Starting phenix.real_space_refine on Tue Apr 16 19:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg5_22311/04_2024/7jg5_22311_updated.pdb" } resolution = 3.4 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= 0.011 sd= 0.277 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4941 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 22570 2.51 5 N 6186 2.21 5 O 6619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E ARG 298": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F GLU 409": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 72": "NH1" <-> "NH2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "b GLU 121": "OE1" <-> "OE2" Residue "b ARG 158": "NH1" <-> "NH2" Residue "d GLU 46": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 75": "OE1" <-> "OE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "d ARG 149": "NH1" <-> "NH2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 239": "NH1" <-> "NH2" Residue "d ARG 353": "NH1" <-> "NH2" Residue "1 ARG 45": "NH1" <-> "NH2" Residue "3 GLU 48": "OE1" <-> "OE2" Residue "3 GLU 65": "OE1" <-> "OE2" Residue "4 GLU 65": "OE1" <-> "OE2" Residue "5 GLU 65": "OE1" <-> "OE2" Residue "6 ARG 45": "NH1" <-> "NH2" Residue "7 GLU 65": "OE1" <-> "OE2" Residue "9 GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35497 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3910 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3787 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3713 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 9, 'UNK:plan-1': 11, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3495 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3525 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2121 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 824 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 70 Chain: "a" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1052 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "d" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2841 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 24, 'ARG:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 218 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 550 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 569 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.67, per 1000 atoms: 0.47 Number of scatterers: 35497 At special positions: 0 Unit cell: (123.6, 136.99, 249.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 13 15.00 Mg 4 11.99 O 6619 8.00 N 6186 7.00 C 22570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 16.10 Conformation dependent library (CDL) restraints added in 7.2 seconds 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 24 sheets defined 57.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.011A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.657A pdb=" N GLY A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 262 Proline residue: A 250 - end of helix removed outlier: 3.852A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.724A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.281A pdb=" N GLN A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 409 removed outlier: 5.381A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.566A pdb=" N ALA A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.043A pdb=" N VAL A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 removed outlier: 4.210A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.639A pdb=" N VAL A 464 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 468 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 470 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 473 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.519A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.978A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.707A pdb=" N GLY B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 243 through 262 Proline residue: B 250 - end of helix removed outlier: 3.692A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 299 through 311 removed outlier: 4.481A pdb=" N PHE B 302 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 307 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU B 310 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 412 removed outlier: 3.858A pdb=" N VAL B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 removed outlier: 4.319A pdb=" N GLN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 4.280A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.114A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 468 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 469 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 473 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 476 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 478 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.038A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 157 No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.047A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 262 Proline residue: C 250 - end of helix removed outlier: 3.563A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.468A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 378 through 381 removed outlier: 3.609A pdb=" N ALA C 381 " --> pdb=" O GLY C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 393 through 409 removed outlier: 5.116A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 removed outlier: 4.222A pdb=" N VAL C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.528A pdb=" N GLN C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.546A pdb=" N THR C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.181A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.902A pdb=" N ARG D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 224 through 245 removed outlier: 4.809A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 removed outlier: 4.264A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.494A pdb=" N ALA D 284 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 289 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU D 292 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.589A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.798A pdb=" N LYS D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 3.567A pdb=" N VAL D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.645A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 423 removed outlier: 4.582A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 452 through 455 removed outlier: 3.870A pdb=" N PHE D 455 " --> pdb=" O GLU D 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 452 through 455' Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.941A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.022A pdb=" N LEU E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.721A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 removed outlier: 4.273A pdb=" N LYS E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.769A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 412 removed outlier: 3.793A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 404 " --> pdb=" O GLN E 400 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 423 removed outlier: 3.826A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR E 423 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 removed outlier: 3.597A pdb=" N GLU E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 454 No H-bonds generated for 'chain 'E' and resid 452 through 454' Processing helix chain 'E' and resid 461 through 470 removed outlier: 3.584A pdb=" N LYS E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 176 Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.710A pdb=" N ALA F 205 " --> pdb=" O TRP F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.600A pdb=" N ARG F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 270 Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.581A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 3.617A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.768A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.559A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.590A pdb=" N SER F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 58 removed outlier: 3.957A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 3.676A pdb=" N GLU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 147 through 162 removed outlier: 3.727A pdb=" N GLU G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 302 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 100 removed outlier: 4.063A pdb=" N LYS H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 116 Processing helix chain 'a' and resid 33 through 52 removed outlier: 3.812A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 80 removed outlier: 3.799A pdb=" N TRP a 66 " --> pdb=" O GLN a 63 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU a 67 " --> pdb=" O LEU a 64 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE a 71 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 108 removed outlier: 3.755A pdb=" N LEU a 90 " --> pdb=" O PRO a 87 " (cutoff:3.500A) Proline residue: a 91 - end of helix removed outlier: 4.747A pdb=" N PHE a 99 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE a 102 " --> pdb=" O PHE a 99 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU a 106 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA a 107 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 removed outlier: 3.779A pdb=" N PHE a 140 " --> pdb=" O ALA a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 171 through 205 removed outlier: 3.965A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU a 179 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.002A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA a 204 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 245 removed outlier: 4.866A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.840A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 removed outlier: 4.477A pdb=" N ILE b 40 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 3.846A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 136 removed outlier: 4.130A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.560A pdb=" N ALA d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 193 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 223 Processing helix chain 'd' and resid 231 through 244 removed outlier: 4.043A pdb=" N LEU d 240 " --> pdb=" O LEU d 236 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP d 243 " --> pdb=" O ARG d 239 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS d 244 " --> pdb=" O LEU d 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 247 through 253 Processing helix chain 'd' and resid 264 through 284 removed outlier: 3.906A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 351 removed outlier: 4.228A pdb=" N LEU d 351 " --> pdb=" O GLN d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 400 removed outlier: 3.646A pdb=" N ARG d 399 " --> pdb=" O GLU d 395 " (cutoff:3.500A) Processing helix chain 'd' and resid 432 through 441 Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 47 through 80 removed outlier: 4.021A pdb=" N GLN 1 50 " --> pdb=" O PRO 1 47 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE 1 54 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR 1 55 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.527A pdb=" N VAL 1 61 " --> pdb=" O PHE 1 58 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU 1 65 " --> pdb=" O GLY 1 62 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE 1 80 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 50 through 79 removed outlier: 4.569A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 49 through 80 removed outlier: 4.114A pdb=" N PHE 3 54 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 3 55 " --> pdb=" O ARG 3 52 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.607A pdb=" N VAL 3 61 " --> pdb=" O PHE 3 58 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 3 66 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 3 69 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE 3 80 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 45 removed outlier: 3.710A pdb=" N ARG 4 45 " --> pdb=" O SER 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 79 removed outlier: 4.181A pdb=" N GLN 4 50 " --> pdb=" O PRO 4 47 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY 4 51 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 4 53 " --> pdb=" O GLN 4 50 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE 4 54 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.682A pdb=" N ALA 4 66 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL 4 79 " --> pdb=" O ALA 4 76 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 45 Processing helix chain '5' and resid 50 through 80 Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 45 removed outlier: 3.550A pdb=" N ALA 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 52 Processing helix chain '6' and resid 54 through 80 removed outlier: 3.962A pdb=" N ALA 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 45 removed outlier: 3.572A pdb=" N ALA 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 81 removed outlier: 3.764A pdb=" N GLN 7 50 " --> pdb=" O PRO 7 47 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY 7 51 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE 7 54 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR 7 55 " --> pdb=" O ARG 7 52 " (cutoff:3.500A) Proline residue: 7 56 - end of helix removed outlier: 3.566A pdb=" N VAL 7 61 " --> pdb=" O PHE 7 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE 7 80 " --> pdb=" O LEU 7 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA 7 81 " --> pdb=" O PHE 7 78 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 45 Processing helix chain '8' and resid 47 through 81 removed outlier: 3.936A pdb=" N GLN 8 50 " --> pdb=" O PRO 8 47 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY 8 51 " --> pdb=" O GLU 8 48 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE 8 54 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR 8 55 " --> pdb=" O ARG 8 52 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.540A pdb=" N PHE 8 80 " --> pdb=" O LEU 8 77 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA 8 81 " --> pdb=" O PHE 8 78 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 47 through 80 removed outlier: 3.638A pdb=" N GLN 9 50 " --> pdb=" O PRO 9 47 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY 9 51 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR 9 55 " --> pdb=" O ARG 9 52 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 4.491A pdb=" N GLU 9 65 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL 9 79 " --> pdb=" O ALA 9 76 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE 9 80 " --> pdb=" O LEU 9 77 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.324A pdb=" N LEU A 63 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 8.721A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 266 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 205 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 268 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A 207 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 270 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 209 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP A 272 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 73 through 77 removed outlier: 6.034A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 355 Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 8.631A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS B 266 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL B 205 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 268 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 207 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 270 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE B 209 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP B 272 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.893A pdb=" N VAL C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU C 69 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 232 through 237 removed outlier: 9.486A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.681A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.980A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 98 through 100 removed outlier: 8.497A pdb=" N PHE D 99 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 215 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA D 329 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE D 159 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR D 331 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.701A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.036A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.387A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.662A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.916A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.565A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 196 through 204 removed outlier: 3.789A pdb=" N THR G 197 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU G 182 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL G 118 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER G 137 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.081A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU H 54 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL H 23 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG H 52 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR H 25 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET H 50 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= X, first strand: chain 'd' and resid 405 through 411 removed outlier: 6.208A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N HIS d 410 " --> pdb=" O ALA d 377 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL d 379 " --> pdb=" O HIS d 410 " (cutoff:3.500A) 2009 hydrogen bonds defined for protein. 5289 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: 15.11 Time building geometry restraints manager: 16.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10772 1.33 - 1.45: 5167 1.45 - 1.57: 19942 1.57 - 1.69: 18 1.69 - 1.82: 191 Bond restraints: 36090 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.53e+01 ... (remaining 36085 not shown) Histogram of bond angle deviations from ideal: 98.51 - 106.06: 830 106.06 - 113.60: 20340 113.60 - 121.14: 18775 121.14 - 128.69: 8905 128.69 - 136.23: 163 Bond angle restraints: 49013 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.44 23.43 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.94 22.93 1.00e+00 1.00e+00 5.26e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.80 22.07 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.50 18.33 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.65 18.18 1.00e+00 1.00e+00 3.31e+02 ... (remaining 49008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19804 18.00 - 36.00: 1305 36.00 - 54.00: 263 54.00 - 72.00: 87 72.00 - 90.00: 72 Dihedral angle restraints: 21531 sinusoidal: 7959 harmonic: 13572 Sorted by residual: dihedral pdb=" CA ALA D 276 " pdb=" C ALA D 276 " pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -149.37 89.37 1 2.00e+01 2.50e-03 2.37e+01 dihedral pdb=" CA ALA F 276 " pdb=" C ALA F 276 " pdb=" N VAL F 277 " pdb=" CA VAL F 277 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 21528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4143 0.045 - 0.089: 1353 0.089 - 0.134: 266 0.134 - 0.178: 18 0.178 - 0.223: 1 Chirality restraints: 5781 Sorted by residual: chirality pdb=" CA GLN b 82 " pdb=" N GLN b 82 " pdb=" C GLN b 82 " pdb=" CB GLN b 82 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP b 70 " pdb=" N ASP b 70 " pdb=" C ASP b 70 " pdb=" CB ASP b 70 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB THR b 67 " pdb=" CA THR b 67 " pdb=" OG1 THR b 67 " pdb=" CG2 THR b 67 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 5778 not shown) Planarity restraints: 6366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 275 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C SER F 275 " -0.040 2.00e-02 2.50e+03 pdb=" O SER F 275 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 276 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 60 " 0.191 9.50e-02 1.11e+02 8.57e-02 4.56e+00 pdb=" NE ARG b 60 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG b 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG b 60 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG b 60 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 275 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C SER E 275 " 0.036 2.00e-02 2.50e+03 pdb=" O SER E 275 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA E 276 " -0.012 2.00e-02 2.50e+03 ... (remaining 6363 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 28 2.25 - 2.92: 15457 2.92 - 3.58: 52914 3.58 - 4.24: 82325 4.24 - 4.90: 141361 Nonbonded interactions: 292085 Sorted by model distance: nonbonded pdb=" CD1 ILE H 39 " pdb=" CA ARG 3 45 " model vdw 1.593 3.890 nonbonded pdb=" O1B ATP B 600 " pdb="MG MG B 601 " model vdw 1.787 2.170 nonbonded pdb=" O ARG H 37 " pdb=" CG PRO 3 47 " model vdw 1.824 3.440 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.825 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.893 2.170 ... (remaining 292080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 294 or (resid 295 through 29 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 297 through \ 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or re \ sid 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) o \ r resid 359 through 400 or (resid 401 through 402 and (name N or name CA or name \ C or name O or name CB )) or resid 403 through 411 or (resid 412 and (name N or \ name CA or name C or name O or name CB )) or resid 413 or (resid 414 through 41 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 420 through \ 461 or (resid 462 through 463 and (name N or name CA or name C or name O or name \ CB )) or resid 464 through 467 or (resid 468 and (name N or name CA or name C o \ r name O or name CB )) or resid 469 or (resid 470 and (name N or name CA or name \ C or name O or name CB )) or resid 471 through 475 or (resid 476 through 477 an \ d (name N or name CA or name C or name O or name CB )) or resid 478 through 494 \ or (resid 495 through 499 and (name N or name CA or name C or name O or name CB \ )) or resid 500 through 505 or (resid 506 and (name N or name CA or name C or na \ me O or name CB )) or resid 507 through 516 or resid 537 through 538 or resid 54 \ 0 or resid 600 through 601)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 44 or (resid 45 and (name N or name CA or na \ me C or name O or name CB )) or resid 46 through 80 or (resid 81 and (name N or \ name CA or name C or name O or name CB )) or resid 82 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 through 19 \ 0 or (resid 191 through 192 and (name N or name CA or name C or name O or name C \ B )) or resid 193 through 294 or (resid 295 through 296 and (name N or name CA o \ r name C or name O or name CB )) or resid 297 through 316 or (resid 317 through \ 318 and (name N or name CA or name C or name O or name CB )) or resid 319 throug \ h 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or \ resid 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) \ or resid 359 through 401 or (resid 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 411 or (resid 412 and (name N or name CA o \ r name C or name O or name CB )) or resid 413 through 416 or (resid 417 through \ 419 and (name N or name CA or name C or name O or name CB )) or resid 420 throug \ h 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 through 467 or (resid 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 475 or (resid 476 through 477 and (name N or n \ ame CA or name C or name O or name CB )) or resid 478 through 493 or (resid 494 \ through 499 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 0 through 505 or (resid 506 and (name N or name CA or name C or name O or name C \ B )) or resid 507 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 516 or resid 518 through 520 or resid 600 through \ 601)) selection = (chain 'C' and (resid 29 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 190 or (resid 191 thr \ ough 192 and (name N or name CA or name C or name O or name CB )) or resid 193 t \ hrough 316 or (resid 317 through 318 and (name N or name CA or name C or name O \ or name CB )) or resid 319 through 400 or (resid 401 through 402 and (name N or \ name CA or name C or name O or name CB )) or resid 403 through 413 or (resid 414 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 through 456 or (resid 457 and (name N or name CA or name C or name O or name \ CB )) or resid 458 through 469 or (resid 470 and (name N or name CA or name C or \ name O or name CB )) or resid 471 through 493 or (resid 494 through 499 and (na \ me N or name CA or name C or name O or name CB )) or resid 500 through 516 or re \ sid 518 through 520 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 285 or ( \ resid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 \ through 362 or (resid 363 through 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 369 or (resid 370 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 380 or (resid 38 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 382 through \ 391 or (resid 392 through 393 and (name N or name CA or name C or name O or name \ CB )) or resid 394 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 424 or (resid 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 137 or (resid 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 220 or (resid 22 \ 1 through 222 and (name N or name CA or name C or name O or name CB )) or resid \ 223 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 461 or (resid 462 through 463 and (name N or name CA or \ name C or name O or name CB )) or resid 464 through 465 or (resid 466 and (name \ N or name CA or name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.030 Extract box with map and model: 8.990 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 98.470 Find NCS groups from input model: 2.610 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.006 0.074 36090 Z= 0.428 Angle : 0.721 23.430 49013 Z= 0.472 Chirality : 0.043 0.223 5781 Planarity : 0.004 0.086 6366 Dihedral : 14.512 89.999 12833 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.51 % Favored : 98.36 % Rotamer: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % 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: -0.99 (0.11), residues: 4761 helix: -0.25 (0.09), residues: 2542 sheet: -0.62 (0.21), residues: 551 loop : -1.08 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 208 HIS 0.006 0.001 HIS C 474 PHE 0.025 0.002 PHE a 99 TYR 0.021 0.002 TYR a 48 ARG 0.009 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 850 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8442 (mm) cc_final: 0.8173 (mm) REVERT: A 78 ILE cc_start: 0.8154 (mt) cc_final: 0.7826 (mm) REVERT: A 153 ILE cc_start: 0.7945 (mt) cc_final: 0.7735 (mt) REVERT: A 272 ASP cc_start: 0.7382 (t0) cc_final: 0.7138 (t0) REVERT: A 444 GLN cc_start: 0.7886 (mt0) cc_final: 0.7449 (mt0) REVERT: B 77 VAL cc_start: 0.8576 (p) cc_final: 0.8213 (m) REVERT: B 83 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6825 (tt0) REVERT: B 159 MET cc_start: 0.7825 (mtp) cc_final: 0.7600 (mtp) REVERT: B 199 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7855 (mmtm) REVERT: B 330 ILE cc_start: 0.7977 (pt) cc_final: 0.7776 (mt) REVERT: B 337 ILE cc_start: 0.8980 (pt) cc_final: 0.8690 (mt) REVERT: B 356 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 488 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 491 LYS cc_start: 0.8319 (mttt) cc_final: 0.8104 (ttmm) REVERT: C 78 ILE cc_start: 0.8584 (mm) cc_final: 0.8340 (mm) REVERT: C 121 GLN cc_start: 0.8508 (tt0) cc_final: 0.8242 (tt0) REVERT: C 153 ILE cc_start: 0.8065 (mm) cc_final: 0.7757 (mt) REVERT: C 336 ASP cc_start: 0.7656 (t0) cc_final: 0.7401 (t0) REVERT: C 404 GLU cc_start: 0.8023 (tp30) cc_final: 0.7525 (tt0) REVERT: C 429 GLU cc_start: 0.7514 (tp30) cc_final: 0.7296 (tp30) REVERT: D 74 VAL cc_start: 0.8527 (t) cc_final: 0.8280 (p) REVERT: D 87 SER cc_start: 0.8501 (m) cc_final: 0.8233 (p) REVERT: D 175 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (t0) REVERT: D 219 GLN cc_start: 0.6512 (mm-40) cc_final: 0.6223 (mm-40) REVERT: D 235 LEU cc_start: 0.7936 (tp) cc_final: 0.7732 (tp) REVERT: E 13 VAL cc_start: 0.8248 (m) cc_final: 0.8047 (t) REVERT: E 34 ASN cc_start: 0.8185 (m-40) cc_final: 0.7946 (m-40) REVERT: E 164 VAL cc_start: 0.8588 (m) cc_final: 0.8256 (t) REVERT: E 173 MET cc_start: 0.7581 (mmm) cc_final: 0.7339 (mmt) REVERT: E 287 MET cc_start: 0.8051 (tpp) cc_final: 0.7529 (tpp) REVERT: E 292 GLU cc_start: 0.7415 (tp30) cc_final: 0.7122 (tp30) REVERT: E 413 SER cc_start: 0.8294 (m) cc_final: 0.7866 (t) REVERT: F 71 ASP cc_start: 0.7745 (t0) cc_final: 0.7512 (t0) REVERT: F 79 VAL cc_start: 0.8642 (t) cc_final: 0.8318 (m) REVERT: F 173 MET cc_start: 0.6724 (mmt) cc_final: 0.6172 (mmt) REVERT: F 196 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6201 (tm-30) REVERT: F 209 VAL cc_start: 0.8427 (t) cc_final: 0.8154 (p) REVERT: F 212 ASP cc_start: 0.7480 (t0) cc_final: 0.7120 (t0) REVERT: F 222 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7336 (mm-30) REVERT: F 391 ILE cc_start: 0.7994 (tt) cc_final: 0.7775 (mp) REVERT: F 414 GLN cc_start: 0.8484 (tt0) cc_final: 0.8143 (tt0) REVERT: F 466 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7748 (tttm) REVERT: G 41 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7525 (mm-30) REVERT: G 162 MET cc_start: 0.7571 (tpp) cc_final: 0.7266 (mmt) REVERT: G 207 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7581 (mt-10) REVERT: G 208 VAL cc_start: 0.8688 (t) cc_final: 0.8364 (p) REVERT: a 228 ILE cc_start: 0.8245 (mt) cc_final: 0.7939 (mt) REVERT: d 89 GLU cc_start: 0.7736 (tt0) cc_final: 0.7281 (mt-10) REVERT: d 295 GLN cc_start: 0.9133 (tp40) cc_final: 0.8893 (tp-100) REVERT: 3 53 LEU cc_start: 0.7575 (tp) cc_final: 0.7341 (tp) REVERT: 7 43 ILE cc_start: 0.8221 (mm) cc_final: 0.7928 (mt) outliers start: 5 outliers final: 1 residues processed: 855 average time/residue: 0.4979 time to fit residues: 679.2834 Evaluate side-chains 614 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 612 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 0.0980 chunk 360 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 373 optimal weight: 0.7980 chunk 144 optimal weight: 0.0070 chunk 226 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 432 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 263 ASN B 259 HIS B 305 HIS C 399 GLN C 420 GLN C 453 GLN C 455 HIS C 512 GLN D 326 HIS D 370 GLN D 425 GLN E 219 GLN E 383 GLN F 219 GLN G 25 GLN a 146 HIS d 116 GLN d 410 HIS 9 50 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36090 Z= 0.199 Angle : 0.565 8.213 49013 Z= 0.300 Chirality : 0.042 0.193 5781 Planarity : 0.005 0.053 6366 Dihedral : 6.539 88.971 5242 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.15 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.67 (0.12), residues: 4761 helix: 1.13 (0.10), residues: 2543 sheet: -0.16 (0.21), residues: 557 loop : -0.26 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 212 HIS 0.004 0.001 HIS H 38 PHE 0.027 0.001 PHE D 456 TYR 0.015 0.001 TYR a 145 ARG 0.005 0.000 ARG G 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 658 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8433 (mm) cc_final: 0.8158 (mm) REVERT: A 78 ILE cc_start: 0.8114 (mt) cc_final: 0.7833 (mm) REVERT: A 92 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7737 (mttm) REVERT: A 104 ASP cc_start: 0.7609 (m-30) cc_final: 0.7354 (m-30) REVERT: A 308 LEU cc_start: 0.8011 (tp) cc_final: 0.7689 (tt) REVERT: A 399 GLN cc_start: 0.7557 (mt0) cc_final: 0.7259 (mt0) REVERT: A 490 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8018 (mttm) REVERT: A 512 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 77 VAL cc_start: 0.8609 (p) cc_final: 0.8274 (m) REVERT: B 83 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6834 (tt0) REVERT: B 159 MET cc_start: 0.7798 (mtp) cc_final: 0.7596 (mtp) REVERT: B 384 LYS cc_start: 0.7826 (tppt) cc_final: 0.7428 (tptt) REVERT: B 491 LYS cc_start: 0.8502 (mttt) cc_final: 0.8195 (ttmm) REVERT: C 78 ILE cc_start: 0.8525 (mm) cc_final: 0.8280 (mm) REVERT: C 153 ILE cc_start: 0.8077 (mm) cc_final: 0.7841 (mt) REVERT: C 207 VAL cc_start: 0.8381 (t) cc_final: 0.7947 (m) REVERT: C 308 LEU cc_start: 0.7745 (tp) cc_final: 0.7538 (tt) REVERT: C 310 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7126 (mm-30) REVERT: C 404 GLU cc_start: 0.7962 (tp30) cc_final: 0.7713 (tt0) REVERT: C 429 GLU cc_start: 0.7460 (tp30) cc_final: 0.7163 (tp30) REVERT: C 491 LYS cc_start: 0.8376 (ptpt) cc_final: 0.7978 (ttpp) REVERT: D 87 SER cc_start: 0.8493 (m) cc_final: 0.8181 (p) REVERT: D 175 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7911 (t0) REVERT: D 228 MET cc_start: 0.7449 (mtp) cc_final: 0.7150 (mtp) REVERT: D 248 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6743 (p0) REVERT: D 342 ILE cc_start: 0.8215 (mm) cc_final: 0.7969 (mp) REVERT: D 443 THR cc_start: 0.8641 (p) cc_final: 0.8408 (t) REVERT: E 13 VAL cc_start: 0.8198 (m) cc_final: 0.7975 (t) REVERT: E 34 ASN cc_start: 0.8372 (m-40) cc_final: 0.8045 (m-40) REVERT: E 173 MET cc_start: 0.7636 (mmm) cc_final: 0.7430 (mmt) REVERT: E 292 GLU cc_start: 0.7364 (tp30) cc_final: 0.7111 (tp30) REVERT: E 305 MET cc_start: 0.7716 (mtp) cc_final: 0.7425 (mtp) REVERT: E 378 ARG cc_start: 0.7651 (tpt-90) cc_final: 0.7414 (tpt-90) REVERT: E 413 SER cc_start: 0.8305 (m) cc_final: 0.7895 (t) REVERT: F 70 THR cc_start: 0.8369 (p) cc_final: 0.8155 (p) REVERT: F 71 ASP cc_start: 0.7715 (t0) cc_final: 0.7480 (t0) REVERT: F 173 MET cc_start: 0.6142 (mmt) cc_final: 0.5882 (mmt) REVERT: F 185 SER cc_start: 0.8345 (t) cc_final: 0.7752 (p) REVERT: F 196 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6209 (tm-30) REVERT: F 212 ASP cc_start: 0.7509 (t0) cc_final: 0.7163 (t0) REVERT: F 222 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7332 (mm-30) REVERT: F 314 ASP cc_start: 0.7589 (t70) cc_final: 0.6772 (t70) REVERT: F 316 THR cc_start: 0.8684 (m) cc_final: 0.8148 (t) REVERT: F 360 ILE cc_start: 0.8823 (mt) cc_final: 0.8519 (mt) REVERT: F 414 GLN cc_start: 0.8432 (tt0) cc_final: 0.8157 (tt0) REVERT: F 436 ILE cc_start: 0.7615 (mm) cc_final: 0.7371 (mt) REVERT: G 6 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7303 (mtm-85) REVERT: G 41 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7554 (mm-30) REVERT: G 162 MET cc_start: 0.7463 (tpp) cc_final: 0.7222 (mmt) REVERT: G 202 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7818 (ttp80) REVERT: H 37 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6227 (mtm-85) REVERT: H 50 MET cc_start: 0.7876 (tmm) cc_final: 0.7629 (tmm) REVERT: a 62 VAL cc_start: 0.7342 (m) cc_final: 0.7134 (p) REVERT: a 228 ILE cc_start: 0.8321 (mt) cc_final: 0.7986 (mt) REVERT: d 89 GLU cc_start: 0.7783 (tt0) cc_final: 0.7581 (tt0) REVERT: d 295 GLN cc_start: 0.8932 (tp40) cc_final: 0.8714 (tp-100) REVERT: d 346 SER cc_start: 0.9206 (m) cc_final: 0.8800 (p) REVERT: 3 47 PRO cc_start: 0.6629 (Cg_exo) cc_final: 0.6424 (Cg_endo) REVERT: 7 43 ILE cc_start: 0.8205 (mm) cc_final: 0.7884 (mt) REVERT: 7 75 MET cc_start: 0.7056 (tmm) cc_final: 0.6639 (tmm) outliers start: 64 outliers final: 33 residues processed: 689 average time/residue: 0.3627 time to fit residues: 415.2435 Evaluate side-chains 646 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 611 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 359 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 433 optimal weight: 0.9990 chunk 467 optimal weight: 8.9990 chunk 385 optimal weight: 7.9990 chunk 429 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 347 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 435 GLN C 258 GLN ** C 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN E 121 HIS F 219 GLN G 93 ASN a 146 HIS 4 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36090 Z= 0.232 Angle : 0.538 8.504 49013 Z= 0.282 Chirality : 0.041 0.180 5781 Planarity : 0.004 0.061 6366 Dihedral : 6.228 86.162 5241 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.91 % Favored : 97.96 % Rotamer: Outliers : 2.53 % Allowed : 13.58 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % 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: 1.03 (0.12), residues: 4761 helix: 1.48 (0.10), residues: 2513 sheet: -0.08 (0.21), residues: 578 loop : -0.13 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 212 HIS 0.004 0.001 HIS D 326 PHE 0.031 0.001 PHE D 456 TYR 0.015 0.001 TYR a 145 ARG 0.006 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 629 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8412 (mm) cc_final: 0.8139 (mm) REVERT: A 78 ILE cc_start: 0.8163 (mt) cc_final: 0.7830 (mm) REVERT: A 92 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7704 (mttm) REVERT: A 157 ASP cc_start: 0.7705 (t70) cc_final: 0.7446 (t0) REVERT: A 308 LEU cc_start: 0.8084 (tp) cc_final: 0.7801 (tt) REVERT: A 490 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8037 (mttm) REVERT: A 512 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 77 VAL cc_start: 0.8592 (p) cc_final: 0.8290 (m) REVERT: B 83 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6905 (tt0) REVERT: B 356 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6803 (mt-10) REVERT: B 384 LYS cc_start: 0.7792 (tppt) cc_final: 0.7467 (tptt) REVERT: B 491 LYS cc_start: 0.8564 (mttt) cc_final: 0.8200 (ttmm) REVERT: C 78 ILE cc_start: 0.8516 (mm) cc_final: 0.8309 (mm) REVERT: C 142 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7675 (mtt-85) REVERT: C 153 ILE cc_start: 0.8096 (mm) cc_final: 0.7743 (mt) REVERT: C 173 ASP cc_start: 0.7174 (t0) cc_final: 0.6911 (t0) REVERT: C 207 VAL cc_start: 0.8401 (t) cc_final: 0.8042 (p) REVERT: C 308 LEU cc_start: 0.7797 (tp) cc_final: 0.7555 (tt) REVERT: C 310 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 404 GLU cc_start: 0.8027 (tp30) cc_final: 0.7673 (tt0) REVERT: C 429 GLU cc_start: 0.7452 (tp30) cc_final: 0.7135 (tp30) REVERT: C 450 LEU cc_start: 0.7922 (mp) cc_final: 0.7662 (mm) REVERT: C 470 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7389 (mt-10) REVERT: D 248 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6708 (p0) REVERT: D 256 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (tp) REVERT: E 34 ASN cc_start: 0.8421 (m-40) cc_final: 0.8100 (m-40) REVERT: E 120 ILE cc_start: 0.8145 (pt) cc_final: 0.7897 (pt) REVERT: E 173 MET cc_start: 0.7632 (mmm) cc_final: 0.7416 (mmt) REVERT: E 239 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7099 (mt-10) REVERT: E 292 GLU cc_start: 0.7426 (tp30) cc_final: 0.7212 (tp30) REVERT: E 378 ARG cc_start: 0.7660 (tpt-90) cc_final: 0.7423 (tpt-90) REVERT: E 413 SER cc_start: 0.8346 (m) cc_final: 0.8009 (t) REVERT: F 71 ASP cc_start: 0.7754 (t0) cc_final: 0.7480 (t0) REVERT: F 185 SER cc_start: 0.8336 (t) cc_final: 0.7789 (p) REVERT: F 196 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6204 (tm-30) REVERT: F 212 ASP cc_start: 0.7510 (t0) cc_final: 0.7173 (t0) REVERT: F 314 ASP cc_start: 0.7584 (t70) cc_final: 0.6727 (t70) REVERT: F 316 THR cc_start: 0.8615 (m) cc_final: 0.8057 (t) REVERT: F 360 ILE cc_start: 0.8822 (mt) cc_final: 0.8513 (mt) REVERT: F 436 ILE cc_start: 0.7620 (mm) cc_final: 0.7346 (mt) REVERT: G 6 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7291 (mtm-85) REVERT: G 63 LEU cc_start: 0.8620 (mp) cc_final: 0.8288 (pp) REVERT: G 79 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7187 (m) REVERT: G 83 SER cc_start: 0.8779 (m) cc_final: 0.8304 (p) REVERT: G 162 MET cc_start: 0.7532 (tpp) cc_final: 0.7250 (mmt) REVERT: H 7 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5648 (mt-10) REVERT: H 31 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7319 (mt-10) REVERT: H 50 MET cc_start: 0.7940 (tmm) cc_final: 0.7722 (tmm) REVERT: a 62 VAL cc_start: 0.7396 (m) cc_final: 0.7176 (p) REVERT: a 228 ILE cc_start: 0.8262 (mt) cc_final: 0.7965 (mt) REVERT: d 1 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5850 (ppp) REVERT: d 295 GLN cc_start: 0.8942 (tp40) cc_final: 0.8733 (tp-100) REVERT: d 346 SER cc_start: 0.9212 (m) cc_final: 0.8810 (p) REVERT: 3 47 PRO cc_start: 0.7131 (Cg_exo) cc_final: 0.6867 (Cg_endo) REVERT: 5 75 MET cc_start: 0.4405 (ttp) cc_final: 0.3451 (ttp) REVERT: 7 43 ILE cc_start: 0.8194 (mm) cc_final: 0.7851 (mt) REVERT: 7 75 MET cc_start: 0.7143 (tmm) cc_final: 0.6833 (tmm) REVERT: 9 75 MET cc_start: 0.8168 (ttp) cc_final: 0.7939 (ttp) outliers start: 88 outliers final: 58 residues processed: 673 average time/residue: 0.4705 time to fit residues: 533.6884 Evaluate side-chains 645 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 583 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 225 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 206 optimal weight: 0.6980 chunk 290 optimal weight: 0.7980 chunk 434 optimal weight: 0.9990 chunk 460 optimal weight: 30.0000 chunk 227 optimal weight: 3.9990 chunk 411 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 455 HIS D 247 GLN E 117 HIS G 184 HIS a 146 HIS d 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36090 Z= 0.195 Angle : 0.509 7.370 49013 Z= 0.267 Chirality : 0.041 0.192 5781 Planarity : 0.004 0.062 6366 Dihedral : 5.883 83.505 5239 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.98 % Rotamer: Outliers : 3.04 % Allowed : 15.01 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % 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: 1.22 (0.13), residues: 4761 helix: 1.66 (0.11), residues: 2522 sheet: -0.01 (0.21), residues: 580 loop : -0.09 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 212 HIS 0.004 0.001 HIS a 146 PHE 0.039 0.001 PHE D 456 TYR 0.016 0.001 TYR a 145 ARG 0.006 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 618 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8420 (mm) cc_final: 0.8122 (mm) REVERT: A 52 THR cc_start: 0.8755 (m) cc_final: 0.8390 (t) REVERT: A 78 ILE cc_start: 0.8119 (mt) cc_final: 0.7780 (mm) REVERT: A 92 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7690 (mttm) REVERT: A 157 ASP cc_start: 0.7679 (t70) cc_final: 0.7405 (t0) REVERT: A 308 LEU cc_start: 0.8103 (tp) cc_final: 0.7821 (tt) REVERT: A 490 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8064 (mttm) REVERT: A 512 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 77 VAL cc_start: 0.8655 (p) cc_final: 0.8335 (m) REVERT: B 83 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6895 (tt0) REVERT: B 267 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8055 (p) REVERT: B 384 LYS cc_start: 0.7737 (tppt) cc_final: 0.7413 (tptt) REVERT: B 491 LYS cc_start: 0.8586 (mttt) cc_final: 0.8201 (ttmm) REVERT: C 102 VAL cc_start: 0.8309 (p) cc_final: 0.7868 (t) REVERT: C 153 ILE cc_start: 0.8044 (mm) cc_final: 0.7786 (mt) REVERT: C 173 ASP cc_start: 0.7288 (t0) cc_final: 0.6966 (t0) REVERT: C 207 VAL cc_start: 0.8423 (t) cc_final: 0.8009 (m) REVERT: C 308 LEU cc_start: 0.7790 (tp) cc_final: 0.7560 (tt) REVERT: C 310 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 384 LYS cc_start: 0.7478 (ttpp) cc_final: 0.7253 (ttpp) REVERT: C 404 GLU cc_start: 0.8035 (tp30) cc_final: 0.7671 (tt0) REVERT: C 429 GLU cc_start: 0.7416 (tp30) cc_final: 0.7070 (tp30) REVERT: C 449 PHE cc_start: 0.8254 (t80) cc_final: 0.8053 (t80) REVERT: D 248 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6697 (p0) REVERT: D 256 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7936 (tp) REVERT: E 34 ASN cc_start: 0.8396 (m-40) cc_final: 0.8067 (m-40) REVERT: E 120 ILE cc_start: 0.8117 (pt) cc_final: 0.7877 (pt) REVERT: E 173 MET cc_start: 0.7637 (mmm) cc_final: 0.7422 (mmt) REVERT: E 239 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: E 292 GLU cc_start: 0.7406 (tp30) cc_final: 0.7175 (tp30) REVERT: E 413 SER cc_start: 0.8339 (m) cc_final: 0.8019 (t) REVERT: F 26 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7604 (mmm-85) REVERT: F 70 THR cc_start: 0.8401 (p) cc_final: 0.8188 (p) REVERT: F 71 ASP cc_start: 0.7670 (t0) cc_final: 0.7283 (t0) REVERT: F 185 SER cc_start: 0.8283 (t) cc_final: 0.7811 (p) REVERT: F 196 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6206 (tm-30) REVERT: F 212 ASP cc_start: 0.7508 (t0) cc_final: 0.7177 (t0) REVERT: F 305 MET cc_start: 0.7366 (tpp) cc_final: 0.7095 (ttt) REVERT: F 314 ASP cc_start: 0.7552 (t70) cc_final: 0.6968 (t70) REVERT: F 436 ILE cc_start: 0.7620 (mm) cc_final: 0.7346 (mt) REVERT: G 6 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7269 (mtm-85) REVERT: G 83 SER cc_start: 0.8768 (m) cc_final: 0.8307 (p) REVERT: G 162 MET cc_start: 0.7510 (tpp) cc_final: 0.7223 (mmt) REVERT: H 7 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5705 (mt-10) REVERT: H 31 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7299 (mt-10) REVERT: a 228 ILE cc_start: 0.8221 (mt) cc_final: 0.7935 (mt) REVERT: d 346 SER cc_start: 0.9196 (m) cc_final: 0.8826 (p) REVERT: d 400 ILE cc_start: 0.8944 (mt) cc_final: 0.8676 (mt) REVERT: 7 75 MET cc_start: 0.7207 (tmm) cc_final: 0.6563 (tmm) REVERT: 9 75 MET cc_start: 0.8177 (ttp) cc_final: 0.7903 (ttp) outliers start: 106 outliers final: 66 residues processed: 680 average time/residue: 0.4473 time to fit residues: 509.5023 Evaluate side-chains 659 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 589 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 392 optimal weight: 20.0000 chunk 318 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN D 97 HIS ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36090 Z= 0.251 Angle : 0.534 8.547 49013 Z= 0.276 Chirality : 0.042 0.203 5781 Planarity : 0.004 0.064 6366 Dihedral : 5.876 85.691 5239 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 3.56 % Allowed : 15.76 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % 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: 1.26 (0.13), residues: 4761 helix: 1.70 (0.11), residues: 2524 sheet: 0.02 (0.22), residues: 578 loop : -0.11 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.005 0.001 HIS D 326 PHE 0.048 0.001 PHE D 456 TYR 0.014 0.001 TYR a 145 ARG 0.007 0.000 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 606 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8391 (mm) cc_final: 0.8126 (mm) REVERT: A 92 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7778 (mttm) REVERT: A 308 LEU cc_start: 0.8200 (tp) cc_final: 0.7942 (tt) REVERT: A 490 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8108 (mttm) REVERT: B 77 VAL cc_start: 0.8607 (p) cc_final: 0.8286 (m) REVERT: B 83 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6880 (tt0) REVERT: B 277 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: B 384 LYS cc_start: 0.7765 (tppt) cc_final: 0.7449 (tptt) REVERT: B 491 LYS cc_start: 0.8632 (mttt) cc_final: 0.8221 (ttmm) REVERT: C 102 VAL cc_start: 0.8355 (p) cc_final: 0.7895 (t) REVERT: C 153 ILE cc_start: 0.8054 (mm) cc_final: 0.7853 (mt) REVERT: C 189 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7505 (mp10) REVERT: C 384 LYS cc_start: 0.7468 (ttpp) cc_final: 0.7260 (ttpp) REVERT: C 404 GLU cc_start: 0.8099 (tp30) cc_final: 0.7723 (tt0) REVERT: C 429 GLU cc_start: 0.7497 (tp30) cc_final: 0.7113 (tp30) REVERT: C 449 PHE cc_start: 0.8322 (t80) cc_final: 0.8048 (t80) REVERT: C 470 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7362 (mt-10) REVERT: D 256 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7881 (tp) REVERT: D 266 VAL cc_start: 0.7843 (m) cc_final: 0.7608 (p) REVERT: D 269 LEU cc_start: 0.8975 (mt) cc_final: 0.8757 (mp) REVERT: D 305 MET cc_start: 0.7849 (tpp) cc_final: 0.7320 (ttm) REVERT: D 420 GLU cc_start: 0.7357 (tp30) cc_final: 0.7039 (tp30) REVERT: E 34 ASN cc_start: 0.8419 (m-40) cc_final: 0.8047 (m-40) REVERT: E 120 ILE cc_start: 0.8086 (pt) cc_final: 0.7864 (pt) REVERT: E 173 MET cc_start: 0.7633 (mmm) cc_final: 0.7428 (mmt) REVERT: E 185 SER cc_start: 0.8099 (t) cc_final: 0.7899 (m) REVERT: E 239 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: E 249 VAL cc_start: 0.8161 (t) cc_final: 0.7914 (m) REVERT: E 287 MET cc_start: 0.8063 (tpp) cc_final: 0.7630 (tpp) REVERT: E 292 GLU cc_start: 0.7427 (tp30) cc_final: 0.7189 (tp30) REVERT: E 353 SER cc_start: 0.8695 (t) cc_final: 0.8335 (m) REVERT: E 413 SER cc_start: 0.8431 (m) cc_final: 0.8103 (t) REVERT: F 26 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7663 (mmm-85) REVERT: F 70 THR cc_start: 0.8476 (p) cc_final: 0.8234 (p) REVERT: F 71 ASP cc_start: 0.7699 (t0) cc_final: 0.7362 (t0) REVERT: F 185 SER cc_start: 0.8274 (t) cc_final: 0.7799 (p) REVERT: F 212 ASP cc_start: 0.7527 (t0) cc_final: 0.7166 (t0) REVERT: F 277 VAL cc_start: 0.8949 (m) cc_final: 0.8571 (p) REVERT: F 310 VAL cc_start: 0.8460 (t) cc_final: 0.8228 (m) REVERT: F 314 ASP cc_start: 0.7509 (t70) cc_final: 0.6970 (t70) REVERT: F 360 ILE cc_start: 0.8825 (mt) cc_final: 0.8498 (mt) REVERT: G 83 SER cc_start: 0.8752 (m) cc_final: 0.8298 (p) REVERT: G 162 MET cc_start: 0.7543 (tpp) cc_final: 0.7215 (mmt) REVERT: G 202 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7936 (ttp-170) REVERT: H 7 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5888 (mt-10) REVERT: H 31 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7317 (mt-10) REVERT: a 228 ILE cc_start: 0.8179 (mt) cc_final: 0.7878 (mt) REVERT: d 346 SER cc_start: 0.9206 (m) cc_final: 0.8839 (p) REVERT: d 400 ILE cc_start: 0.8911 (mt) cc_final: 0.8670 (mt) REVERT: d 428 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6760 (mt) REVERT: 5 75 MET cc_start: 0.4679 (ttp) cc_final: 0.3945 (ttp) REVERT: 7 20 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6911 (mm) REVERT: 7 75 MET cc_start: 0.7331 (tmm) cc_final: 0.7085 (tmm) outliers start: 124 outliers final: 85 residues processed: 677 average time/residue: 0.3817 time to fit residues: 433.4941 Evaluate side-chains 667 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 577 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain d residue 428 ILE Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 75 MET Chi-restraints excluded: chain 7 residue 20 ILE Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 0.8980 chunk 414 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 460 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 241 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: