Starting phenix.real_space_refine on Sat Aug 10 17:20:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvc_22506/08_2024/7jvc_22506.cif" } resolution = 3.3 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= 0.005 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18591 2.51 5 N 5092 2.21 5 O 5750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1111": "OE1" <-> "OE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29562 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7354 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 276 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 327 Chain: "L" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1094 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 692 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 295 Chain: "B" Number of atoms: 7353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7353 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 276 Chain: "C" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 327 Chain: "D" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1088 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 299 Chain: "E" Number of atoms: 7353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7353 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 276 Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 327 Chain: "G" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1090 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 299 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.70, per 1000 atoms: 0.56 Number of scatterers: 29562 At special positions: 0 Unit cell: (150.15, 157.5, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5750 8.00 N 5092 7.00 C 18591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.05 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.01 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A 343 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E 343 " " NAG W 1 " - " ASN E1098 " " NAG X 1 " - " ASN E1134 " Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 6.7 seconds 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 84 sheets defined 20.9% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.757A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.816A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 removed outlier: 5.316A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.648A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.817A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 through 965 removed outlier: 5.316A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.647A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU D 86 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.757A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.816A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.734A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 947 through 965 removed outlier: 5.317A pdb=" N ASN E 953 " --> pdb=" O GLN E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.648A pdb=" N ARG E 983 " --> pdb=" O ASP E 979 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 71 No H-bonds generated for 'chain 'G' and resid 69 through 71' Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 131 Processing helix chain 'G' and resid 186 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.172A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.543A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.466A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.343A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.195A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.526A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.533A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.095A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.061A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS H 96 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP H 109 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AC7, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER L 205 " --> pdb=" O HIS L 202 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.171A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.465A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.194A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.527A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.533A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.094A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET C 34 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS C 96 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP C 109 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG C 98 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA C 143 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 190 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY C 145 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 188 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 147 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER C 186 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 149 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 184 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA C 143 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 190 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY C 145 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 188 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 147 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER C 186 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 149 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 184 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AF8, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AF9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL D 10 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN D 38 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL D 10 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR D 177 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR D 177 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER D 205 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.172A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.465A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.344A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.526A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.534A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.094A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AI2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS F 96 " --> pdb=" O TRP F 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP F 109 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG F 98 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 190 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 188 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU F 147 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER F 186 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS F 149 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU F 184 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 190 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 188 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU F 147 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER F 186 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS F 149 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU F 184 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 157 through 160 Processing sheet with id=AI7, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN G 38 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR G 177 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR G 177 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER G 205 " --> pdb=" O HIS G 202 " (cutoff:3.500A) 1530 hydrogen bonds defined for protein. 3987 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: 17.74 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6015 1.32 - 1.45: 8475 1.45 - 1.58: 15440 1.58 - 1.72: 15 1.72 - 1.85: 153 Bond restraints: 30098 Sorted by residual: bond pdb=" CD GLN B 607 " pdb=" NE2 GLN B 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" CD GLN A 607 " pdb=" NE2 GLN A 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" CD GLN E 607 " pdb=" NE2 GLN E 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.64e+01 bond pdb=" C5 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 30093 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.28: 848 105.28 - 112.49: 15442 112.49 - 119.70: 9539 119.70 - 126.91: 15333 126.91 - 134.12: 116 Bond angle restraints: 41278 Sorted by residual: angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.14 -5.48 7.20e-01 1.93e+00 5.78e+01 angle pdb=" C LEU E 861 " pdb=" N PRO E 862 " pdb=" CA PRO E 862 " ideal model delta sigma weight residual 119.66 125.11 -5.45 7.20e-01 1.93e+00 5.73e+01 angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 125.11 -5.45 7.20e-01 1.93e+00 5.72e+01 angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.49 -7.46 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.65e+01 ... (remaining 41273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 18242 21.30 - 42.60: 376 42.60 - 63.90: 91 63.90 - 85.20: 33 85.20 - 106.50: 18 Dihedral angle restraints: 18760 sinusoidal: 6460 harmonic: 12300 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 91 " pdb=" CB CYS D 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.58 42.42 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 91 " pdb=" CB CYS G 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.60 42.40 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.63 42.37 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 18757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3857 0.084 - 0.168: 966 0.168 - 0.252: 180 0.252 - 0.336: 91 0.336 - 0.420: 54 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.74e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.60e+01 ... (remaining 5145 not shown) Planarity restraints: 5475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.045 2.00e-02 2.50e+03 4.66e-02 2.71e+01 pdb=" CG ASN B 709 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 709 " -0.045 2.00e-02 2.50e+03 4.65e-02 2.71e+01 pdb=" CG ASN E 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 709 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG E1309 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.045 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" CG ASN A 709 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.072 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.057 2.00e-02 2.50e+03 ... (remaining 5472 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 12736 2.92 - 3.42: 25830 3.42 - 3.91: 46762 3.91 - 4.41: 51599 4.41 - 4.90: 86934 Nonbonded interactions: 223861 Sorted by model distance: nonbonded pdb=" NZ LYS E 811 " pdb=" OD2 ASP E 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.444 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.444 3.120 ... (remaining 223856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB )) or resid 515 through 1145 or resid 1301 through 1311 \ )) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = (chain 'G' and (resid 1 through 55 or (resid 56 through 57 and (name N or name C \ A or name C or name O or name CB )) or resid 58 through 214)) selection = (chain 'L' and (resid 1 through 55 or (resid 56 through 57 and (name N or name C \ A or name C or name O or name CB )) or resid 58 through 91 or (resid 92 through \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throug \ h 214)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'V' } 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 86.330 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.013 0.127 30098 Z= 0.898 Angle : 1.418 8.008 41278 Z= 0.963 Chirality : 0.091 0.420 5148 Planarity : 0.005 0.024 5427 Dihedral : 10.638 106.500 10639 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.71 (0.12), residues: 4194 helix: -0.40 (0.17), residues: 753 sheet: 1.28 (0.14), residues: 1245 loop : 0.46 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP E1102 HIS 0.009 0.002 HIS E1083 PHE 0.021 0.003 PHE B 347 TYR 0.025 0.004 TYR E 674 ARG 0.003 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 453 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.6443 (p-90) cc_final: 0.5814 (p-90) REVERT: A 377 PHE cc_start: 0.7073 (t80) cc_final: 0.6871 (t80) REVERT: B 396 TYR cc_start: 0.6999 (m-80) cc_final: 0.6794 (m-80) REVERT: E 271 GLN cc_start: 0.7134 (mt0) cc_final: 0.6911 (tt0) REVERT: E 317 ASN cc_start: 0.7846 (m-40) cc_final: 0.7110 (m-40) REVERT: E 353 TRP cc_start: 0.6269 (p-90) cc_final: 0.5613 (p-90) REVERT: E 396 TYR cc_start: 0.6957 (m-80) cc_final: 0.6691 (m-80) outliers start: 3 outliers final: 0 residues processed: 454 average time/residue: 0.3826 time to fit residues: 279.6321 Evaluate side-chains 168 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.5980 chunk 322 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 217 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 333 optimal weight: 0.9990 chunk 129 optimal weight: 50.0000 chunk 203 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 386 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN A 607 GLN A 965 GLN B 207 HIS B 607 GLN E 207 HIS E 321 GLN E 388 ASN E 607 GLN E 703 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30098 Z= 0.241 Angle : 0.620 13.084 41278 Z= 0.322 Chirality : 0.047 0.328 5148 Planarity : 0.004 0.032 5427 Dihedral : 6.568 67.242 5793 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.41 % Favored : 98.52 % Rotamer: Outliers : 1.40 % Allowed : 7.91 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4194 helix: 0.78 (0.19), residues: 741 sheet: 1.39 (0.14), residues: 1317 loop : 0.41 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 104 HIS 0.008 0.001 HIS E1083 PHE 0.018 0.002 PHE B 65 TYR 0.026 0.002 TYR E1138 ARG 0.008 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.6398 (p-90) cc_final: 0.5700 (p-90) REVERT: B 231 ILE cc_start: 0.8704 (mm) cc_final: 0.8366 (mm) REVERT: B 554 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: B 725 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: E 231 ILE cc_start: 0.8662 (mm) cc_final: 0.8437 (mm) REVERT: E 353 TRP cc_start: 0.6053 (p-90) cc_final: 0.5365 (p-90) REVERT: E 377 PHE cc_start: 0.6947 (t80) cc_final: 0.5238 (p90) outliers start: 33 outliers final: 16 residues processed: 239 average time/residue: 0.3600 time to fit residues: 146.1912 Evaluate side-chains 175 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 773 GLU Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 387 optimal weight: 0.8980 chunk 418 optimal weight: 20.0000 chunk 345 optimal weight: 0.6980 chunk 384 optimal weight: 1.9990 chunk 132 optimal weight: 50.0000 chunk 310 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 914 ASN A 926 GLN A1048 HIS B 321 GLN B 388 ASN B1048 HIS E1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30098 Z= 0.307 Angle : 0.593 15.782 41278 Z= 0.304 Chirality : 0.046 0.368 5148 Planarity : 0.004 0.037 5427 Dihedral : 5.281 50.521 5793 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.27 % Allowed : 8.92 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.11 (0.13), residues: 4194 helix: 1.20 (0.19), residues: 720 sheet: 1.43 (0.13), residues: 1296 loop : 0.22 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.006 0.002 HIS E1083 PHE 0.016 0.002 PHE E 318 TYR 0.018 0.001 TYR E1067 ARG 0.011 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6364 (m-80) cc_final: 0.5596 (t80) REVERT: A 353 TRP cc_start: 0.6452 (p-90) cc_final: 0.5762 (p-90) REVERT: A 377 PHE cc_start: 0.6687 (t80) cc_final: 0.5290 (p90) REVERT: B 377 PHE cc_start: 0.6940 (t80) cc_final: 0.5492 (p90) REVERT: B 674 TYR cc_start: 0.7870 (t80) cc_final: 0.7582 (t80) REVERT: B 725 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: E 377 PHE cc_start: 0.6824 (t80) cc_final: 0.5414 (p90) REVERT: E 900 MET cc_start: 0.8137 (mtp) cc_final: 0.7888 (mtp) outliers start: 30 outliers final: 22 residues processed: 198 average time/residue: 0.3533 time to fit residues: 120.2492 Evaluate side-chains 174 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 260 optimal weight: 50.0000 chunk 388 optimal weight: 50.0000 chunk 411 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 368 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN B 914 ASN B1071 GLN E 901 GLN E1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 30098 Z= 0.455 Angle : 0.652 16.247 41278 Z= 0.331 Chirality : 0.049 0.402 5148 Planarity : 0.005 0.042 5427 Dihedral : 5.242 38.473 5793 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.28 % Allowed : 9.64 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.74 (0.13), residues: 4194 helix: 1.15 (0.20), residues: 705 sheet: 0.88 (0.13), residues: 1389 loop : 0.09 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.008 0.002 HIS A 207 PHE 0.022 0.002 PHE E 275 TYR 0.023 0.002 TYR B1067 ARG 0.007 0.001 ARG E1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 3.088 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6243 (m-80) cc_final: 0.5716 (t80) REVERT: A 377 PHE cc_start: 0.6919 (t80) cc_final: 0.5615 (p90) REVERT: B 674 TYR cc_start: 0.8095 (t80) cc_final: 0.7849 (t80) REVERT: E 900 MET cc_start: 0.8225 (mtp) cc_final: 0.7987 (mtp) outliers start: 54 outliers final: 37 residues processed: 202 average time/residue: 0.3402 time to fit residues: 120.9871 Evaluate side-chains 175 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 351 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 210 optimal weight: 0.0980 chunk 369 optimal weight: 0.6980 chunk 103 optimal weight: 40.0000 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 901 GLN A 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30098 Z= 0.188 Angle : 0.529 17.094 41278 Z= 0.265 Chirality : 0.046 0.548 5148 Planarity : 0.004 0.038 5427 Dihedral : 4.801 38.587 5793 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 10.36 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.91 (0.13), residues: 4194 helix: 1.58 (0.20), residues: 708 sheet: 0.97 (0.14), residues: 1356 loop : 0.10 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS E1083 PHE 0.021 0.001 PHE E 374 TYR 0.015 0.001 TYR E1067 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 3.162 Fit side-chains REVERT: A 133 PHE cc_start: 0.6137 (m-80) cc_final: 0.5462 (t80) REVERT: A 377 PHE cc_start: 0.6908 (t80) cc_final: 0.5447 (p90) REVERT: B 674 TYR cc_start: 0.7907 (t80) cc_final: 0.7675 (t80) REVERT: E 133 PHE cc_start: 0.6383 (m-80) cc_final: 0.5734 (t80) REVERT: E 900 MET cc_start: 0.8126 (mtp) cc_final: 0.7880 (mtp) outliers start: 42 outliers final: 26 residues processed: 187 average time/residue: 0.3392 time to fit residues: 111.6395 Evaluate side-chains 168 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 412 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 136 optimal weight: 0.0020 chunk 216 optimal weight: 0.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 901 GLN B 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 30098 Z= 0.347 Angle : 0.572 16.777 41278 Z= 0.287 Chirality : 0.047 0.582 5148 Planarity : 0.004 0.042 5427 Dihedral : 5.013 40.633 5793 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.73 % Allowed : 10.27 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.79 (0.13), residues: 4194 helix: 1.45 (0.20), residues: 708 sheet: 0.88 (0.14), residues: 1362 loop : 0.05 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 PHE 0.017 0.002 PHE E 374 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG E1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 149 time to evaluate : 3.130 Fit side-chains REVERT: A 133 PHE cc_start: 0.6238 (m-80) cc_final: 0.5820 (t80) REVERT: A 377 PHE cc_start: 0.6948 (t80) cc_final: 0.5647 (p90) REVERT: B 135 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.4076 (m-80) REVERT: B 674 TYR cc_start: 0.8044 (t80) cc_final: 0.7795 (t80) REVERT: E 133 PHE cc_start: 0.6351 (m-80) cc_final: 0.5410 (t80) REVERT: E 900 MET cc_start: 0.8202 (mtp) cc_final: 0.7932 (mtp) outliers start: 41 outliers final: 33 residues processed: 180 average time/residue: 0.3395 time to fit residues: 108.2011 Evaluate side-chains 173 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 346 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 256 optimal weight: 0.0270 chunk 250 optimal weight: 40.0000 chunk 189 optimal weight: 1.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30098 Z= 0.191 Angle : 0.513 17.147 41278 Z= 0.255 Chirality : 0.045 0.525 5148 Planarity : 0.004 0.040 5427 Dihedral : 4.725 43.355 5793 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.61 % Allowed : 10.74 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.87 (0.13), residues: 4194 helix: 1.43 (0.20), residues: 747 sheet: 0.97 (0.14), residues: 1356 loop : 0.08 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS A1083 PHE 0.015 0.001 PHE E 133 TYR 0.014 0.001 TYR E1067 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 3.322 Fit side-chains REVERT: A 133 PHE cc_start: 0.6050 (m-80) cc_final: 0.5809 (t80) REVERT: B 135 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: B 674 TYR cc_start: 0.7969 (t80) cc_final: 0.7737 (t80) REVERT: E 539 VAL cc_start: 0.8707 (m) cc_final: 0.8500 (m) REVERT: E 900 MET cc_start: 0.8145 (mtp) cc_final: 0.7878 (mtp) outliers start: 38 outliers final: 28 residues processed: 179 average time/residue: 0.3313 time to fit residues: 104.8540 Evaluate side-chains 171 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 40.0000 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 261 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 322 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30098 Z= 0.212 Angle : 0.516 17.036 41278 Z= 0.257 Chirality : 0.045 0.508 5148 Planarity : 0.004 0.040 5427 Dihedral : 4.640 42.466 5793 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.69 % Allowed : 10.87 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 0.89 (0.13), residues: 4194 helix: 1.46 (0.20), residues: 747 sheet: 1.00 (0.14), residues: 1356 loop : 0.08 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A1083 PHE 0.012 0.001 PHE B 898 TYR 0.014 0.001 TYR B1067 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 3.142 Fit side-chains REVERT: A 133 PHE cc_start: 0.6125 (m-80) cc_final: 0.5887 (t80) REVERT: A 377 PHE cc_start: 0.7240 (t80) cc_final: 0.5591 (p90) REVERT: B 135 PHE cc_start: 0.4310 (OUTLIER) cc_final: 0.3968 (m-80) REVERT: B 674 TYR cc_start: 0.8004 (t80) cc_final: 0.7774 (t80) REVERT: E 900 MET cc_start: 0.8175 (mtp) cc_final: 0.7879 (mtp) outliers start: 40 outliers final: 31 residues processed: 180 average time/residue: 0.3431 time to fit residues: 108.9478 Evaluate side-chains 174 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.9980 chunk 393 optimal weight: 30.0000 chunk 358 optimal weight: 0.6980 chunk 382 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 300 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 chunk 345 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 381 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30098 Z= 0.188 Angle : 0.504 17.004 41278 Z= 0.250 Chirality : 0.045 0.444 5148 Planarity : 0.004 0.039 5427 Dihedral : 4.490 42.085 5793 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.56 % Allowed : 11.08 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.01 (0.13), residues: 4194 helix: 1.71 (0.20), residues: 720 sheet: 1.11 (0.14), residues: 1323 loop : 0.10 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1083 PHE 0.011 0.001 PHE E 318 TYR 0.013 0.001 TYR B1067 ARG 0.006 0.000 ARG E 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 3.172 Fit side-chains REVERT: B 135 PHE cc_start: 0.4285 (OUTLIER) cc_final: 0.3949 (m-80) REVERT: B 326 ILE cc_start: 0.8611 (mm) cc_final: 0.8410 (pt) REVERT: B 674 TYR cc_start: 0.7989 (t80) cc_final: 0.7768 (t80) REVERT: E 900 MET cc_start: 0.8160 (mtp) cc_final: 0.7865 (mtp) outliers start: 37 outliers final: 30 residues processed: 177 average time/residue: 0.3299 time to fit residues: 102.9181 Evaluate side-chains 179 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.2519 > 50: distance: 13 - 101: 32.152 distance: 16 - 98: 12.940 distance: 23 - 91: 6.474 distance: 26 - 88: 14.916 distance: 33 - 81: 20.999 distance: 36 - 78: 18.480 distance: 52 - 86: 32.331 distance: 55 - 83: 26.838 distance: 70 - 73: 14.548 distance: 73 - 74: 14.903 distance: 74 - 75: 21.298 distance: 74 - 77: 11.947 distance: 75 - 76: 32.879 distance: 75 - 78: 10.634 distance: 78 - 79: 19.285 distance: 79 - 80: 19.704 distance: 79 - 82: 35.163 distance: 80 - 81: 23.365 distance: 80 - 83: 32.606 distance: 83 - 84: 42.616 distance: 84 - 85: 22.482 distance: 84 - 87: 30.776 distance: 85 - 86: 14.417 distance: 85 - 88: 14.225 distance: 88 - 89: 34.768 distance: 89 - 90: 12.481 distance: 89 - 92: 27.887 distance: 90 - 91: 18.884 distance: 90 - 93: 12.054 distance: 93 - 94: 40.153 distance: 94 - 95: 38.761 distance: 94 - 97: 40.639 distance: 95 - 96: 41.646 distance: 95 - 98: 17.767 distance: 98 - 99: 23.130 distance: 99 - 100: 30.590 distance: 99 - 102: 32.566 distance: 100 - 101: 37.749 distance: 100 - 103: 11.187 distance: 103 - 104: 17.650 distance: 104 - 105: 29.065 distance: 104 - 107: 15.329 distance: 105 - 106: 13.667 distance: 105 - 108: 24.525 distance: 106 - 125: 36.760 distance: 108 - 109: 12.809 distance: 108 - 114: 4.901 distance: 109 - 110: 10.295 distance: 109 - 112: 24.667 distance: 110 - 111: 30.942 distance: 110 - 115: 16.130 distance: 111 - 130: 15.051 distance: 112 - 113: 6.366 distance: 113 - 114: 27.928 distance: 115 - 116: 9.835 distance: 116 - 117: 31.451 distance: 116 - 119: 25.944 distance: 117 - 118: 13.086 distance: 117 - 120: 13.240 distance: 120 - 121: 11.207 distance: 121 - 124: 46.612 distance: 122 - 123: 20.928 distance: 122 - 125: 26.895