : 12.16 % Favored : 83.43 % 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: 0.11 (0.13), residues: 3447 helix: 0.62 (0.19), residues: 711 sheet: 0.28 (0.17), residues: 870 loop : -0.14 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 960 HIS 0.008 0.002 HIS C 208 PHE 0.024 0.002 PHE A 473 TYR 0.016 0.002 TYR C 928 ARG 0.005 0.001 ARG B 269 *********************** 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 453 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 322 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7967 (mmmm) REVERT: A 548 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7040 (mt) REVERT: A 595 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7377 (mmtp) REVERT: A 1068 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6937 (t70) REVERT: A 1148 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: B 509 ASP cc_start: 0.6131 (OUTLIER) cc_final: 0.5905 (p0) REVERT: B 796 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: B 818 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: B 1148 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: C 252 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6339 (pt0) REVERT: C 406 ASN cc_start: 0.7240 (m-40) cc_final: 0.6956 (m-40) REVERT: C 818 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: C 842 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: C 1056 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: C 1084 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7297 (tp-100) outliers start: 131 outliers final: 68 residues processed: 413 average time/residue: 1.1259 time to fit residues: 564.8202 Evaluate side-chains 367 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 285 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.0570 chunk 189 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 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: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 832 ASN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 194 HIS B 280 GLN B 681 HIS B 819 GLN B 832 ASN B1009 GLN B1169 ASN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 280 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN C1042 ASN C1169 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29316 Z= 0.214 Angle : 0.643 25.892 39906 Z= 0.324 Chirality : 0.047 0.427 4848 Planarity : 0.004 0.051 4971 Dihedral : 8.422 67.045 6516 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.23 % Allowed : 13.91 % Favored : 82.86 % 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: 0.23 (0.14), residues: 3447 helix: 1.11 (0.20), residues: 705 sheet: 0.10 (0.17), residues: 891 loop : -0.10 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.004 0.001 HIS C 167 PHE 0.020 0.001 PHE A 473 TYR 0.011 0.001 TYR C 928 ARG 0.003 0.000 ARG C 542 *********************** 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: 96 poor density : 327 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7038 (mt) REVERT: A 1068 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6935 (t70) REVERT: A 1148 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: B 600 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 796 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: B 818 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: B 1148 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 406 ASN cc_start: 0.7155 (m-40) cc_final: 0.6857 (m-40) REVERT: C 818 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: C 842 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: C 1056 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: C 1084 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7295 (tp-100) outliers start: 96 outliers final: 43 residues processed: 398 average time/residue: 1.1228 time to fit residues: 544.4531 Evaluate side-chains 356 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 302 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 195 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 812 ASN A 832 ASN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 427 GLN B 681 HIS ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN B 832 ASN B1009 GLN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 427 GLN C 815 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29316 Z= 0.227 Angle : 0.661 28.895 39906 Z= 0.330 Chirality : 0.047 0.422 4848 Planarity : 0.004 0.051 4971 Dihedral : 8.073 65.396 6516 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.49 % Allowed : 14.08 % Favored : 82.43 % 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: 0.17 (0.14), residues: 3447 helix: 1.10 (0.20), residues: 711 sheet: 0.08 (0.17), residues: 888 loop : -0.16 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 960 HIS 0.003 0.001 HIS B 486 PHE 0.021 0.002 PHE C 473 TYR 0.016 0.001 TYR C 909 ARG 0.004 0.000 ARG C 542 *********************** 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 423 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 319 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.7001 (mt) REVERT: A 595 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7278 (mmtp) REVERT: A 1068 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6902 (t70) REVERT: A 1148 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: B 600 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7872 (mt) REVERT: B 796 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: B 818 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: C 252 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6332 (pt0) REVERT: C 406 ASN cc_start: 0.7175 (m-40) cc_final: 0.6859 (m-40) REVERT: C 818 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: C 1056 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: C 1084 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7271 (tp-100) outliers start: 104 outliers final: 59 residues processed: 390 average time/residue: 1.1340 time to fit residues: 539.9500 Evaluate side-chains 374 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 304 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 280 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 332 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 202 optimal weight: 0.0270 chunk 153 optimal weight: 1.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A 832 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 280 GLN B 681 HIS B 815 GLN B 832 ASN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 261 GLN C 987 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29316 Z= 0.303 Angle : 0.699 29.228 39906 Z= 0.350 Chirality : 0.048 0.434 4848 Planarity : 0.004 0.050 4971 Dihedral : 8.071 65.291 6516 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.83 % Allowed : 14.25 % Favored : 81.92 % 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: 0.09 (0.13), residues: 3447 helix: 0.99 (0.20), residues: 711 sheet: 0.04 (0.17), residues: 891 loop : -0.21 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.004 0.001 HIS C 208 PHE 0.023 0.002 PHE C 473 TYR 0.017 0.002 TYR B 909 ARG 0.004 0.000 ARG C 542 *********************** 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 415 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 301 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7854 (mmmm) REVERT: A 548 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7025 (mt) REVERT: A 595 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7233 (mmtp) REVERT: A 1068 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6940 (t70) REVERT: A 1148 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 509 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5915 (p0) REVERT: B 600 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7913 (mt) REVERT: B 796 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: B 818 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: C 252 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6335 (pt0) REVERT: C 818 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: C 842 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: C 1056 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: C 1084 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7216 (tp-100) outliers start: 114 outliers final: 75 residues processed: 380 average time/residue: 1.1363 time to fit residues: 524.2485 Evaluate side-chains 381 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 292 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 198 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A1009 GLN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 681 HIS B 815 GLN B1009 GLN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 ASN C 987 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 29316 Z= 0.204 Angle : 0.645 27.673 39906 Z= 0.323 Chirality : 0.046 0.422 4848 Planarity : 0.004 0.053 4971 Dihedral : 7.578 62.434 6516 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.19 % Allowed : 15.09 % Favored : 81.72 % 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: 0.12 (0.13), residues: 3447 helix: 1.10 (0.20), residues: 714 sheet: 0.07 (0.17), residues: 858 loop : -0.24 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.003 0.001 HIS C 167 PHE 0.022 0.001 PHE C 473 TYR 0.011 0.001 TYR B1141 ARG 0.004 0.000 ARG C 542 *********************** 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 414 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 319 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7666 (p) REVERT: A 595 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7190 (mmtp) REVERT: A 1068 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6901 (t70) REVERT: B 796 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: B 818 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: C 252 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6299 (pt0) REVERT: C 406 ASN cc_start: 0.7005 (m-40) cc_final: 0.6692 (m-40) REVERT: C 612 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7477 (m) REVERT: C 818 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 842 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: C 1056 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: C 1084 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7373 (tp-100) outliers start: 95 outliers final: 57 residues processed: 382 average time/residue: 1.1379 time to fit residues: 529.2023 Evaluate side-chains 370 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 302 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.8980 chunk 318 optimal weight: 0.9990 chunk 290 optimal weight: 0.2980 chunk 309 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 134 optimal weight: 0.0030 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 308 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A1009 GLN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 280 GLN B 599 GLN B 733 GLN B 815 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN C 987 GLN C1009 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29316 Z= 0.187 Angle : 0.637 26.488 39906 Z= 0.318 Chirality : 0.046 0.404 4848 Planarity : 0.004 0.056 4971 Dihedral : 7.143 60.010 6514 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.52 % Allowed : 15.93 % Favored : 81.55 % 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: 0.22 (0.14), residues: 3447 helix: 1.23 (0.20), residues: 711 sheet: 0.07 (0.17), residues: 888 loop : -0.15 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 535 HIS 0.003 0.001 HIS C 167 PHE 0.025 0.001 PHE B 571 TYR 0.021 0.001 TYR B 909 ARG 0.005 0.000 ARG C 542 *********************** 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 388 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 313 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (p) REVERT: A 1068 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6901 (t70) REVERT: B 815 GLN cc_start: 0.7042 (tp40) cc_final: 0.6811 (tp-100) REVERT: B 818 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: C 252 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: C 818 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: C 842 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: C 1056 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: C 1084 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7369 (tp-100) outliers start: 75 outliers final: 45 residues processed: 364 average time/residue: 1.1161 time to fit residues: 494.4623 Evaluate side-chains 351 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 298 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 3.9990 chunk 327 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 273 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 211 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A1009 GLN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 280 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 987 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 29316 Z= 0.207 Angle : 0.749 57.515 39906 Z= 0.393 Chirality : 0.047 0.674 4848 Planarity : 0.004 0.057 4971 Dihedral : 7.076 59.843 6514 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.18 % Allowed : 16.40 % Favored : 81.42 % 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: 0.22 (0.14), residues: 3447 helix: 1.20 (0.20), residues: 711 sheet: 0.06 (0.16), residues: 918 loop : -0.14 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 535 HIS 0.003 0.001 HIS C 167 PHE 0.026 0.001 PHE B 571 TYR 0.032 0.001 TYR B 909 ARG 0.005 0.000 ARG C 542 ********************** 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 366 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.4887 (t80) REVERT: A 1068 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6903 (t70) REVERT: B 818 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: C 252 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6290 (pt0) REVERT: C 818 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: C 842 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: C 1056 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7255 (tt0) outliers start: 65 outliers final: 51 residues processed: 345 average time/residue: 1.1047 time to fit residues: 467.6111 Evaluate side-chains 355 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 297 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1008 MET Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 274 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN A1009 GLN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 280 GLN B 815 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 486 HIS C 987 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119026 restraints weight = 32779.424| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.30 r_work: 0.3329 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 29316 Z= 0.276 Angle : 0.676 27.166 39906 Z= 0.337 Chirality : 0.048 0.399 4848 Planarity : 0.004 0.056 4971 Dihedral : 7.208 60.357 6514 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.69 % Allowed : 15.99 % Favored : 81.32 % 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: 0.14 (0.14), residues: 3447 helix: 1.05 (0.20), residues: 711 sheet: 0.05 (0.16), residues: 948 loop : -0.17 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 960 HIS 0.003 0.001 HIS C 208 PHE 0.026 0.002 PHE B 571 TYR 0.013 0.001 TYR B 928 ARG 0.005 0.000 ARG C 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10083.43 seconds wall clock time: 182 minutes 1.04 seconds (10921.04 seconds total)