Starting phenix.real_space_refine on Sat Mar 23 19:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/03_2024/7nyd_12651.pdb" } resolution = 3.27 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 256 5.16 5 C 24072 2.51 5 N 6598 2.21 5 O 7500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "E ARG 381": "NH1" <-> "NH2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 122": "NH1" <-> "NH2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G GLU 319": "OE1" <-> "OE2" Residue "G GLU 336": "OE1" <-> "OE2" Residue "G ARG 348": "NH1" <-> "NH2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G GLU 418": "OE1" <-> "OE2" Residue "G ARG 425": "NH1" <-> "NH2" Residue "G ARG 475": "NH1" <-> "NH2" Residue "G ARG 487": "NH1" <-> "NH2" Residue "G GLU 519": "OE1" <-> "OE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C GLU 579": "OE1" <-> "OE2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C GLU 644": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 532": "OE1" <-> "OE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 588": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B GLU 690": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H ARG 122": "NH1" <-> "NH2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H GLU 279": "OE1" <-> "OE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H GLU 313": "OE1" <-> "OE2" Residue "H GLU 319": "OE1" <-> "OE2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 348": "NH1" <-> "NH2" Residue "H ARG 475": "NH1" <-> "NH2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A GLU 940": "OE1" <-> "OE2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A GLU 1076": "OE1" <-> "OE2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A GLU 1197": "OE1" <-> "OE2" Residue "A GLU 1231": "OE1" <-> "OE2" Residue "A GLU 1258": "OE1" <-> "OE2" Residue "A GLU 1259": "OE1" <-> "OE2" Residue "A ARG 1261": "NH1" <-> "NH2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A TYR 1478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1511": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38430 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3914 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 2 Chain: "E" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3819 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3259 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 5977 Classifications: {'peptide': 809} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 88} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 763} Chain breaks: 2 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5631 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2517 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 308} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1319 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "A" Number of atoms: 11744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 11744 Classifications: {'peptide': 1542} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1475} Chain breaks: 3 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 413 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 279 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CA': 1, 'BMA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CA': 1, 'BMA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 20.81, per 1000 atoms: 0.54 Number of scatterers: 38430 At special positions: 0 Unit cell: (236.622, 256.515, 170.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 256 16.00 O 7500 8.00 N 6598 7.00 C 24072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 449 " - pdb=" SG CYS D 496 " distance=2.04 Simple disulfide: pdb=" SG CYS D 451 " - pdb=" SG CYS D 467 " distance=2.05 Simple disulfide: pdb=" SG CYS D 454 " - pdb=" SG CYS D 469 " distance=2.04 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 480 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 44 " distance=2.01 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 54 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 78 " distance=2.04 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 91 " distance=2.02 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS F 40 " distance=2.19 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 514 " distance=2.02 Simple disulfide: pdb=" SG CYS E 469 " - pdb=" SG CYS E 485 " distance=2.05 Simple disulfide: pdb=" SG CYS E 472 " - pdb=" SG CYS E 487 " distance=2.04 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.02 Simple disulfide: pdb=" SG CYS E 521 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 532 " - pdb=" SG CYS E 544 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 57 " distance=2.02 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 73 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 86 " - pdb=" SG CYS G 104 " distance=2.02 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 113 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 160 " distance=2.05 Simple disulfide: pdb=" SG CYS G 489 " - pdb=" SG CYS G 505 " distance=2.03 Simple disulfide: pdb=" SG CYS G 492 " - pdb=" SG CYS G 507 " distance=2.03 Simple disulfide: pdb=" SG CYS G 509 " - pdb=" SG CYS G 518 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 41 " distance=2.04 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 51 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 57 " distance=1.99 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 87 " distance=2.00 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 143 " distance=2.05 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 538 " distance=2.04 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 483 " distance=2.04 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 451 " distance=2.01 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 464 " distance=2.05 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 523 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 513 " distance=2.04 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 591 " distance=2.02 Simple disulfide: pdb=" SG CYS C 577 " - pdb=" SG CYS C 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 666 " distance=2.02 Simple disulfide: pdb=" SG CYS C 783 " - pdb=" SG CYS C 816 " distance=2.02 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 40 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 44 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 106 " distance=2.01 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 399 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 602 " distance=2.02 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 549 " distance=2.05 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 520 " distance=2.05 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 531 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 580 " distance=2.04 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 665 " distance=2.04 Simple disulfide: pdb=" SG CYS B 651 " - pdb=" SG CYS B 678 " distance=2.01 Simple disulfide: pdb=" SG CYS B 683 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 711 " - pdb=" SG CYS B 740 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 86 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 359 " - pdb=" SG CYS H 384 " distance=2.04 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 792 " distance=2.04 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 651 " distance=2.02 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 865 " distance=2.02 Simple disulfide: pdb=" SG CYS A 848 " - pdb=" SG CYS A1509 " distance=2.04 Simple disulfide: pdb=" SG CYS A1083 " - pdb=" SG CYS A1141 " distance=2.03 Simple disulfide: pdb=" SG CYS A1357 " - pdb=" SG CYS A1487 " distance=2.04 Simple disulfide: pdb=" SG CYS A1387 " - pdb=" SG CYS A1456 " distance=2.04 Simple disulfide: pdb=" SG CYS A1502 " - pdb=" SG CYS A1507 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B1001 " - " ASN B 303 " " NAG G 601 " - " ASN G 394 " " NAG H 601 " - " ASN H 394 " " NAG I 1 " - " ASN D 189 " " NAG J 1 " - " ASN E 407 " " NAG K 1 " - " ASN A 893 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.07 Conformation dependent library (CDL) restraints added in 7.6 seconds 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9194 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 72 sheets defined 19.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.512A pdb=" N LEU D 85 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.902A pdb=" N TYR D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 391 through 403 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 427 through 447 Processing helix chain 'D' and resid 448 through 451 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.983A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.694A pdb=" N ALA E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 397 through 407 Processing helix chain 'E' and resid 411 through 421 removed outlier: 3.567A pdb=" N LYS E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 439 removed outlier: 4.315A pdb=" N LEU E 438 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 439 " --> pdb=" O HIS E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 434 through 439' Processing helix chain 'E' and resid 446 through 464 removed outlier: 3.509A pdb=" N GLN E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET E 462 " --> pdb=" O ASP E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 102 through 106 removed outlier: 4.141A pdb=" N GLY G 105 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP G 106 " --> pdb=" O ASP G 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 106' Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.644A pdb=" N PHE G 317 " --> pdb=" O GLU G 313 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 320 " --> pdb=" O ALA G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 423 removed outlier: 3.748A pdb=" N GLU G 421 " --> pdb=" O PHE G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 441 Processing helix chain 'G' and resid 456 through 459 Processing helix chain 'G' and resid 465 through 483 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.611A pdb=" N TYR C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 411 through 431 removed outlier: 3.678A pdb=" N LEU C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.508A pdb=" N LEU C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 771 through 775 removed outlier: 3.546A pdb=" N CYS C 775 " --> pdb=" O ALA C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 804 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.562A pdb=" N ARG B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 329 through 341 removed outlier: 4.031A pdb=" N ILE B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.817A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 473 removed outlier: 3.611A pdb=" N VAL B 473 " --> pdb=" O VAL B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 473' Processing helix chain 'B' and resid 478 through 498 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 606 through 610 removed outlier: 3.673A pdb=" N MET B 609 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 610' Processing helix chain 'H' and resid 96 through 100 removed outlier: 4.577A pdb=" N GLY H 100 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 4.218A pdb=" N ASP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.964A pdb=" N THR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.580A pdb=" N ASP H 301 " --> pdb=" O THR H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 343 through 348 Processing helix chain 'H' and resid 352 through 361 Processing helix chain 'H' and resid 412 through 425 Processing helix chain 'H' and resid 430 through 441 removed outlier: 3.644A pdb=" N PHE H 434 " --> pdb=" O ASP H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 459 Processing helix chain 'H' and resid 465 through 484 removed outlier: 3.742A pdb=" N ASP H 479 " --> pdb=" O ARG H 475 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE H 481 " --> pdb=" O ILE H 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.695A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 93 through 97 removed outlier: 4.109A pdb=" N ALA F 96 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 97 " --> pdb=" O LEU F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 97' Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 172 through 176 removed outlier: 4.098A pdb=" N VAL F 176 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.693A pdb=" N LEU A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.508A pdb=" N ALA A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 991 through 1010 Proline residue: A 999 - end of helix removed outlier: 3.584A pdb=" N TYR A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1040 removed outlier: 3.547A pdb=" N LYS A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1073 removed outlier: 4.018A pdb=" N LYS A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1093 removed outlier: 3.620A pdb=" N ILE A1082 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.880A pdb=" N ASN A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1179 removed outlier: 3.931A pdb=" N LEU A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1197 removed outlier: 3.563A pdb=" N ARG A1188 " --> pdb=" O HIS A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1244 Processing helix chain 'A' and resid 1245 through 1257 Proline residue: A1251 - end of helix Processing helix chain 'A' and resid 1268 through 1290 removed outlier: 3.517A pdb=" N THR A1272 " --> pdb=" O SER A1268 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A1290 " --> pdb=" O VAL A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1422 Processing helix chain 'A' and resid 1422 through 1427 Processing helix chain 'A' and resid 1526 through 1536 removed outlier: 3.537A pdb=" N ARG A1530 " --> pdb=" O SER A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1557 removed outlier: 4.245A pdb=" N VAL A1557 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1592 removed outlier: 3.788A pdb=" N GLU A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1656 Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.760A pdb=" N SER D 39 " --> pdb=" O CYS D 467 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N CYS D 469 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.485A pdb=" N GLY D 124 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 166 current: chain 'D' and resid 220 through 252 removed outlier: 6.952A pdb=" N LEU D 296 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS D 249 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 294 " --> pdb=" O HIS D 249 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 251 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR D 292 " --> pdb=" O LYS D 251 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 351 through 374 current: chain 'E' and resid 133 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 133 through 136 current: chain 'E' and resid 246 through 273 removed outlier: 5.380A pdb=" N ASN E 247 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N SER E 339 " --> pdb=" O ASN E 247 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU E 249 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE E 337 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS E 251 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU E 335 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN E 253 " --> pdb=" O GLU E 333 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU E 333 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS E 255 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS E 331 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE E 257 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS E 329 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 259 " --> pdb=" O ILE E 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 327 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG E 261 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU E 325 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE E 263 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR E 323 " --> pdb=" O PHE E 263 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYS E 265 " --> pdb=" O TYR E 321 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR E 321 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN E 267 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY E 319 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR E 313 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 336 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 378 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR E 338 " --> pdb=" O LYS E 376 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 376 through 394 current: chain 'G' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 145 through 147 current: chain 'G' and resid 261 through 287 removed outlier: 5.335A pdb=" N LEU G 331 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG G 284 " --> pdb=" O GLY G 329 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY G 329 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL G 286 " --> pdb=" O SER G 327 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER G 327 " --> pdb=" O VAL G 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 409 current: chain 'C' and resid 129 through 132 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 132 current: chain 'C' and resid 205 through 241 removed outlier: 6.878A pdb=" N LEU C 287 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA C 238 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C 285 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE C 240 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN C 283 " --> pdb=" O PHE C 240 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 351 current: chain 'B' and resid 182 through 186 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 182 through 186 current: chain 'B' and resid 269 through 306 removed outlier: 7.033A pdb=" N LEU B 350 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 303 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 348 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 305 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 346 " --> pdb=" O THR B 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 424 current: chain 'H' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 267 through 272 current: chain 'H' and resid 324 through 336 Processing sheet with id=AA8, first strand: chain 'D' and resid 506 through 509 Processing sheet with id=AA9, first strand: chain 'E' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB4, first strand: chain 'E' and resid 527 through 529 Processing sheet with id=AB5, first strand: chain 'G' and resid 20 through 24 removed outlier: 6.422A pdb=" N ASP G 21 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE G 49 " --> pdb=" O ASP G 21 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG G 23 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 39 through 43 Processing sheet with id=AB7, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'G' and resid 127 through 128 removed outlier: 6.884A pdb=" N GLU G 127 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 499 through 501 Processing sheet with id=AC1, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AC2, first strand: chain 'C' and resid 23 through 27 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AC5, first strand: chain 'C' and resid 443 through 446 removed outlier: 4.138A pdb=" N LEU C 443 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 459 through 460 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AC8, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC9, first strand: chain 'C' and resid 581 through 584 Processing sheet with id=AD1, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AD2, first strand: chain 'C' and resid 619 through 620 removed outlier: 3.605A pdb=" N LEU C 650 " --> pdb=" O SER C 658 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 658 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 715 through 719 Processing sheet with id=AD4, first strand: chain 'C' and resid 758 through 760 Processing sheet with id=AD5, first strand: chain 'C' and resid 789 through 794 removed outlier: 6.872A pdb=" N CYS C 783 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 21 through 26 Processing sheet with id=AD7, first strand: chain 'B' and resid 62 through 63 removed outlier: 6.741A pdb=" N LEU B 62 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 78 through 82 Processing sheet with id=AD9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AE1, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AE2, first strand: chain 'B' and resid 510 through 513 Processing sheet with id=AE3, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AE4, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AE5, first strand: chain 'B' and resid 623 through 624 Processing sheet with id=AE6, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AE7, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AE8, first strand: chain 'B' and resid 682 through 684 Processing sheet with id=AE9, first strand: chain 'B' and resid 694 through 695 removed outlier: 4.658A pdb=" N GLU B 708 " --> pdb=" O THR B 695 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 84 through 86 removed outlier: 3.728A pdb=" N ARG H 90 " --> pdb=" O CYS H 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.581A pdb=" N THR H 170 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 29 through 37 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 75 through 83 current: chain 'F' and resid 104 through 111 removed outlier: 6.943A pdb=" N VAL F 117 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR F 110 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE F 115 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 62 through 67 removed outlier: 9.084A pdb=" N ASN A 20 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.574A pdb=" N SER A 49 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AF7, first strand: chain 'A' and resid 107 through 112 Processing sheet with id=AF8, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.854A pdb=" N THR A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A 157 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 143 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET A 155 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 209 through 215 removed outlier: 3.650A pdb=" N LYS A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 219 through 220 removed outlier: 5.727A pdb=" N LEU A 305 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.775A pdb=" N LYS A 335 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 369 through 377 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 385 current: chain 'A' and resid 431 through 437 Processing sheet with id=AG4, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AG5, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AG6, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.755A pdb=" N SER A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER A 487 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 480 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 527 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 554 through 557 Processing sheet with id=AG8, first strand: chain 'A' and resid 580 through 588 removed outlier: 4.819A pdb=" N ALA A 586 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 756 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 588 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 754 " --> pdb=" O ASP A 588 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 754 through 762 current: chain 'A' and resid 790 through 793 Processing sheet with id=AG9, first strand: chain 'A' and resid 805 through 810 removed outlier: 3.916A pdb=" N LYS A 824 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 815 through 816 removed outlier: 5.793A pdb=" N VAL A 815 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 835 through 836 Processing sheet with id=AH3, first strand: chain 'A' and resid 916 through 926 removed outlier: 5.552A pdb=" N VAL A 961 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG A1318 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY A 963 " --> pdb=" O LEU A1316 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU A1316 " --> pdb=" O GLY A 963 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 938 through 941 removed outlier: 6.241A pdb=" N MET A1293 " --> pdb=" O LYS A1309 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS A1309 " --> pdb=" O MET A1293 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A1295 " --> pdb=" O ASN A1307 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A1307 " --> pdb=" O ILE A1295 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A1297 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 1199 through 1201 Processing sheet with id=AH6, first strand: chain 'A' and resid 1359 through 1366 Processing sheet with id=AH7, first strand: chain 'A' and resid 1432 through 1438 removed outlier: 4.104A pdb=" N ASP A1434 " --> pdb=" O GLN A1445 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS A1485 " --> pdb=" O GLU A1479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 1498 through 1499 Processing sheet with id=AH9, first strand: chain 'A' and resid 1560 through 1566 removed outlier: 6.581A pdb=" N LYS A1560 " --> pdb=" O THR A1548 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A1544 " --> pdb=" O LEU A1564 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE A1566 " --> pdb=" O ALA A1542 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A1542 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1543 " --> pdb=" O ILE A1601 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.36 Time building geometry restraints manager: 18.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6959 1.30 - 1.43: 10006 1.43 - 1.56: 21940 1.56 - 1.69: 3 1.69 - 1.82: 322 Bond restraints: 39230 Sorted by residual: bond pdb=" C ASP C 173 " pdb=" O ASP C 173 " ideal model delta sigma weight residual 1.234 1.174 0.061 1.11e-02 8.12e+03 2.97e+01 bond pdb=" CA SER C 15 " pdb=" C SER C 15 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.42e-02 4.96e+03 2.69e+01 bond pdb=" C SER C 15 " pdb=" O SER C 15 " ideal model delta sigma weight residual 1.233 1.171 0.063 1.28e-02 6.10e+03 2.39e+01 bond pdb=" CA TRP C 14 " pdb=" C TRP C 14 " ideal model delta sigma weight residual 1.527 1.466 0.060 1.35e-02 5.49e+03 2.01e+01 bond pdb=" C ILE A 887 " pdb=" O ILE A 887 " ideal model delta sigma weight residual 1.236 1.289 -0.052 1.19e-02 7.06e+03 1.94e+01 ... (remaining 39225 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.00: 704 105.00 - 112.63: 17538 112.63 - 120.25: 18721 120.25 - 127.88: 15897 127.88 - 135.50: 286 Bond angle restraints: 53146 Sorted by residual: angle pdb=" CA PHE A1209 " pdb=" CB PHE A1209 " pdb=" CG PHE A1209 " ideal model delta sigma weight residual 113.80 125.59 -11.79 1.00e+00 1.00e+00 1.39e+02 angle pdb=" N PRO D 518 " pdb=" CA PRO D 518 " pdb=" C PRO D 518 " ideal model delta sigma weight residual 110.70 121.22 -10.52 1.22e+00 6.72e-01 7.44e+01 angle pdb=" CA ASP E 201 " pdb=" CB ASP E 201 " pdb=" CG ASP E 201 " ideal model delta sigma weight residual 112.60 120.51 -7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA PHE B 633 " pdb=" CB PHE B 633 " pdb=" CG PHE B 633 " ideal model delta sigma weight residual 113.80 121.55 -7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" CA ASN H 465 " pdb=" CB ASN H 465 " pdb=" CG ASN H 465 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.00e+00 1.00e+00 4.99e+01 ... (remaining 53141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 23129 27.20 - 54.39: 769 54.39 - 81.58: 136 81.58 - 108.78: 52 108.78 - 135.97: 21 Dihedral angle restraints: 24107 sinusoidal: 9788 harmonic: 14319 Sorted by residual: dihedral pdb=" CB CYS A 838 " pdb=" SG CYS A 838 " pdb=" SG CYS A 865 " pdb=" CB CYS A 865 " ideal model delta sinusoidal sigma weight residual -86.00 -171.56 85.56 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS D 503 " pdb=" SG CYS D 503 " pdb=" SG CYS D 536 " pdb=" CB CYS D 536 " ideal model delta sinusoidal sigma weight residual -86.00 -149.89 63.89 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" C ARG H 348 " pdb=" N ARG H 348 " pdb=" CA ARG H 348 " pdb=" CB ARG H 348 " ideal model delta harmonic sigma weight residual -122.60 -139.08 16.48 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 24104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 5389 0.174 - 0.348: 443 0.348 - 0.522: 16 0.522 - 0.696: 0 0.696 - 0.870: 3 Chirality restraints: 5851 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.45e+01 ... (remaining 5848 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.356 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG J 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " -0.353 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG B1001 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 601 " 0.332 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG H 601 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG H 601 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG H 601 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG H 601 " 0.124 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 10 2.21 - 2.88: 13378 2.88 - 3.55: 51956 3.55 - 4.23: 88192 4.23 - 4.90: 148063 Nonbonded interactions: 301599 Sorted by model distance: nonbonded pdb=" NH2 ARG D 67 " pdb=" OE2 GLU D 69 " model vdw 1.536 2.520 nonbonded pdb=" CG2 ILE A 887 " pdb=" O VAL A 911 " model vdw 1.908 3.460 nonbonded pdb=" O ASP E 88 " pdb="CA CA E 603 " model vdw 1.972 2.510 nonbonded pdb=" OD1 ASN H 394 " pdb=" C2 NAG H 601 " model vdw 2.044 3.470 nonbonded pdb=" NE2 GLN H 471 " pdb=" O3 BMA G 602 " model vdw 2.079 2.520 ... (remaining 301594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.380 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 107.480 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.084 39230 Z= 0.825 Angle : 1.843 13.886 53146 Z= 1.220 Chirality : 0.104 0.870 5851 Planarity : 0.017 0.307 6944 Dihedral : 15.561 135.974 14634 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 0.66 % Allowed : 3.79 % Favored : 95.55 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -1.14 (0.11), residues: 4890 helix: -1.76 (0.15), residues: 746 sheet: 0.44 (0.14), residues: 1250 loop : -1.03 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.200 0.027 TRP A 542 HIS 0.027 0.004 HIS H 467 PHE 0.108 0.015 PHE H 191 TYR 0.233 0.023 TYR H 335 ARG 0.018 0.001 ARG G 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1275 time to evaluate : 4.564 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: D 52 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8714 (mm-30) REVERT: D 71 PHE cc_start: 0.7959 (t80) cc_final: 0.7536 (t80) REVERT: D 116 TRP cc_start: 0.8554 (m-10) cc_final: 0.8285 (m100) REVERT: D 128 PHE cc_start: 0.8882 (m-80) cc_final: 0.8523 (m-80) REVERT: D 141 TYR cc_start: 0.8484 (t80) cc_final: 0.8139 (t80) REVERT: D 155 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7872 (ttm110) REVERT: D 253 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8065 (mtpt) REVERT: D 268 LYS cc_start: 0.8047 (mttt) cc_final: 0.7346 (mtpp) REVERT: D 269 ARG cc_start: 0.8443 (mtt180) cc_final: 0.8130 (ttp-110) REVERT: D 303 THR cc_start: 0.8786 (t) cc_final: 0.8405 (m) REVERT: D 387 GLN cc_start: 0.8605 (pt0) cc_final: 0.7953 (pt0) REVERT: D 405 ASN cc_start: 0.8844 (t0) cc_final: 0.8582 (t0) REVERT: D 432 ARG cc_start: 0.8707 (mtt180) cc_final: 0.7968 (ttm110) REVERT: D 443 GLN cc_start: 0.9067 (tt0) cc_final: 0.8851 (tt0) REVERT: D 446 VAL cc_start: 0.8950 (m) cc_final: 0.7681 (p) REVERT: D 465 SER cc_start: 0.8555 (m) cc_final: 0.8161 (p) REVERT: E 14 TRP cc_start: 0.8437 (m100) cc_final: 0.7214 (m100) REVERT: E 31 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8122 (mtm180) REVERT: E 50 ASP cc_start: 0.8875 (t0) cc_final: 0.8516 (t0) REVERT: E 139 ASP cc_start: 0.9166 (t0) cc_final: 0.8825 (t0) REVERT: E 160 TYR cc_start: 0.8557 (t80) cc_final: 0.8180 (t80) REVERT: E 161 ASP cc_start: 0.8902 (t0) cc_final: 0.8670 (t0) REVERT: E 163 THR cc_start: 0.8322 (p) cc_final: 0.7997 (t) REVERT: E 182 PHE cc_start: 0.8394 (m-80) cc_final: 0.7693 (m-80) REVERT: E 267 GLN cc_start: 0.8724 (mt0) cc_final: 0.8211 (mt0) REVERT: E 275 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8695 (tttp) REVERT: E 277 ASP cc_start: 0.8673 (m-30) cc_final: 0.8435 (t0) REVERT: E 279 MET cc_start: 0.8063 (tpp) cc_final: 0.7794 (tpp) REVERT: E 394 ARG cc_start: 0.8854 (mtt90) cc_final: 0.8481 (ttm110) REVERT: E 408 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7903 (ttp-110) REVERT: E 429 PHE cc_start: 0.7995 (p90) cc_final: 0.7517 (p90) REVERT: E 446 LEU cc_start: 0.8654 (mt) cc_final: 0.8425 (mp) REVERT: E 451 GLN cc_start: 0.8337 (mt0) cc_final: 0.7944 (tp40) REVERT: E 479 ILE cc_start: 0.8210 (mt) cc_final: 0.7429 (tt) REVERT: E 530 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6685 (mtp-110) REVERT: E 531 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7145 (tt0) REVERT: G 40 MET cc_start: 0.7247 (mtm) cc_final: 0.6470 (ttp) REVERT: G 109 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.3002 (m-30) REVERT: G 157 ASN cc_start: 0.8478 (t0) cc_final: 0.7899 (t0) REVERT: G 173 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7939 (mtp-110) REVERT: G 177 ASN cc_start: 0.8592 (m-40) cc_final: 0.8332 (m-40) REVERT: G 191 PHE cc_start: 0.8517 (t80) cc_final: 0.8132 (t80) REVERT: G 313 GLU cc_start: 0.8253 (tp30) cc_final: 0.7876 (tp30) REVERT: G 461 VAL cc_start: 0.7945 (t) cc_final: 0.6665 (m) REVERT: C 14 TRP cc_start: 0.6499 (m100) cc_final: 0.6139 (m100) REVERT: C 42 VAL cc_start: 0.8250 (m) cc_final: 0.7880 (p) REVERT: C 44 ASN cc_start: 0.8133 (m-40) cc_final: 0.7601 (m-40) REVERT: C 93 ASP cc_start: 0.8599 (p0) cc_final: 0.7668 (p0) REVERT: C 155 TYR cc_start: 0.8736 (m-80) cc_final: 0.8528 (m-80) REVERT: C 295 PHE cc_start: 0.8674 (t80) cc_final: 0.8290 (t80) REVERT: C 304 GLN cc_start: 0.8792 (tt0) cc_final: 0.8282 (tm-30) REVERT: C 495 LYS cc_start: 0.8548 (mttm) cc_final: 0.8250 (mttm) REVERT: C 517 THR cc_start: 0.7925 (m) cc_final: 0.7310 (t) REVERT: C 537 HIS cc_start: 0.9147 (p-80) cc_final: 0.8922 (p-80) REVERT: C 615 MET cc_start: 0.7509 (mtm) cc_final: 0.6854 (mtm) REVERT: C 653 SER cc_start: 0.6332 (OUTLIER) cc_final: 0.6020 (p) REVERT: C 661 MET cc_start: 0.8408 (mpp) cc_final: 0.8181 (mpp) REVERT: B 23 GLN cc_start: 0.8169 (pt0) cc_final: 0.7940 (pt0) REVERT: B 27 ARG cc_start: 0.8418 (mtt90) cc_final: 0.8212 (mtt90) REVERT: B 33 LYS cc_start: 0.7974 (tptt) cc_final: 0.7620 (tptt) REVERT: B 39 PHE cc_start: 0.8303 (m-80) cc_final: 0.8068 (m-80) REVERT: B 76 ILE cc_start: 0.8777 (mm) cc_final: 0.8257 (tp) REVERT: B 101 VAL cc_start: 0.8438 (p) cc_final: 0.7096 (t) REVERT: B 122 LYS cc_start: 0.8851 (mttt) cc_final: 0.8559 (mmtm) REVERT: B 198 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8298 (ptpt) REVERT: B 216 GLU cc_start: 0.8957 (tp30) cc_final: 0.8521 (mm-30) REVERT: B 218 VAL cc_start: 0.8940 (t) cc_final: 0.8262 (p) REVERT: B 226 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8374 (tm-30) REVERT: B 358 TYR cc_start: 0.9110 (t80) cc_final: 0.8743 (t80) REVERT: B 470 VAL cc_start: 0.8740 (p) cc_final: 0.8466 (m) REVERT: B 498 ASP cc_start: 0.8235 (t70) cc_final: 0.6914 (m-30) REVERT: B 566 ARG cc_start: 0.7707 (ptt90) cc_final: 0.7005 (ptt90) REVERT: B 568 CYS cc_start: 0.9054 (m) cc_final: 0.8701 (t) REVERT: B 596 GLU cc_start: 0.8164 (tp30) cc_final: 0.7926 (pm20) REVERT: B 607 GLU cc_start: 0.7769 (pt0) cc_final: 0.7517 (pt0) REVERT: B 625 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8741 (tt0) REVERT: B 630 GLU cc_start: 0.7787 (tt0) cc_final: 0.7399 (pm20) REVERT: B 645 GLU cc_start: 0.7003 (tt0) cc_final: 0.6745 (mm-30) REVERT: B 648 GLU cc_start: 0.8101 (tt0) cc_final: 0.7767 (pm20) REVERT: B 673 GLN cc_start: 0.8650 (tt0) cc_final: 0.8432 (tp40) REVERT: H 93 LYS cc_start: 0.8089 (mptt) cc_final: 0.7765 (mptt) REVERT: H 96 LEU cc_start: 0.7349 (mt) cc_final: 0.6992 (mp) REVERT: H 152 ASP cc_start: 0.8831 (t0) cc_final: 0.8550 (t0) REVERT: H 176 TRP cc_start: 0.8221 (t60) cc_final: 0.7368 (t60) REVERT: H 189 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7566 (mtpt) REVERT: H 192 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7593 (mtp-110) REVERT: H 290 ARG cc_start: 0.8949 (mpt90) cc_final: 0.8465 (mmt-90) REVERT: H 291 ASP cc_start: 0.8590 (t0) cc_final: 0.7621 (t0) REVERT: H 294 LEU cc_start: 0.7156 (mm) cc_final: 0.6928 (mt) REVERT: H 301 ASP cc_start: 0.8442 (t0) cc_final: 0.7680 (t0) REVERT: H 349 LYS cc_start: 0.5991 (mptm) cc_final: 0.5633 (ptmt) REVERT: H 357 LYS cc_start: 0.8689 (tttm) cc_final: 0.8431 (tmtt) REVERT: H 448 ILE cc_start: 0.8450 (mt) cc_final: 0.8219 (mp) REVERT: F 27 PHE cc_start: 0.7171 (t80) cc_final: 0.6930 (t80) REVERT: F 51 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7850 (mm-30) REVERT: F 118 LEU cc_start: 0.7499 (mp) cc_final: 0.7287 (mp) REVERT: F 130 LEU cc_start: 0.8702 (tp) cc_final: 0.8501 (tt) REVERT: F 150 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8390 (pt0) REVERT: F 167 PHE cc_start: 0.8755 (m-80) cc_final: 0.8361 (m-80) REVERT: F 173 GLN cc_start: 0.8154 (tt0) cc_final: 0.7949 (tt0) REVERT: A 3 GLN cc_start: 0.8825 (mt0) cc_final: 0.8529 (mp10) REVERT: A 24 GLN cc_start: 0.8864 (tp40) cc_final: 0.8433 (tp40) REVERT: A 104 ASP cc_start: 0.7835 (t0) cc_final: 0.7330 (m-30) REVERT: A 114 LYS cc_start: 0.9176 (mtmt) cc_final: 0.7730 (ttmt) REVERT: A 134 LEU cc_start: 0.7948 (tp) cc_final: 0.7549 (mt) REVERT: A 138 LYS cc_start: 0.8664 (mttt) cc_final: 0.8261 (mtpp) REVERT: A 175 ASN cc_start: 0.8953 (t0) cc_final: 0.8723 (t0) REVERT: A 178 TYR cc_start: 0.8682 (m-80) cc_final: 0.7906 (m-10) REVERT: A 191 PHE cc_start: 0.8863 (m-80) cc_final: 0.8269 (m-80) REVERT: A 193 THR cc_start: 0.8645 (p) cc_final: 0.8140 (m) REVERT: A 196 THR cc_start: 0.9035 (m) cc_final: 0.8747 (t) REVERT: A 223 LYS cc_start: 0.9219 (tttt) cc_final: 0.8987 (mmmt) REVERT: A 225 PHE cc_start: 0.8795 (t80) cc_final: 0.8433 (t80) REVERT: A 242 VAL cc_start: 0.8561 (t) cc_final: 0.8103 (p) REVERT: A 244 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8383 (tm-30) REVERT: A 249 ILE cc_start: 0.8376 (mm) cc_final: 0.8008 (mm) REVERT: A 265 MET cc_start: 0.8714 (mmt) cc_final: 0.8480 (pmm) REVERT: A 304 TYR cc_start: 0.8564 (m-80) cc_final: 0.7781 (m-10) REVERT: A 323 GLU cc_start: 0.8700 (pt0) cc_final: 0.8392 (pt0) REVERT: A 325 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7644 (Cg_exo) REVERT: A 357 VAL cc_start: 0.8924 (t) cc_final: 0.8577 (m) REVERT: A 414 GLU cc_start: 0.8362 (pt0) cc_final: 0.8144 (tm-30) REVERT: A 415 PHE cc_start: 0.8696 (p90) cc_final: 0.8410 (p90) REVERT: A 426 GLU cc_start: 0.8485 (tt0) cc_final: 0.8027 (tp30) REVERT: A 475 ILE cc_start: 0.8630 (pt) cc_final: 0.8093 (mt) REVERT: A 541 VAL cc_start: 0.8826 (p) cc_final: 0.8130 (m) REVERT: A 547 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7688 (pp20) REVERT: A 569 THR cc_start: 0.8609 (m) cc_final: 0.8150 (t) REVERT: A 654 ILE cc_start: 0.8474 (pt) cc_final: 0.6868 (tt) REVERT: A 770 PHE cc_start: 0.8824 (p90) cc_final: 0.8545 (p90) REVERT: A 779 TRP cc_start: 0.8869 (m100) cc_final: 0.8024 (m100) REVERT: A 780 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 835 MET cc_start: 0.7375 (ptt) cc_final: 0.7078 (mtt) REVERT: A 880 PHE cc_start: 0.7128 (m-80) cc_final: 0.6781 (m-80) REVERT: A 904 ILE cc_start: 0.6404 (tt) cc_final: 0.5899 (pt) REVERT: A 935 ILE cc_start: 0.8133 (tt) cc_final: 0.7296 (pt) REVERT: A 944 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8642 (mtp-110) REVERT: A 947 LEU cc_start: 0.8157 (mt) cc_final: 0.7881 (pp) REVERT: A 952 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8447 (mmtm) REVERT: A 954 GLU cc_start: 0.8782 (tt0) cc_final: 0.8424 (tm-30) REVERT: A 961 VAL cc_start: 0.8659 (p) cc_final: 0.8120 (t) REVERT: A 981 ILE cc_start: 0.8588 (mt) cc_final: 0.8374 (mt) REVERT: A 1008 GLU cc_start: 0.8542 (tp30) cc_final: 0.8315 (tt0) REVERT: A 1045 ASP cc_start: 0.7230 (m-30) cc_final: 0.7008 (t70) REVERT: A 1052 LYS cc_start: 0.8397 (mttt) cc_final: 0.8048 (mtmm) REVERT: A 1060 LEU cc_start: 0.8424 (tp) cc_final: 0.7470 (tt) REVERT: A 1096 ASP cc_start: 0.8580 (p0) cc_final: 0.8163 (t70) REVERT: A 1125 TYR cc_start: 0.7622 (t80) cc_final: 0.7255 (t80) REVERT: A 1143 LEU cc_start: 0.8404 (mt) cc_final: 0.8041 (mt) REVERT: A 1197 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8903 (tp30) REVERT: A 1211 LYS cc_start: 0.8805 (mttt) cc_final: 0.8045 (mttm) REVERT: A 1235 TYR cc_start: 0.8238 (m-80) cc_final: 0.7250 (m-10) REVERT: A 1295 ILE cc_start: 0.8429 (mt) cc_final: 0.7566 (tp) REVERT: A 1297 VAL cc_start: 0.8405 (p) cc_final: 0.7626 (t) REVERT: A 1301 HIS cc_start: 0.8426 (m-70) cc_final: 0.8159 (m-70) REVERT: A 1310 MET cc_start: 0.8161 (mmm) cc_final: 0.7941 (mmm) REVERT: A 1316 LEU cc_start: 0.8992 (tp) cc_final: 0.8503 (pt) outliers start: 27 outliers final: 16 residues processed: 1294 average time/residue: 0.5956 time to fit residues: 1213.9383 Evaluate side-chains 1099 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1081 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 413 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain H residue 348 ARG Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 887 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 chunk 205 optimal weight: 50.0000 chunk 126 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 233 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 240 HIS D 249 HIS D 260 HIS D 380 HIS D 437 GLN D 443 GLN D 455 GLN E 135 GLN E 423 ASN E 488 GLN E 539 ASN G 153 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN C 18 ASN C 73 GLN C 135 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN B 274 HIS H 195 HIS H 289 ASN ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN F 78 GLN A 54 HIS A 208 HIS A 280 GLN A 356 GLN A 482 ASN A 595 GLN ** A 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN A1103 ASN A1417 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 39230 Z= 0.280 Angle : 0.793 12.875 53146 Z= 0.421 Chirality : 0.049 0.446 5851 Planarity : 0.005 0.052 6944 Dihedral : 11.857 113.736 5802 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.79 % Allowed : 11.37 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 4890 helix: -0.51 (0.18), residues: 766 sheet: 0.24 (0.13), residues: 1400 loop : -1.00 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 542 HIS 0.008 0.001 HIS B 274 PHE 0.025 0.002 PHE A1004 TYR 0.024 0.002 TYR H 172 ARG 0.006 0.001 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1064 time to evaluate : 4.447 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8655 (m-80) cc_final: 0.8397 (m-80) REVERT: D 32 TYR cc_start: 0.8611 (p90) cc_final: 0.8338 (p90) REVERT: D 41 PHE cc_start: 0.8674 (m-10) cc_final: 0.8134 (m-80) REVERT: D 116 TRP cc_start: 0.8609 (m-10) cc_final: 0.8309 (m100) REVERT: D 253 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8068 (mtpt) REVERT: D 268 LYS cc_start: 0.7931 (mttt) cc_final: 0.7252 (ttmm) REVERT: D 269 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8258 (ttp-110) REVERT: D 398 TRP cc_start: 0.8476 (t60) cc_final: 0.8236 (t60) REVERT: D 432 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8045 (ttm110) REVERT: D 446 VAL cc_start: 0.8636 (m) cc_final: 0.7171 (p) REVERT: D 465 SER cc_start: 0.8603 (m) cc_final: 0.8235 (p) REVERT: E 10 GLN cc_start: 0.8245 (mt0) cc_final: 0.8023 (pt0) REVERT: E 14 TRP cc_start: 0.8416 (m100) cc_final: 0.7268 (m100) REVERT: E 139 ASP cc_start: 0.9171 (t0) cc_final: 0.8773 (t0) REVERT: E 163 THR cc_start: 0.8172 (p) cc_final: 0.7853 (t) REVERT: E 273 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7185 (mmm) REVERT: E 277 ASP cc_start: 0.8635 (m-30) cc_final: 0.8419 (t0) REVERT: E 279 MET cc_start: 0.7978 (tpp) cc_final: 0.7711 (tpp) REVERT: E 416 TRP cc_start: 0.8320 (t60) cc_final: 0.7945 (t60) REVERT: E 429 PHE cc_start: 0.8094 (p90) cc_final: 0.7887 (p90) REVERT: E 430 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8030 (mm-30) REVERT: E 451 GLN cc_start: 0.8341 (mt0) cc_final: 0.7920 (tp-100) REVERT: E 479 ILE cc_start: 0.8156 (mt) cc_final: 0.7276 (tt) REVERT: E 509 ASP cc_start: 0.8840 (p0) cc_final: 0.8377 (p0) REVERT: E 530 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6886 (mtm180) REVERT: E 531 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7084 (tt0) REVERT: G 24 MET cc_start: 0.8170 (mtp) cc_final: 0.7772 (mtt) REVERT: G 40 MET cc_start: 0.7452 (mtm) cc_final: 0.6440 (ttp) REVERT: G 109 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.4513 (m-30) REVERT: G 296 THR cc_start: 0.8158 (m) cc_final: 0.5915 (t) REVERT: G 428 VAL cc_start: 0.8035 (t) cc_final: 0.7397 (m) REVERT: G 437 TRP cc_start: 0.7964 (t60) cc_final: 0.7637 (t60) REVERT: G 461 VAL cc_start: 0.7808 (t) cc_final: 0.6557 (m) REVERT: C 42 VAL cc_start: 0.7895 (m) cc_final: 0.7634 (p) REVERT: C 93 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8271 (p0) REVERT: C 155 TYR cc_start: 0.8750 (m-80) cc_final: 0.8344 (m-80) REVERT: C 257 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8261 (tt0) REVERT: C 303 LYS cc_start: 0.8667 (tttt) cc_final: 0.8444 (mmmm) REVERT: C 427 LEU cc_start: 0.8761 (mt) cc_final: 0.8510 (mp) REVERT: C 487 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: C 495 LYS cc_start: 0.8395 (mttm) cc_final: 0.8143 (mttm) REVERT: C 517 THR cc_start: 0.7900 (m) cc_final: 0.7221 (t) REVERT: C 537 HIS cc_start: 0.9191 (p-80) cc_final: 0.8943 (p-80) REVERT: C 590 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8601 (ttm170) REVERT: C 615 MET cc_start: 0.7529 (mtm) cc_final: 0.6936 (mtm) REVERT: B 23 GLN cc_start: 0.8201 (pt0) cc_final: 0.7988 (pt0) REVERT: B 27 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8266 (mtt90) REVERT: B 39 PHE cc_start: 0.8110 (m-80) cc_final: 0.7895 (m-80) REVERT: B 76 ILE cc_start: 0.8732 (mm) cc_final: 0.8031 (tp) REVERT: B 101 VAL cc_start: 0.8516 (p) cc_final: 0.7378 (t) REVERT: B 216 GLU cc_start: 0.8963 (tp30) cc_final: 0.8734 (tp30) REVERT: B 226 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8324 (tm-30) REVERT: B 243 ASN cc_start: 0.7565 (p0) cc_final: 0.7313 (t0) REVERT: B 358 TYR cc_start: 0.9181 (t80) cc_final: 0.8659 (t80) REVERT: B 366 LYS cc_start: 0.8938 (mttt) cc_final: 0.8727 (mmtt) REVERT: B 492 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8802 (tm-30) REVERT: B 498 ASP cc_start: 0.8166 (t70) cc_final: 0.6954 (m-30) REVERT: B 566 ARG cc_start: 0.7760 (ptt90) cc_final: 0.6723 (ptt90) REVERT: B 568 CYS cc_start: 0.9117 (m) cc_final: 0.8872 (t) REVERT: B 630 GLU cc_start: 0.7942 (tt0) cc_final: 0.7604 (pm20) REVERT: B 634 ILE cc_start: 0.8138 (mt) cc_final: 0.7785 (tt) REVERT: B 648 GLU cc_start: 0.8188 (tt0) cc_final: 0.7911 (pm20) REVERT: H 93 LYS cc_start: 0.8041 (mptt) cc_final: 0.7770 (mptt) REVERT: H 96 LEU cc_start: 0.7455 (mt) cc_final: 0.7119 (mp) REVERT: H 152 ASP cc_start: 0.8890 (t0) cc_final: 0.8586 (t0) REVERT: H 164 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7760 (ptt90) REVERT: H 176 TRP cc_start: 0.8270 (t60) cc_final: 0.7396 (t60) REVERT: H 189 LYS cc_start: 0.8351 (tmtt) cc_final: 0.7986 (tttm) REVERT: H 192 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7446 (mtp-110) REVERT: H 279 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8575 (tm-30) REVERT: H 290 ARG cc_start: 0.8856 (mpt90) cc_final: 0.8590 (mmt-90) REVERT: H 291 ASP cc_start: 0.8419 (t0) cc_final: 0.7617 (t0) REVERT: H 294 LEU cc_start: 0.7319 (mm) cc_final: 0.7095 (mt) REVERT: H 301 ASP cc_start: 0.8469 (t0) cc_final: 0.8045 (t0) REVERT: H 357 LYS cc_start: 0.8722 (tttm) cc_final: 0.8442 (tmtt) REVERT: H 448 ILE cc_start: 0.8271 (mt) cc_final: 0.7995 (mp) REVERT: H 471 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8158 (tp40) REVERT: H 484 PHE cc_start: 0.6530 (m-80) cc_final: 0.5610 (m-80) REVERT: F 23 ASP cc_start: 0.7837 (t0) cc_final: 0.7427 (p0) REVERT: F 27 PHE cc_start: 0.7248 (t80) cc_final: 0.7023 (t80) REVERT: F 69 PHE cc_start: 0.8161 (m-80) cc_final: 0.7875 (m-80) REVERT: F 112 TYR cc_start: 0.7880 (m-80) cc_final: 0.7679 (m-80) REVERT: F 118 LEU cc_start: 0.7385 (mp) cc_final: 0.7071 (mp) REVERT: A 3 GLN cc_start: 0.8845 (mt0) cc_final: 0.8619 (mm-40) REVERT: A 175 ASN cc_start: 0.8974 (t0) cc_final: 0.8769 (t0) REVERT: A 178 TYR cc_start: 0.8629 (m-80) cc_final: 0.7879 (m-10) REVERT: A 191 PHE cc_start: 0.8940 (m-80) cc_final: 0.8395 (m-80) REVERT: A 193 THR cc_start: 0.8505 (p) cc_final: 0.8124 (m) REVERT: A 196 THR cc_start: 0.9032 (m) cc_final: 0.8698 (t) REVERT: A 225 PHE cc_start: 0.8823 (t80) cc_final: 0.8246 (t80) REVERT: A 242 VAL cc_start: 0.8474 (t) cc_final: 0.7841 (p) REVERT: A 244 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8459 (tm-30) REVERT: A 249 ILE cc_start: 0.8486 (mm) cc_final: 0.8062 (mm) REVERT: A 258 LYS cc_start: 0.8910 (tptt) cc_final: 0.8614 (mmtm) REVERT: A 265 MET cc_start: 0.8863 (mmt) cc_final: 0.8581 (pmm) REVERT: A 357 VAL cc_start: 0.8799 (t) cc_final: 0.8451 (m) REVERT: A 415 PHE cc_start: 0.8663 (p90) cc_final: 0.8364 (p90) REVERT: A 426 GLU cc_start: 0.8352 (tt0) cc_final: 0.7995 (tm-30) REVERT: A 475 ILE cc_start: 0.8437 (pt) cc_final: 0.7991 (mm) REVERT: A 541 VAL cc_start: 0.8929 (p) cc_final: 0.8262 (m) REVERT: A 569 THR cc_start: 0.8667 (m) cc_final: 0.8209 (t) REVERT: A 582 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 654 ILE cc_start: 0.8358 (pt) cc_final: 0.6903 (tt) REVERT: A 764 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7825 (mtm-85) REVERT: A 767 GLN cc_start: 0.8832 (tt0) cc_final: 0.8566 (mp10) REVERT: A 780 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 835 MET cc_start: 0.7201 (ptt) cc_final: 0.6928 (mtt) REVERT: A 880 PHE cc_start: 0.7363 (m-80) cc_final: 0.7034 (m-80) REVERT: A 904 ILE cc_start: 0.6316 (tt) cc_final: 0.5810 (pt) REVERT: A 935 ILE cc_start: 0.8294 (tt) cc_final: 0.7648 (pt) REVERT: A 944 ARG cc_start: 0.8933 (mtt180) cc_final: 0.8645 (mtp-110) REVERT: A 947 LEU cc_start: 0.8160 (mt) cc_final: 0.7925 (pp) REVERT: A 954 GLU cc_start: 0.8705 (tt0) cc_final: 0.8384 (tm-30) REVERT: A 981 ILE cc_start: 0.8539 (mt) cc_final: 0.7924 (tt) REVERT: A 1045 ASP cc_start: 0.7418 (m-30) cc_final: 0.6903 (t0) REVERT: A 1052 LYS cc_start: 0.8445 (mttt) cc_final: 0.8113 (mtmm) REVERT: A 1060 LEU cc_start: 0.8505 (tp) cc_final: 0.7260 (tt) REVERT: A 1120 ARG cc_start: 0.7952 (tpt170) cc_final: 0.7588 (tmm160) REVERT: A 1121 GLU cc_start: 0.8256 (tt0) cc_final: 0.7962 (mt-10) REVERT: A 1143 LEU cc_start: 0.8400 (mt) cc_final: 0.8200 (mt) REVERT: A 1197 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8872 (tp30) REVERT: A 1239 THR cc_start: 0.8412 (m) cc_final: 0.7183 (p) REVERT: A 1248 TYR cc_start: 0.8466 (t80) cc_final: 0.8088 (t80) REVERT: A 1287 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8435 (mmtt) REVERT: A 1295 ILE cc_start: 0.8359 (mt) cc_final: 0.7296 (tt) REVERT: A 1297 VAL cc_start: 0.8484 (p) cc_final: 0.7783 (t) outliers start: 114 outliers final: 63 residues processed: 1114 average time/residue: 0.5688 time to fit residues: 998.8104 Evaluate side-chains 1072 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1004 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 482 ASN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 359 CYS Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 164 LYS Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 948 ASP Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1267 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 369 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 444 optimal weight: 2.9990 chunk 480 optimal weight: 8.9990 chunk 396 optimal weight: 3.9990 chunk 441 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 360 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN G 99 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS G 281 HIS G 289 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN C 347 ASN B 47 GLN B 177 HIS ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN H 465 ASN H 471 GLN F 78 GLN A 52 HIS ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 HIS A 271 ASN A 301 ASN A 337 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN A 976 GLN A1112 GLN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 39230 Z= 0.420 Angle : 0.763 11.192 53146 Z= 0.403 Chirality : 0.050 0.381 5851 Planarity : 0.005 0.065 6944 Dihedral : 10.006 114.428 5773 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.08 % Allowed : 14.13 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 4890 helix: -0.54 (0.18), residues: 776 sheet: -0.12 (0.13), residues: 1450 loop : -1.16 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 451 HIS 0.011 0.002 HIS C 260 PHE 0.023 0.003 PHE A1266 TYR 0.032 0.003 TYR E 323 ARG 0.010 0.001 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1055 time to evaluate : 4.647 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8707 (p90) cc_final: 0.8331 (p90) REVERT: D 71 PHE cc_start: 0.8167 (t80) cc_final: 0.7570 (t80) REVERT: D 116 TRP cc_start: 0.8578 (m-10) cc_final: 0.8318 (m100) REVERT: D 253 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8061 (mtpt) REVERT: D 268 LYS cc_start: 0.8096 (mttt) cc_final: 0.7431 (mtpp) REVERT: D 269 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8432 (ttp-110) REVERT: D 432 ARG cc_start: 0.8653 (mtt180) cc_final: 0.7893 (ttm110) REVERT: D 446 VAL cc_start: 0.8562 (m) cc_final: 0.7251 (p) REVERT: D 465 SER cc_start: 0.8676 (m) cc_final: 0.8305 (p) REVERT: D 511 GLN cc_start: 0.8385 (mp10) cc_final: 0.8044 (mp10) REVERT: E 14 TRP cc_start: 0.8574 (m100) cc_final: 0.7476 (m100) REVERT: E 139 ASP cc_start: 0.9221 (t0) cc_final: 0.8756 (t0) REVERT: E 166 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7100 (ttp-170) REVERT: E 273 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7179 (mmm) REVERT: E 277 ASP cc_start: 0.8535 (m-30) cc_final: 0.8300 (t0) REVERT: E 279 MET cc_start: 0.8033 (tpp) cc_final: 0.7757 (tpp) REVERT: E 416 TRP cc_start: 0.8263 (t60) cc_final: 0.7984 (t60) REVERT: E 435 HIS cc_start: 0.8572 (p90) cc_final: 0.8235 (p-80) REVERT: E 479 ILE cc_start: 0.8164 (mt) cc_final: 0.7272 (tt) REVERT: E 480 LEU cc_start: 0.8288 (mt) cc_final: 0.8006 (tt) REVERT: E 509 ASP cc_start: 0.8815 (p0) cc_final: 0.8410 (p0) REVERT: G 40 MET cc_start: 0.7127 (mtm) cc_final: 0.6386 (ttp) REVERT: G 52 PHE cc_start: 0.7549 (m-80) cc_final: 0.7128 (m-80) REVERT: G 109 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.4232 (m-30) REVERT: G 168 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 296 THR cc_start: 0.8146 (m) cc_final: 0.6949 (p) REVERT: G 331 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7640 (mt) REVERT: G 437 TRP cc_start: 0.7913 (t60) cc_final: 0.7505 (t60) REVERT: G 461 VAL cc_start: 0.7814 (t) cc_final: 0.6673 (m) REVERT: C 14 TRP cc_start: 0.6850 (m100) cc_final: 0.6607 (m100) REVERT: C 26 ARG cc_start: 0.8040 (ptt90) cc_final: 0.7811 (ptt90) REVERT: C 42 VAL cc_start: 0.7884 (m) cc_final: 0.7592 (p) REVERT: C 47 GLU cc_start: 0.8581 (pt0) cc_final: 0.8266 (pt0) REVERT: C 93 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8343 (p0) REVERT: C 185 TYR cc_start: 0.8516 (t80) cc_final: 0.8177 (t80) REVERT: C 427 LEU cc_start: 0.8652 (mt) cc_final: 0.8403 (mp) REVERT: C 487 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: C 495 LYS cc_start: 0.8479 (mttm) cc_final: 0.8224 (mttm) REVERT: C 537 HIS cc_start: 0.9103 (p-80) cc_final: 0.8869 (p-80) REVERT: C 615 MET cc_start: 0.7103 (mtm) cc_final: 0.6581 (mtm) REVERT: C 631 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 27 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8290 (mtt90) REVERT: B 39 PHE cc_start: 0.8123 (m-80) cc_final: 0.7914 (m-80) REVERT: B 54 TRP cc_start: 0.8833 (p90) cc_final: 0.8483 (p90) REVERT: B 76 ILE cc_start: 0.8768 (mm) cc_final: 0.8126 (tp) REVERT: B 135 LEU cc_start: 0.8158 (mt) cc_final: 0.7805 (mt) REVERT: B 138 ASN cc_start: 0.7808 (p0) cc_final: 0.6129 (p0) REVERT: B 140 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8834 (mm-30) REVERT: B 227 ASP cc_start: 0.8526 (t0) cc_final: 0.8239 (t0) REVERT: B 243 ASN cc_start: 0.7669 (p0) cc_final: 0.7422 (t0) REVERT: B 412 PHE cc_start: 0.8890 (t80) cc_final: 0.8559 (t80) REVERT: B 454 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.6772 (p) REVERT: B 492 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8785 (tm-30) REVERT: B 498 ASP cc_start: 0.8246 (t70) cc_final: 0.6672 (m-30) REVERT: B 566 ARG cc_start: 0.7819 (ptt90) cc_final: 0.7211 (ptt90) REVERT: B 568 CYS cc_start: 0.9215 (m) cc_final: 0.8959 (t) REVERT: B 606 ASP cc_start: 0.7964 (t0) cc_final: 0.7649 (t0) REVERT: B 630 GLU cc_start: 0.8050 (tt0) cc_final: 0.7687 (pm20) REVERT: B 648 GLU cc_start: 0.8286 (tt0) cc_final: 0.7953 (pm20) REVERT: H 93 LYS cc_start: 0.7953 (mptt) cc_final: 0.7664 (mptt) REVERT: H 96 LEU cc_start: 0.7446 (mt) cc_final: 0.7069 (mp) REVERT: H 133 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7507 (ttm110) REVERT: H 152 ASP cc_start: 0.8863 (t0) cc_final: 0.8617 (t0) REVERT: H 164 ARG cc_start: 0.8181 (ptt90) cc_final: 0.7949 (ptt90) REVERT: H 279 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8614 (tm-30) REVERT: H 301 ASP cc_start: 0.8500 (t0) cc_final: 0.8197 (t0) REVERT: H 341 LEU cc_start: 0.7051 (mt) cc_final: 0.6034 (mp) REVERT: H 357 LYS cc_start: 0.8748 (tttm) cc_final: 0.8325 (tptp) REVERT: H 437 TRP cc_start: 0.6875 (t60) cc_final: 0.6580 (t60) REVERT: H 448 ILE cc_start: 0.8357 (mt) cc_final: 0.8113 (mp) REVERT: H 480 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: F 27 PHE cc_start: 0.7319 (t80) cc_final: 0.6847 (t80) REVERT: F 112 TYR cc_start: 0.8060 (m-80) cc_final: 0.7738 (m-80) REVERT: A 3 GLN cc_start: 0.8957 (mt0) cc_final: 0.8685 (mm-40) REVERT: A 30 GLU cc_start: 0.8697 (tt0) cc_final: 0.8453 (tm-30) REVERT: A 193 THR cc_start: 0.8599 (p) cc_final: 0.8119 (m) REVERT: A 196 THR cc_start: 0.8943 (m) cc_final: 0.8657 (t) REVERT: A 225 PHE cc_start: 0.8705 (t80) cc_final: 0.8159 (t80) REVERT: A 242 VAL cc_start: 0.8433 (t) cc_final: 0.7774 (p) REVERT: A 244 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8443 (tm-30) REVERT: A 249 ILE cc_start: 0.8611 (mm) cc_final: 0.7969 (tp) REVERT: A 258 LYS cc_start: 0.8907 (tptt) cc_final: 0.8630 (mmtm) REVERT: A 273 MET cc_start: 0.7899 (mtm) cc_final: 0.7644 (mmm) REVERT: A 304 TYR cc_start: 0.8427 (m-10) cc_final: 0.7137 (m-10) REVERT: A 307 ILE cc_start: 0.8074 (tt) cc_final: 0.7267 (pt) REVERT: A 323 GLU cc_start: 0.8645 (pt0) cc_final: 0.8156 (tm-30) REVERT: A 357 VAL cc_start: 0.8939 (t) cc_final: 0.8547 (m) REVERT: A 359 ASP cc_start: 0.8101 (m-30) cc_final: 0.7852 (m-30) REVERT: A 415 PHE cc_start: 0.8674 (p90) cc_final: 0.8410 (p90) REVERT: A 426 GLU cc_start: 0.8330 (tt0) cc_final: 0.7906 (tp30) REVERT: A 431 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8586 (ptm-80) REVERT: A 475 ILE cc_start: 0.8451 (pt) cc_final: 0.8005 (mm) REVERT: A 524 VAL cc_start: 0.8679 (t) cc_final: 0.8469 (m) REVERT: A 541 VAL cc_start: 0.8878 (p) cc_final: 0.8264 (m) REVERT: A 569 THR cc_start: 0.8757 (m) cc_final: 0.8300 (t) REVERT: A 588 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8644 (t0) REVERT: A 637 THR cc_start: 0.8989 (t) cc_final: 0.8778 (p) REVERT: A 764 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7929 (mtm-85) REVERT: A 767 GLN cc_start: 0.8810 (tt0) cc_final: 0.8537 (mp10) REVERT: A 778 THR cc_start: 0.9209 (m) cc_final: 0.8808 (t) REVERT: A 779 TRP cc_start: 0.8890 (m100) cc_final: 0.8173 (m100) REVERT: A 780 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8623 (mt-10) REVERT: A 793 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 835 MET cc_start: 0.7076 (ptt) cc_final: 0.6756 (mtt) REVERT: A 841 MET cc_start: 0.8227 (ttp) cc_final: 0.8022 (ttp) REVERT: A 880 PHE cc_start: 0.7433 (m-80) cc_final: 0.7026 (m-80) REVERT: A 894 PHE cc_start: 0.7422 (m-10) cc_final: 0.7184 (m-10) REVERT: A 924 VAL cc_start: 0.8114 (m) cc_final: 0.7873 (p) REVERT: A 944 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8630 (mtp-110) REVERT: A 952 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8639 (mptp) REVERT: A 954 GLU cc_start: 0.8844 (tt0) cc_final: 0.8544 (tm-30) REVERT: A 961 VAL cc_start: 0.8513 (p) cc_final: 0.7975 (t) REVERT: A 981 ILE cc_start: 0.8561 (mt) cc_final: 0.7930 (tt) REVERT: A 993 GLU cc_start: 0.7874 (tt0) cc_final: 0.7657 (pt0) REVERT: A 1045 ASP cc_start: 0.7615 (m-30) cc_final: 0.7161 (t70) REVERT: A 1052 LYS cc_start: 0.8435 (mttt) cc_final: 0.8111 (mtmm) REVERT: A 1060 LEU cc_start: 0.8572 (tp) cc_final: 0.7305 (tt) REVERT: A 1120 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7762 (tpt170) REVERT: A 1140 ILE cc_start: 0.8465 (pt) cc_final: 0.8193 (tt) REVERT: A 1167 THR cc_start: 0.8769 (m) cc_final: 0.8529 (p) REVERT: A 1197 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8938 (tp30) REVERT: A 1287 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8458 (mmtt) REVERT: A 1295 ILE cc_start: 0.8435 (mt) cc_final: 0.7415 (tt) REVERT: A 1296 ASP cc_start: 0.8255 (t0) cc_final: 0.8003 (t0) REVERT: A 1297 VAL cc_start: 0.8580 (p) cc_final: 0.7852 (t) outliers start: 167 outliers final: 101 residues processed: 1128 average time/residue: 0.5705 time to fit residues: 1020.4908 Evaluate side-chains 1117 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1006 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 464 LYS Chi-restraints excluded: chain G residue 482 ASN Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 359 CYS Chi-restraints excluded: chain H residue 480 TYR Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 948 ASP Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 230 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 212 optimal weight: 40.0000 chunk 298 optimal weight: 2.9990 chunk 446 optimal weight: 0.2980 chunk 472 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 423 optimal weight: 0.0470 chunk 127 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 126 ASN D 495 ASN E 10 GLN E 423 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 223 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN H 471 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS A1242 ASN A1274 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 39230 Z= 0.219 Angle : 0.663 10.484 53146 Z= 0.346 Chirality : 0.045 0.354 5851 Planarity : 0.005 0.052 6944 Dihedral : 8.818 114.847 5771 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.03 % Allowed : 16.33 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.11), residues: 4890 helix: -0.07 (0.18), residues: 776 sheet: -0.04 (0.13), residues: 1433 loop : -1.01 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 451 HIS 0.006 0.001 HIS G 275 PHE 0.022 0.002 PHE C 147 TYR 0.029 0.002 TYR A 448 ARG 0.007 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1032 time to evaluate : 4.377 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 PHE cc_start: 0.8607 (m-10) cc_final: 0.8402 (m-10) REVERT: D 71 PHE cc_start: 0.8100 (t80) cc_final: 0.7499 (t80) REVERT: D 116 TRP cc_start: 0.8556 (m-10) cc_final: 0.8301 (m100) REVERT: D 253 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8113 (ttmt) REVERT: D 255 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8204 (ttm-80) REVERT: D 268 LYS cc_start: 0.8021 (mttt) cc_final: 0.7799 (mttm) REVERT: D 269 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8380 (ttp-110) REVERT: D 306 MET cc_start: 0.8825 (tmm) cc_final: 0.8202 (tmm) REVERT: D 432 ARG cc_start: 0.8578 (mtt180) cc_final: 0.7820 (ttm110) REVERT: D 443 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: D 446 VAL cc_start: 0.8478 (m) cc_final: 0.7174 (p) REVERT: D 465 SER cc_start: 0.8645 (m) cc_final: 0.8240 (p) REVERT: D 511 GLN cc_start: 0.8225 (mp10) cc_final: 0.7879 (mp10) REVERT: E 14 TRP cc_start: 0.8420 (m100) cc_final: 0.7416 (m100) REVERT: E 139 ASP cc_start: 0.9234 (t0) cc_final: 0.8849 (t0) REVERT: E 181 ASN cc_start: 0.8895 (m-40) cc_final: 0.8681 (t0) REVERT: E 273 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7165 (mmm) REVERT: E 416 TRP cc_start: 0.8307 (t60) cc_final: 0.7965 (t60) REVERT: E 435 HIS cc_start: 0.8527 (p90) cc_final: 0.8169 (p-80) REVERT: E 451 GLN cc_start: 0.8317 (mt0) cc_final: 0.8103 (mm-40) REVERT: E 464 PHE cc_start: 0.8771 (m-80) cc_final: 0.8493 (m-80) REVERT: E 479 ILE cc_start: 0.8115 (mt) cc_final: 0.7219 (tt) REVERT: E 480 LEU cc_start: 0.8210 (mt) cc_final: 0.7971 (tt) REVERT: E 509 ASP cc_start: 0.8781 (p0) cc_final: 0.8404 (p0) REVERT: E 531 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7203 (tt0) REVERT: G 34 ASP cc_start: 0.8338 (m-30) cc_final: 0.8036 (t0) REVERT: G 40 MET cc_start: 0.7042 (mtm) cc_final: 0.5961 (ppp) REVERT: G 52 PHE cc_start: 0.7579 (m-80) cc_final: 0.7150 (m-80) REVERT: G 108 SER cc_start: 0.8510 (t) cc_final: 0.7997 (m) REVERT: G 109 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.4369 (m-30) REVERT: G 168 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8321 (p) REVERT: G 296 THR cc_start: 0.7976 (m) cc_final: 0.6796 (p) REVERT: G 331 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7673 (mt) REVERT: G 428 VAL cc_start: 0.8070 (t) cc_final: 0.7357 (m) REVERT: G 461 VAL cc_start: 0.7824 (t) cc_final: 0.6594 (m) REVERT: C 14 TRP cc_start: 0.6895 (m100) cc_final: 0.6588 (m100) REVERT: C 42 VAL cc_start: 0.7762 (m) cc_final: 0.7479 (p) REVERT: C 44 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8194 (t0) REVERT: C 426 TYR cc_start: 0.7919 (t80) cc_final: 0.6886 (t80) REVERT: C 427 LEU cc_start: 0.8553 (mt) cc_final: 0.8233 (mp) REVERT: C 487 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7708 (m-10) REVERT: C 495 LYS cc_start: 0.8457 (mttm) cc_final: 0.8219 (mttm) REVERT: C 497 ARG cc_start: 0.7857 (ptt180) cc_final: 0.7475 (ptt180) REVERT: C 517 THR cc_start: 0.7885 (m) cc_final: 0.7091 (t) REVERT: C 537 HIS cc_start: 0.9050 (p-80) cc_final: 0.8801 (p-80) REVERT: C 615 MET cc_start: 0.6952 (mtm) cc_final: 0.6462 (mtm) REVERT: C 618 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8214 (mt) REVERT: C 631 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 649 PHE cc_start: 0.8063 (m-80) cc_final: 0.7522 (m-10) REVERT: B 27 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8314 (mtt90) REVERT: B 39 PHE cc_start: 0.8065 (m-80) cc_final: 0.7854 (m-80) REVERT: B 76 ILE cc_start: 0.8772 (mm) cc_final: 0.8107 (tp) REVERT: B 226 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8350 (tm-30) REVERT: B 227 ASP cc_start: 0.8506 (t0) cc_final: 0.8211 (t0) REVERT: B 243 ASN cc_start: 0.7672 (p0) cc_final: 0.7428 (t0) REVERT: B 283 GLN cc_start: 0.8712 (tt0) cc_final: 0.8259 (tm-30) REVERT: B 412 PHE cc_start: 0.8872 (t80) cc_final: 0.8541 (t80) REVERT: B 454 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.6343 (p) REVERT: B 492 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8792 (tm-30) REVERT: B 498 ASP cc_start: 0.8117 (t70) cc_final: 0.6534 (m-30) REVERT: B 606 ASP cc_start: 0.7771 (t0) cc_final: 0.7437 (t0) REVERT: B 610 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8202 (mmmt) REVERT: B 630 GLU cc_start: 0.8054 (tt0) cc_final: 0.7685 (pm20) REVERT: B 639 GLN cc_start: 0.7013 (pp30) cc_final: 0.6705 (pp30) REVERT: B 648 GLU cc_start: 0.8276 (tt0) cc_final: 0.7939 (pm20) REVERT: B 695 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7614 (p) REVERT: H 93 LYS cc_start: 0.7903 (mptt) cc_final: 0.7617 (mptt) REVERT: H 96 LEU cc_start: 0.7432 (mt) cc_final: 0.7057 (mp) REVERT: H 133 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7424 (ttm110) REVERT: H 145 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: H 152 ASP cc_start: 0.8863 (t0) cc_final: 0.8611 (t0) REVERT: H 164 ARG cc_start: 0.8113 (ptt90) cc_final: 0.7897 (ptt90) REVERT: H 189 LYS cc_start: 0.8157 (tttm) cc_final: 0.7922 (tppt) REVERT: H 272 MET cc_start: 0.3442 (ppp) cc_final: 0.3088 (ppp) REVERT: H 305 LEU cc_start: 0.7696 (mt) cc_final: 0.7326 (mt) REVERT: H 341 LEU cc_start: 0.6961 (mt) cc_final: 0.5792 (mp) REVERT: H 357 LYS cc_start: 0.8705 (tttm) cc_final: 0.8384 (tptp) REVERT: H 434 PHE cc_start: 0.7408 (m-10) cc_final: 0.7194 (m-10) REVERT: H 448 ILE cc_start: 0.8253 (mt) cc_final: 0.8053 (mp) REVERT: H 480 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: F 23 ASP cc_start: 0.7843 (t0) cc_final: 0.7628 (t0) REVERT: F 27 PHE cc_start: 0.7305 (t80) cc_final: 0.6833 (t80) REVERT: F 112 TYR cc_start: 0.8152 (m-80) cc_final: 0.7704 (m-80) REVERT: F 158 GLN cc_start: 0.8217 (mt0) cc_final: 0.7981 (tt0) REVERT: A 3 GLN cc_start: 0.8937 (mt0) cc_final: 0.8726 (mp-120) REVERT: A 193 THR cc_start: 0.8509 (p) cc_final: 0.8185 (m) REVERT: A 196 THR cc_start: 0.8983 (m) cc_final: 0.8646 (t) REVERT: A 225 PHE cc_start: 0.8648 (t80) cc_final: 0.7976 (t80) REVERT: A 242 VAL cc_start: 0.8359 (t) cc_final: 0.7683 (p) REVERT: A 244 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8452 (tm-30) REVERT: A 249 ILE cc_start: 0.8480 (mm) cc_final: 0.7507 (tt) REVERT: A 255 GLU cc_start: 0.8534 (pt0) cc_final: 0.8332 (pm20) REVERT: A 258 LYS cc_start: 0.8887 (tptt) cc_final: 0.8639 (mmtm) REVERT: A 304 TYR cc_start: 0.8320 (m-10) cc_final: 0.7047 (m-10) REVERT: A 307 ILE cc_start: 0.8000 (tt) cc_final: 0.7186 (pt) REVERT: A 323 GLU cc_start: 0.8610 (pt0) cc_final: 0.8118 (tm-30) REVERT: A 357 VAL cc_start: 0.8954 (t) cc_final: 0.8566 (m) REVERT: A 359 ASP cc_start: 0.8169 (m-30) cc_final: 0.7937 (m-30) REVERT: A 426 GLU cc_start: 0.8304 (tt0) cc_final: 0.7894 (tp30) REVERT: A 462 GLU cc_start: 0.8819 (pt0) cc_final: 0.8568 (pt0) REVERT: A 475 ILE cc_start: 0.8450 (pt) cc_final: 0.8019 (mm) REVERT: A 524 VAL cc_start: 0.8620 (t) cc_final: 0.8410 (m) REVERT: A 526 TYR cc_start: 0.8618 (p90) cc_final: 0.8342 (p90) REVERT: A 569 THR cc_start: 0.8744 (m) cc_final: 0.8302 (t) REVERT: A 582 VAL cc_start: 0.8959 (p) cc_final: 0.8625 (t) REVERT: A 588 ASP cc_start: 0.8851 (t70) cc_final: 0.8494 (t70) REVERT: A 637 THR cc_start: 0.8954 (t) cc_final: 0.8654 (p) REVERT: A 654 ILE cc_start: 0.8315 (pt) cc_final: 0.8031 (pt) REVERT: A 764 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7900 (mtm-85) REVERT: A 767 GLN cc_start: 0.8811 (tt0) cc_final: 0.8521 (mp10) REVERT: A 779 TRP cc_start: 0.8860 (m100) cc_final: 0.8191 (m100) REVERT: A 780 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8786 (mt-10) REVERT: A 792 CYS cc_start: 0.8160 (t) cc_final: 0.7900 (p) REVERT: A 793 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 835 MET cc_start: 0.7119 (ptt) cc_final: 0.6771 (mtt) REVERT: A 841 MET cc_start: 0.8203 (ttp) cc_final: 0.7921 (ttp) REVERT: A 880 PHE cc_start: 0.7408 (m-80) cc_final: 0.7006 (m-80) REVERT: A 894 PHE cc_start: 0.7358 (m-10) cc_final: 0.7044 (m-10) REVERT: A 924 VAL cc_start: 0.7988 (m) cc_final: 0.7740 (p) REVERT: A 944 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8624 (mtp-110) REVERT: A 952 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8603 (mptt) REVERT: A 954 GLU cc_start: 0.8812 (tt0) cc_final: 0.8506 (tm-30) REVERT: A 961 VAL cc_start: 0.8433 (p) cc_final: 0.7824 (t) REVERT: A 981 ILE cc_start: 0.8520 (mt) cc_final: 0.7923 (tp) REVERT: A 1008 GLU cc_start: 0.8594 (tp30) cc_final: 0.8282 (mt-10) REVERT: A 1045 ASP cc_start: 0.7634 (m-30) cc_final: 0.7160 (t70) REVERT: A 1052 LYS cc_start: 0.8338 (mttt) cc_final: 0.8042 (mppt) REVERT: A 1060 LEU cc_start: 0.8572 (tp) cc_final: 0.7213 (tt) REVERT: A 1168 PHE cc_start: 0.8512 (t80) cc_final: 0.7906 (t80) REVERT: A 1187 PHE cc_start: 0.8584 (t80) cc_final: 0.8098 (t80) REVERT: A 1197 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8800 (tp30) REVERT: A 1287 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8367 (mptt) REVERT: A 1295 ILE cc_start: 0.8389 (mt) cc_final: 0.7386 (tt) REVERT: A 1296 ASP cc_start: 0.8258 (t0) cc_final: 0.8015 (t0) REVERT: A 1297 VAL cc_start: 0.8557 (p) cc_final: 0.7799 (t) REVERT: A 1310 MET cc_start: 0.7804 (mmm) cc_final: 0.7361 (mmm) outliers start: 165 outliers final: 104 residues processed: 1107 average time/residue: 0.5590 time to fit residues: 975.0622 Evaluate side-chains 1115 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 998 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 723 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 480 TYR Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 838 CYS Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 3.9990 chunk 268 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 351 optimal weight: 0.0000 chunk 195 optimal weight: 0.5980 chunk 403 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 424 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 495 ASN E 10 GLN E 423 ASN ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 ASN H 471 GLN F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN A1070 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN A1165 GLN A1184 HIS A1301 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39230 Z= 0.192 Angle : 0.632 11.754 53146 Z= 0.327 Chirality : 0.044 0.332 5851 Planarity : 0.004 0.054 6944 Dihedral : 8.128 113.968 5769 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.81 % Allowed : 17.92 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4890 helix: 0.18 (0.18), residues: 770 sheet: 0.01 (0.13), residues: 1413 loop : -0.94 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 451 HIS 0.005 0.001 HIS C 280 PHE 0.024 0.002 PHE C 147 TYR 0.023 0.002 TYR E 297 ARG 0.007 0.000 ARG G 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1016 time to evaluate : 4.306 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: 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: D 32 TYR cc_start: 0.8696 (p90) cc_final: 0.8402 (p90) REVERT: D 41 PHE cc_start: 0.8592 (m-10) cc_final: 0.8361 (m-10) REVERT: D 71 PHE cc_start: 0.8104 (t80) cc_final: 0.7476 (t80) REVERT: D 116 TRP cc_start: 0.8530 (m-10) cc_final: 0.8294 (m100) REVERT: D 253 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8019 (ttmt) REVERT: D 268 LYS cc_start: 0.7874 (mttt) cc_final: 0.7625 (mttm) REVERT: D 306 MET cc_start: 0.8804 (tmm) cc_final: 0.8179 (tmm) REVERT: D 429 SER cc_start: 0.8934 (m) cc_final: 0.8705 (t) REVERT: D 432 ARG cc_start: 0.8552 (mtt180) cc_final: 0.7763 (ttm110) REVERT: D 443 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: D 446 VAL cc_start: 0.8459 (m) cc_final: 0.7113 (p) REVERT: D 465 SER cc_start: 0.8564 (m) cc_final: 0.8247 (p) REVERT: D 495 ASN cc_start: 0.7940 (p0) cc_final: 0.7503 (p0) REVERT: E 14 TRP cc_start: 0.8390 (m100) cc_final: 0.7603 (m100) REVERT: E 54 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7914 (p) REVERT: E 182 PHE cc_start: 0.8473 (m-80) cc_final: 0.8253 (m-10) REVERT: E 267 GLN cc_start: 0.8809 (mt0) cc_final: 0.8317 (tt0) REVERT: E 416 TRP cc_start: 0.8291 (t60) cc_final: 0.7907 (t60) REVERT: E 429 PHE cc_start: 0.7900 (p90) cc_final: 0.7645 (p90) REVERT: E 451 GLN cc_start: 0.8300 (mt0) cc_final: 0.8089 (mm-40) REVERT: E 464 PHE cc_start: 0.8704 (m-80) cc_final: 0.8411 (m-80) REVERT: E 479 ILE cc_start: 0.8097 (mt) cc_final: 0.7115 (tt) REVERT: E 480 LEU cc_start: 0.8273 (mt) cc_final: 0.7976 (tt) REVERT: E 531 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7242 (tt0) REVERT: G 34 ASP cc_start: 0.8278 (m-30) cc_final: 0.8005 (t70) REVERT: G 40 MET cc_start: 0.7123 (mtm) cc_final: 0.6033 (ppp) REVERT: G 52 PHE cc_start: 0.7590 (m-80) cc_final: 0.7163 (m-80) REVERT: G 103 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: G 108 SER cc_start: 0.8563 (t) cc_final: 0.7489 (m) REVERT: G 109 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.3083 (m-30) REVERT: G 168 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (p) REVERT: G 296 THR cc_start: 0.7993 (m) cc_final: 0.5575 (t) REVERT: G 428 VAL cc_start: 0.8063 (t) cc_final: 0.7302 (m) REVERT: C 14 TRP cc_start: 0.6855 (m100) cc_final: 0.6573 (m100) REVERT: C 42 VAL cc_start: 0.7738 (m) cc_final: 0.7455 (p) REVERT: C 44 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8262 (t0) REVERT: C 93 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7467 (p0) REVERT: C 304 GLN cc_start: 0.8943 (mt0) cc_final: 0.8295 (tm-30) REVERT: C 426 TYR cc_start: 0.7833 (t80) cc_final: 0.6935 (t80) REVERT: C 427 LEU cc_start: 0.8579 (mt) cc_final: 0.8263 (mp) REVERT: C 487 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7640 (m-10) REVERT: C 495 LYS cc_start: 0.8477 (mttm) cc_final: 0.8186 (mttm) REVERT: C 497 ARG cc_start: 0.7805 (ptt180) cc_final: 0.7519 (ptt180) REVERT: C 517 THR cc_start: 0.7894 (m) cc_final: 0.7078 (t) REVERT: C 537 HIS cc_start: 0.9033 (p-80) cc_final: 0.8807 (p-80) REVERT: C 615 MET cc_start: 0.6979 (mtm) cc_final: 0.6477 (mtm) REVERT: C 618 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8295 (mt) REVERT: C 649 PHE cc_start: 0.8071 (m-80) cc_final: 0.7564 (m-10) REVERT: B 39 PHE cc_start: 0.8049 (m-80) cc_final: 0.7845 (m-80) REVERT: B 54 TRP cc_start: 0.8806 (p90) cc_final: 0.8458 (p90) REVERT: B 76 ILE cc_start: 0.8812 (mm) cc_final: 0.8154 (tp) REVERT: B 138 ASN cc_start: 0.7634 (p0) cc_final: 0.6166 (p0) REVERT: B 142 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.6993 (p0) REVERT: B 226 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8379 (tm-30) REVERT: B 243 ASN cc_start: 0.7666 (p0) cc_final: 0.7433 (t0) REVERT: B 283 GLN cc_start: 0.8706 (tt0) cc_final: 0.8251 (tm-30) REVERT: B 412 PHE cc_start: 0.8910 (t80) cc_final: 0.8553 (t80) REVERT: B 454 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.6027 (p) REVERT: B 492 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8790 (tm-30) REVERT: B 498 ASP cc_start: 0.8007 (t70) cc_final: 0.6530 (m-30) REVERT: B 606 ASP cc_start: 0.7739 (t0) cc_final: 0.7418 (t0) REVERT: B 610 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8145 (mmmt) REVERT: B 611 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8492 (mp0) REVERT: B 630 GLU cc_start: 0.8069 (tt0) cc_final: 0.7704 (pm20) REVERT: B 648 GLU cc_start: 0.8269 (tt0) cc_final: 0.7941 (pm20) REVERT: B 695 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7631 (p) REVERT: H 93 LYS cc_start: 0.7869 (mptt) cc_final: 0.7582 (mptt) REVERT: H 96 LEU cc_start: 0.7470 (mt) cc_final: 0.7087 (mp) REVERT: H 133 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7409 (ttm110) REVERT: H 145 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6269 (m-30) REVERT: H 272 MET cc_start: 0.3142 (ppp) cc_final: 0.2885 (ppp) REVERT: H 291 ASP cc_start: 0.8325 (t0) cc_final: 0.8079 (t0) REVERT: H 341 LEU cc_start: 0.6955 (mt) cc_final: 0.5582 (mp) REVERT: H 357 LYS cc_start: 0.8696 (tttm) cc_final: 0.8432 (tptp) REVERT: H 448 ILE cc_start: 0.8218 (mt) cc_final: 0.7962 (mp) REVERT: F 23 ASP cc_start: 0.7861 (t0) cc_final: 0.7629 (t0) REVERT: F 69 PHE cc_start: 0.7885 (m-80) cc_final: 0.7667 (m-80) REVERT: F 112 TYR cc_start: 0.8138 (m-80) cc_final: 0.7675 (m-80) REVERT: F 128 VAL cc_start: 0.8105 (m) cc_final: 0.7642 (p) REVERT: F 158 GLN cc_start: 0.8273 (mt0) cc_final: 0.7933 (tt0) REVERT: A 193 THR cc_start: 0.8497 (p) cc_final: 0.8139 (m) REVERT: A 196 THR cc_start: 0.8995 (m) cc_final: 0.8655 (t) REVERT: A 216 GLU cc_start: 0.8626 (tp30) cc_final: 0.8315 (pt0) REVERT: A 225 PHE cc_start: 0.8474 (t80) cc_final: 0.7801 (t80) REVERT: A 242 VAL cc_start: 0.8315 (t) cc_final: 0.7665 (p) REVERT: A 244 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8467 (tm-30) REVERT: A 249 ILE cc_start: 0.8403 (mm) cc_final: 0.7723 (tp) REVERT: A 258 LYS cc_start: 0.8853 (tptt) cc_final: 0.8589 (mmtm) REVERT: A 273 MET cc_start: 0.7934 (mtm) cc_final: 0.7691 (mmm) REVERT: A 307 ILE cc_start: 0.7927 (tt) cc_final: 0.7443 (pt) REVERT: A 357 VAL cc_start: 0.8973 (t) cc_final: 0.8593 (m) REVERT: A 359 ASP cc_start: 0.8112 (m-30) cc_final: 0.7252 (p0) REVERT: A 373 ASN cc_start: 0.8005 (m110) cc_final: 0.7721 (m110) REVERT: A 426 GLU cc_start: 0.8212 (tt0) cc_final: 0.7845 (tp30) REVERT: A 462 GLU cc_start: 0.8820 (pt0) cc_final: 0.8486 (pt0) REVERT: A 475 ILE cc_start: 0.8430 (pt) cc_final: 0.8004 (mm) REVERT: A 524 VAL cc_start: 0.8571 (t) cc_final: 0.8299 (m) REVERT: A 526 TYR cc_start: 0.8655 (p90) cc_final: 0.8362 (p90) REVERT: A 569 THR cc_start: 0.8729 (m) cc_final: 0.8278 (t) REVERT: A 582 VAL cc_start: 0.8936 (p) cc_final: 0.8587 (t) REVERT: A 637 THR cc_start: 0.8943 (t) cc_final: 0.8657 (p) REVERT: A 654 ILE cc_start: 0.8281 (pt) cc_final: 0.7974 (pt) REVERT: A 764 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7884 (mtm-85) REVERT: A 766 LYS cc_start: 0.8346 (tttt) cc_final: 0.8146 (tppt) REVERT: A 767 GLN cc_start: 0.8823 (tt0) cc_final: 0.8525 (mp10) REVERT: A 779 TRP cc_start: 0.8827 (m100) cc_final: 0.8172 (m100) REVERT: A 780 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 782 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8348 (mt0) REVERT: A 793 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8013 (m) REVERT: A 835 MET cc_start: 0.7141 (ptt) cc_final: 0.6769 (mtt) REVERT: A 880 PHE cc_start: 0.7370 (m-80) cc_final: 0.6990 (m-80) REVERT: A 892 ILE cc_start: 0.8068 (mt) cc_final: 0.7859 (mm) REVERT: A 895 SER cc_start: 0.7302 (m) cc_final: 0.7074 (p) REVERT: A 924 VAL cc_start: 0.7936 (m) cc_final: 0.7699 (p) REVERT: A 944 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8635 (mtp-110) REVERT: A 952 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8581 (mptt) REVERT: A 954 GLU cc_start: 0.8805 (tt0) cc_final: 0.8499 (tm-30) REVERT: A 961 VAL cc_start: 0.8364 (p) cc_final: 0.7921 (t) REVERT: A 981 ILE cc_start: 0.8507 (mt) cc_final: 0.7912 (tp) REVERT: A 993 GLU cc_start: 0.7785 (pt0) cc_final: 0.7516 (mm-30) REVERT: A 1042 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.7856 (ttt-90) REVERT: A 1045 ASP cc_start: 0.7648 (m-30) cc_final: 0.7266 (t70) REVERT: A 1052 LYS cc_start: 0.8305 (mttt) cc_final: 0.7973 (mtmm) REVERT: A 1060 LEU cc_start: 0.8567 (tp) cc_final: 0.7133 (tt) REVERT: A 1168 PHE cc_start: 0.8504 (t80) cc_final: 0.7914 (t80) REVERT: A 1187 PHE cc_start: 0.8554 (t80) cc_final: 0.8090 (t80) REVERT: A 1197 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8791 (tp30) REVERT: A 1287 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8358 (mmtt) REVERT: A 1297 VAL cc_start: 0.8477 (p) cc_final: 0.7842 (t) REVERT: A 1310 MET cc_start: 0.7727 (mmm) cc_final: 0.7487 (mmm) outliers start: 156 outliers final: 98 residues processed: 1089 average time/residue: 0.5222 time to fit residues: 892.7699 Evaluate side-chains 1096 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 984 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 473 optimal weight: 7.9990 chunk 392 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN E 423 ASN E 432 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN B 367 ASN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 574 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN A1005 HIS ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN A1184 HIS A1247 ASN ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 39230 Z= 0.389 Angle : 0.713 17.045 53146 Z= 0.372 Chirality : 0.048 0.311 5851 Planarity : 0.005 0.073 6944 Dihedral : 8.039 115.912 5769 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.72 % Allowed : 18.11 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.03 (0.11), residues: 4890 helix: -0.04 (0.18), residues: 770 sheet: -0.24 (0.13), residues: 1442 loop : -1.11 (0.11), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 451 HIS 0.018 0.001 HIS C 280 PHE 0.027 0.002 PHE F 42 TYR 0.029 0.002 TYR C 281 ARG 0.010 0.001 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1000 time to evaluate : 4.471 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: 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: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8755 (p90) cc_final: 0.8339 (p90) REVERT: D 41 PHE cc_start: 0.8625 (m-10) cc_final: 0.8403 (m-10) REVERT: D 71 PHE cc_start: 0.8160 (t80) cc_final: 0.7530 (t80) REVERT: D 78 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7371 (mtm180) REVERT: D 102 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8746 (ttp80) REVERT: D 116 TRP cc_start: 0.8559 (m-10) cc_final: 0.8318 (m100) REVERT: D 253 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8138 (ttmt) REVERT: D 268 LYS cc_start: 0.8069 (mttt) cc_final: 0.7856 (mttm) REVERT: D 306 MET cc_start: 0.8853 (tmm) cc_final: 0.8300 (tmm) REVERT: D 432 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8299 (mtp-110) REVERT: D 446 VAL cc_start: 0.8335 (m) cc_final: 0.6673 (p) REVERT: D 465 SER cc_start: 0.8663 (m) cc_final: 0.8328 (p) REVERT: E 14 TRP cc_start: 0.8467 (m100) cc_final: 0.7881 (m100) REVERT: E 54 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7940 (p) REVERT: E 139 ASP cc_start: 0.9150 (t0) cc_final: 0.8797 (t70) REVERT: E 166 ARG cc_start: 0.7327 (mtp180) cc_final: 0.7049 (ttt180) REVERT: E 168 TYR cc_start: 0.8986 (p90) cc_final: 0.8741 (p90) REVERT: E 416 TRP cc_start: 0.8295 (t60) cc_final: 0.7919 (t60) REVERT: E 435 HIS cc_start: 0.8598 (p90) cc_final: 0.8254 (p-80) REVERT: E 460 TYR cc_start: 0.7361 (t80) cc_final: 0.7099 (t80) REVERT: E 479 ILE cc_start: 0.8182 (mt) cc_final: 0.7274 (tt) REVERT: E 480 LEU cc_start: 0.8417 (mt) cc_final: 0.8092 (tt) REVERT: E 509 ASP cc_start: 0.8777 (p0) cc_final: 0.8483 (p0) REVERT: E 531 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7207 (tt0) REVERT: G 34 ASP cc_start: 0.8403 (m-30) cc_final: 0.8192 (t0) REVERT: G 40 MET cc_start: 0.7142 (mtm) cc_final: 0.6760 (ttp) REVERT: G 52 PHE cc_start: 0.7582 (m-80) cc_final: 0.7243 (m-80) REVERT: G 103 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.5557 (m-30) REVERT: G 108 SER cc_start: 0.8547 (t) cc_final: 0.7438 (m) REVERT: G 109 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.2510 (m-30) REVERT: G 168 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8399 (p) REVERT: G 296 THR cc_start: 0.8100 (m) cc_final: 0.6861 (p) REVERT: G 331 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7717 (mt) REVERT: G 480 TYR cc_start: 0.8850 (t80) cc_final: 0.8630 (t80) REVERT: C 14 TRP cc_start: 0.6637 (m100) cc_final: 0.6369 (m100) REVERT: C 42 VAL cc_start: 0.7713 (m) cc_final: 0.7448 (p) REVERT: C 44 ASN cc_start: 0.8696 (m110) cc_final: 0.8248 (t0) REVERT: C 93 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8210 (p0) REVERT: C 95 ASP cc_start: 0.7764 (m-30) cc_final: 0.7500 (m-30) REVERT: C 304 GLN cc_start: 0.8904 (mt0) cc_final: 0.8251 (tm-30) REVERT: C 414 VAL cc_start: 0.8170 (t) cc_final: 0.6820 (m) REVERT: C 427 LEU cc_start: 0.8699 (mt) cc_final: 0.8322 (mp) REVERT: C 447 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6612 (pt0) REVERT: C 487 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7574 (m-10) REVERT: C 497 ARG cc_start: 0.7904 (ptt180) cc_final: 0.7565 (ptt180) REVERT: C 517 THR cc_start: 0.7963 (m) cc_final: 0.7252 (t) REVERT: C 615 MET cc_start: 0.6851 (mtm) cc_final: 0.6441 (mtm) REVERT: C 618 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 631 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 27 ARG cc_start: 0.8425 (mtt90) cc_final: 0.8166 (mtt90) REVERT: B 39 PHE cc_start: 0.8066 (m-80) cc_final: 0.7865 (m-80) REVERT: B 54 TRP cc_start: 0.8873 (p90) cc_final: 0.8522 (p90) REVERT: B 76 ILE cc_start: 0.8787 (mm) cc_final: 0.8149 (tp) REVERT: B 227 ASP cc_start: 0.8476 (t0) cc_final: 0.8168 (t0) REVERT: B 228 ASP cc_start: 0.8915 (t70) cc_final: 0.8710 (t0) REVERT: B 243 ASN cc_start: 0.7742 (p0) cc_final: 0.7512 (t0) REVERT: B 358 TYR cc_start: 0.9053 (t80) cc_final: 0.8739 (t80) REVERT: B 417 GLU cc_start: 0.9064 (tp30) cc_final: 0.8797 (tp30) REVERT: B 454 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.6342 (p) REVERT: B 498 ASP cc_start: 0.8160 (t70) cc_final: 0.6961 (m-30) REVERT: B 606 ASP cc_start: 0.7805 (t0) cc_final: 0.7497 (t0) REVERT: B 610 LYS cc_start: 0.8423 (mtmt) cc_final: 0.8184 (mmmt) REVERT: B 611 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8490 (mp0) REVERT: B 630 GLU cc_start: 0.8056 (tt0) cc_final: 0.7689 (pm20) REVERT: B 648 GLU cc_start: 0.8284 (tt0) cc_final: 0.7909 (pm20) REVERT: B 695 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7886 (p) REVERT: H 93 LYS cc_start: 0.7814 (mptt) cc_final: 0.7542 (mptt) REVERT: H 96 LEU cc_start: 0.7491 (mt) cc_final: 0.7089 (mp) REVERT: H 133 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7445 (mtm110) REVERT: H 152 ASP cc_start: 0.8826 (t0) cc_final: 0.8547 (t70) REVERT: H 192 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7617 (mtp85) REVERT: H 279 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8609 (tm-30) REVERT: H 341 LEU cc_start: 0.7055 (mt) cc_final: 0.5830 (mp) REVERT: H 448 ILE cc_start: 0.8245 (mt) cc_final: 0.8024 (mp) REVERT: H 484 PHE cc_start: 0.6074 (m-80) cc_final: 0.3927 (m-10) REVERT: F 23 ASP cc_start: 0.7949 (t0) cc_final: 0.7746 (t0) REVERT: F 112 TYR cc_start: 0.8155 (m-80) cc_final: 0.7804 (m-80) REVERT: A 189 GLU cc_start: 0.8785 (tp30) cc_final: 0.8503 (mp0) REVERT: A 193 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8291 (m) REVERT: A 196 THR cc_start: 0.8960 (m) cc_final: 0.8689 (t) REVERT: A 216 GLU cc_start: 0.8632 (tp30) cc_final: 0.8328 (pt0) REVERT: A 225 PHE cc_start: 0.8643 (t80) cc_final: 0.8035 (t80) REVERT: A 242 VAL cc_start: 0.8384 (t) cc_final: 0.7713 (p) REVERT: A 244 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8430 (tm-30) REVERT: A 249 ILE cc_start: 0.8481 (mm) cc_final: 0.7673 (tt) REVERT: A 258 LYS cc_start: 0.8876 (tptt) cc_final: 0.8617 (mmtm) REVERT: A 273 MET cc_start: 0.7958 (mtm) cc_final: 0.7656 (mmm) REVERT: A 307 ILE cc_start: 0.7926 (tt) cc_final: 0.7361 (pt) REVERT: A 309 VAL cc_start: 0.8285 (p) cc_final: 0.7932 (m) REVERT: A 323 GLU cc_start: 0.8623 (pt0) cc_final: 0.8059 (pp20) REVERT: A 357 VAL cc_start: 0.9024 (t) cc_final: 0.8634 (m) REVERT: A 373 ASN cc_start: 0.8057 (m110) cc_final: 0.7761 (m110) REVERT: A 426 GLU cc_start: 0.8277 (tt0) cc_final: 0.7864 (tp30) REVERT: A 462 GLU cc_start: 0.8780 (pt0) cc_final: 0.8441 (pt0) REVERT: A 475 ILE cc_start: 0.8453 (pt) cc_final: 0.7981 (mm) REVERT: A 524 VAL cc_start: 0.8675 (t) cc_final: 0.8458 (m) REVERT: A 542 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8000 (t60) REVERT: A 569 THR cc_start: 0.8762 (m) cc_final: 0.8343 (t) REVERT: A 582 VAL cc_start: 0.8964 (p) cc_final: 0.8600 (t) REVERT: A 637 THR cc_start: 0.8946 (t) cc_final: 0.8629 (p) REVERT: A 764 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7955 (mtm-85) REVERT: A 779 TRP cc_start: 0.8877 (m100) cc_final: 0.8220 (m100) REVERT: A 780 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 793 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8289 (m) REVERT: A 835 MET cc_start: 0.7157 (ptt) cc_final: 0.6759 (mtt) REVERT: A 880 PHE cc_start: 0.7365 (m-80) cc_final: 0.7022 (m-80) REVERT: A 892 ILE cc_start: 0.8137 (mt) cc_final: 0.7889 (mm) REVERT: A 895 SER cc_start: 0.7409 (m) cc_final: 0.7209 (p) REVERT: A 924 VAL cc_start: 0.8070 (m) cc_final: 0.7767 (p) REVERT: A 944 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8617 (mtp-110) REVERT: A 952 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8610 (mptt) REVERT: A 954 GLU cc_start: 0.8831 (tt0) cc_final: 0.8514 (tm-30) REVERT: A 961 VAL cc_start: 0.8524 (p) cc_final: 0.8046 (t) REVERT: A 981 ILE cc_start: 0.8511 (mt) cc_final: 0.7906 (tp) REVERT: A 993 GLU cc_start: 0.8045 (pt0) cc_final: 0.7648 (tp30) REVERT: A 1042 ARG cc_start: 0.8264 (ttt-90) cc_final: 0.8034 (tmm-80) REVERT: A 1045 ASP cc_start: 0.7730 (m-30) cc_final: 0.7336 (t0) REVERT: A 1052 LYS cc_start: 0.8316 (mttt) cc_final: 0.7972 (mppt) REVERT: A 1060 LEU cc_start: 0.8616 (tp) cc_final: 0.8251 (tp) REVERT: A 1117 VAL cc_start: 0.7529 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 1120 ARG cc_start: 0.7596 (tpt170) cc_final: 0.7312 (tpt170) REVERT: A 1197 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8901 (tp30) REVERT: A 1287 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8367 (mptt) REVERT: A 1295 ILE cc_start: 0.8360 (mt) cc_final: 0.7384 (tt) REVERT: A 1297 VAL cc_start: 0.8465 (p) cc_final: 0.7827 (t) REVERT: A 1310 MET cc_start: 0.7784 (mmm) cc_final: 0.7483 (mmm) outliers start: 193 outliers final: 133 residues processed: 1099 average time/residue: 0.5527 time to fit residues: 960.8406 Evaluate side-chains 1129 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 982 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 409 ARG Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 432 THR Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1342 HIS Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1433 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 345 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 398 optimal weight: 0.8980 chunk 264 optimal weight: 0.7980 chunk 471 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 433 GLN E 10 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN E 432 GLN E 488 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN C 305 ASN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 158 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 39230 Z= 0.251 Angle : 0.676 16.042 53146 Z= 0.349 Chirality : 0.045 0.299 5851 Planarity : 0.005 0.057 6944 Dihedral : 7.625 115.200 5769 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.20 % Allowed : 19.38 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.93 (0.12), residues: 4890 helix: 0.14 (0.19), residues: 770 sheet: -0.17 (0.13), residues: 1414 loop : -1.07 (0.11), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 451 HIS 0.007 0.001 HIS C 280 PHE 0.026 0.002 PHE F 42 TYR 0.027 0.002 TYR A 448 ARG 0.012 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 994 time to evaluate : 4.358 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: 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: D 32 TYR cc_start: 0.8732 (p90) cc_final: 0.8398 (p90) REVERT: D 41 PHE cc_start: 0.8618 (m-10) cc_final: 0.8366 (m-10) REVERT: D 97 ASP cc_start: 0.8480 (p0) cc_final: 0.8138 (p0) REVERT: D 116 TRP cc_start: 0.8541 (m-10) cc_final: 0.8298 (m100) REVERT: D 253 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8122 (ttmt) REVERT: D 268 LYS cc_start: 0.8041 (mttt) cc_final: 0.7797 (mttm) REVERT: D 306 MET cc_start: 0.8837 (tmm) cc_final: 0.8257 (tmm) REVERT: D 432 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8268 (mtp-110) REVERT: D 443 GLN cc_start: 0.8650 (mt0) cc_final: 0.8267 (tm-30) REVERT: D 465 SER cc_start: 0.8622 (m) cc_final: 0.8292 (p) REVERT: E 14 TRP cc_start: 0.8398 (m100) cc_final: 0.7929 (m100) REVERT: E 54 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7878 (p) REVERT: E 126 TYR cc_start: 0.9005 (t80) cc_final: 0.8737 (t80) REVERT: E 139 ASP cc_start: 0.9071 (t0) cc_final: 0.8481 (t0) REVERT: E 166 ARG cc_start: 0.6992 (mtp180) cc_final: 0.6782 (ttt-90) REVERT: E 168 TYR cc_start: 0.8991 (p90) cc_final: 0.8714 (p90) REVERT: E 182 PHE cc_start: 0.8693 (m-10) cc_final: 0.8490 (m-10) REVERT: E 267 GLN cc_start: 0.8816 (mt0) cc_final: 0.8379 (tt0) REVERT: E 435 HIS cc_start: 0.8574 (p90) cc_final: 0.8219 (p-80) REVERT: E 451 GLN cc_start: 0.8318 (mt0) cc_final: 0.8099 (mm-40) REVERT: E 479 ILE cc_start: 0.8134 (mt) cc_final: 0.7220 (tt) REVERT: E 480 LEU cc_start: 0.8392 (mt) cc_final: 0.8059 (tt) REVERT: E 531 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7232 (tt0) REVERT: G 30 TRP cc_start: 0.8565 (m-10) cc_final: 0.8307 (m-10) REVERT: G 40 MET cc_start: 0.7303 (mtm) cc_final: 0.7026 (ptm) REVERT: G 52 PHE cc_start: 0.7562 (m-80) cc_final: 0.7157 (m-80) REVERT: G 103 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.5592 (m-30) REVERT: G 108 SER cc_start: 0.8546 (t) cc_final: 0.7467 (m) REVERT: G 109 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.2657 (m-30) REVERT: G 168 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8370 (p) REVERT: G 296 THR cc_start: 0.8052 (m) cc_final: 0.5840 (t) REVERT: G 428 VAL cc_start: 0.8100 (t) cc_final: 0.7276 (m) REVERT: G 480 TYR cc_start: 0.8829 (t80) cc_final: 0.8601 (t80) REVERT: C 14 TRP cc_start: 0.6625 (m100) cc_final: 0.6358 (m100) REVERT: C 42 VAL cc_start: 0.7643 (m) cc_final: 0.7392 (p) REVERT: C 44 ASN cc_start: 0.8668 (m110) cc_final: 0.8250 (t0) REVERT: C 93 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7591 (p0) REVERT: C 94 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7956 (mm-30) REVERT: C 95 ASP cc_start: 0.7688 (m-30) cc_final: 0.7212 (m-30) REVERT: C 227 GLN cc_start: 0.8086 (mp10) cc_final: 0.7864 (mp10) REVERT: C 257 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8282 (tp30) REVERT: C 304 GLN cc_start: 0.8930 (mt0) cc_final: 0.8270 (tm-30) REVERT: C 414 VAL cc_start: 0.8273 (t) cc_final: 0.7698 (p) REVERT: C 426 TYR cc_start: 0.7836 (t80) cc_final: 0.7137 (t80) REVERT: C 487 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: C 615 MET cc_start: 0.6877 (mtm) cc_final: 0.6397 (mtm) REVERT: C 618 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 631 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 649 PHE cc_start: 0.8165 (m-10) cc_final: 0.7897 (m-10) REVERT: C 660 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.4974 (pt0) REVERT: B 27 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8120 (mtt90) REVERT: B 54 TRP cc_start: 0.8851 (p90) cc_final: 0.8531 (p90) REVERT: B 76 ILE cc_start: 0.8794 (mm) cc_final: 0.8160 (tp) REVERT: B 227 ASP cc_start: 0.8438 (t0) cc_final: 0.8154 (t0) REVERT: B 228 ASP cc_start: 0.8907 (t70) cc_final: 0.8696 (t0) REVERT: B 243 ASN cc_start: 0.7724 (p0) cc_final: 0.7494 (t0) REVERT: B 454 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.6159 (p) REVERT: B 498 ASP cc_start: 0.8059 (t70) cc_final: 0.6596 (m-30) REVERT: B 606 ASP cc_start: 0.7821 (t0) cc_final: 0.7481 (t0) REVERT: B 610 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8089 (mmmt) REVERT: B 611 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8489 (mp0) REVERT: B 630 GLU cc_start: 0.8059 (tt0) cc_final: 0.7689 (pm20) REVERT: B 648 GLU cc_start: 0.8273 (tt0) cc_final: 0.7909 (pm20) REVERT: B 695 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (p) REVERT: H 93 LYS cc_start: 0.7776 (mptt) cc_final: 0.7501 (mptt) REVERT: H 96 LEU cc_start: 0.7514 (mt) cc_final: 0.7104 (mp) REVERT: H 133 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7432 (ttm110) REVERT: H 152 ASP cc_start: 0.8842 (t0) cc_final: 0.8314 (t70) REVERT: H 192 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7600 (mtp85) REVERT: H 272 MET cc_start: 0.3083 (ppp) cc_final: 0.2712 (ppp) REVERT: H 279 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8571 (tm-30) REVERT: H 291 ASP cc_start: 0.8257 (t0) cc_final: 0.7977 (t0) REVERT: H 341 LEU cc_start: 0.6813 (mt) cc_final: 0.5465 (mp) REVERT: H 484 PHE cc_start: 0.6181 (m-80) cc_final: 0.5633 (m-80) REVERT: F 112 TYR cc_start: 0.8183 (m-80) cc_final: 0.7824 (m-80) REVERT: F 128 VAL cc_start: 0.8028 (m) cc_final: 0.7773 (p) REVERT: F 158 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: A 149 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8212 (mp0) REVERT: A 193 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8102 (m) REVERT: A 196 THR cc_start: 0.8973 (m) cc_final: 0.8676 (t) REVERT: A 216 GLU cc_start: 0.8645 (tp30) cc_final: 0.8342 (pt0) REVERT: A 242 VAL cc_start: 0.8364 (t) cc_final: 0.7702 (p) REVERT: A 244 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8457 (tm-30) REVERT: A 249 ILE cc_start: 0.8468 (mm) cc_final: 0.7757 (tp) REVERT: A 258 LYS cc_start: 0.8865 (tptt) cc_final: 0.8596 (mmtm) REVERT: A 273 MET cc_start: 0.7955 (mtm) cc_final: 0.7653 (mmm) REVERT: A 307 ILE cc_start: 0.7857 (tt) cc_final: 0.7343 (pt) REVERT: A 357 VAL cc_start: 0.9002 (t) cc_final: 0.8612 (m) REVERT: A 373 ASN cc_start: 0.8006 (m110) cc_final: 0.7776 (m110) REVERT: A 419 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 426 GLU cc_start: 0.8261 (tt0) cc_final: 0.7857 (tp30) REVERT: A 462 GLU cc_start: 0.8705 (pt0) cc_final: 0.8339 (pt0) REVERT: A 475 ILE cc_start: 0.8439 (pt) cc_final: 0.8062 (mm) REVERT: A 524 VAL cc_start: 0.8608 (t) cc_final: 0.8336 (m) REVERT: A 542 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.7672 (t60) REVERT: A 569 THR cc_start: 0.8745 (m) cc_final: 0.8343 (t) REVERT: A 582 VAL cc_start: 0.8947 (p) cc_final: 0.8585 (t) REVERT: A 637 THR cc_start: 0.8873 (t) cc_final: 0.8588 (p) REVERT: A 755 TRP cc_start: 0.8384 (p-90) cc_final: 0.8107 (p-90) REVERT: A 764 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7941 (mtm-85) REVERT: A 767 GLN cc_start: 0.8835 (tt0) cc_final: 0.8533 (mp10) REVERT: A 779 TRP cc_start: 0.8885 (m100) cc_final: 0.8250 (m100) REVERT: A 780 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 782 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8407 (mt0) REVERT: A 793 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8119 (m) REVERT: A 835 MET cc_start: 0.7249 (ptt) cc_final: 0.6829 (mtt) REVERT: A 880 PHE cc_start: 0.7405 (m-80) cc_final: 0.7043 (m-80) REVERT: A 881 THR cc_start: 0.7850 (p) cc_final: 0.7568 (t) REVERT: A 892 ILE cc_start: 0.8120 (mt) cc_final: 0.7863 (mm) REVERT: A 895 SER cc_start: 0.7316 (m) cc_final: 0.7094 (p) REVERT: A 924 VAL cc_start: 0.7993 (m) cc_final: 0.7711 (p) REVERT: A 944 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8609 (mtp-110) REVERT: A 952 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8587 (mptt) REVERT: A 954 GLU cc_start: 0.8831 (tt0) cc_final: 0.8515 (tm-30) REVERT: A 961 VAL cc_start: 0.8450 (p) cc_final: 0.7933 (t) REVERT: A 981 ILE cc_start: 0.8528 (mt) cc_final: 0.7927 (tp) REVERT: A 1008 GLU cc_start: 0.8477 (tp30) cc_final: 0.8180 (mt-10) REVERT: A 1042 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.8061 (tmm-80) REVERT: A 1045 ASP cc_start: 0.7771 (m-30) cc_final: 0.7335 (t70) REVERT: A 1052 LYS cc_start: 0.8187 (mttt) cc_final: 0.7829 (mppt) REVERT: A 1060 LEU cc_start: 0.8585 (tp) cc_final: 0.8085 (tp) REVERT: A 1117 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7292 (t) REVERT: A 1120 ARG cc_start: 0.7538 (tpt170) cc_final: 0.7208 (tpt170) REVERT: A 1168 PHE cc_start: 0.8523 (t80) cc_final: 0.7869 (t80) REVERT: A 1197 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8847 (tp30) REVERT: A 1287 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8371 (mmtt) REVERT: A 1295 ILE cc_start: 0.8313 (mt) cc_final: 0.7366 (tt) REVERT: A 1297 VAL cc_start: 0.8411 (p) cc_final: 0.7798 (t) outliers start: 172 outliers final: 127 residues processed: 1082 average time/residue: 0.5409 time to fit residues: 923.3080 Evaluate side-chains 1117 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 974 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 409 ARG Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 432 THR Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1127 THR Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1433 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 chunk 321 optimal weight: 8.9990 chunk 233 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 370 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 158 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 39230 Z= 0.289 Angle : 0.680 13.773 53146 Z= 0.352 Chirality : 0.046 0.287 5851 Planarity : 0.005 0.057 6944 Dihedral : 7.346 112.504 5769 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.40 % Allowed : 19.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.97 (0.12), residues: 4890 helix: 0.08 (0.19), residues: 770 sheet: -0.20 (0.13), residues: 1417 loop : -1.08 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 451 HIS 0.013 0.001 HIS C 280 PHE 0.021 0.002 PHE C 147 TYR 0.023 0.002 TYR D 141 ARG 0.014 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 982 time to evaluate : 4.429 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: 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: D 32 TYR cc_start: 0.8744 (p90) cc_final: 0.8417 (p90) REVERT: D 41 PHE cc_start: 0.8628 (m-10) cc_final: 0.8373 (m-10) REVERT: D 97 ASP cc_start: 0.8495 (p0) cc_final: 0.8122 (p0) REVERT: D 116 TRP cc_start: 0.8552 (m-10) cc_final: 0.8244 (m100) REVERT: D 253 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8125 (ttmt) REVERT: D 268 LYS cc_start: 0.8055 (mttt) cc_final: 0.7808 (mttm) REVERT: D 306 MET cc_start: 0.8856 (tmm) cc_final: 0.8240 (tmm) REVERT: D 432 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8260 (mtp-110) REVERT: D 442 PHE cc_start: 0.8322 (t80) cc_final: 0.7761 (t80) REVERT: D 443 GLN cc_start: 0.8683 (tt0) cc_final: 0.8276 (tm-30) REVERT: D 465 SER cc_start: 0.8660 (m) cc_final: 0.8316 (p) REVERT: E 14 TRP cc_start: 0.8390 (m100) cc_final: 0.7943 (m100) REVERT: E 54 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 139 ASP cc_start: 0.9064 (t0) cc_final: 0.8709 (t70) REVERT: E 168 TYR cc_start: 0.9020 (p90) cc_final: 0.8800 (p90) REVERT: E 182 PHE cc_start: 0.8726 (m-10) cc_final: 0.8500 (m-10) REVERT: E 267 GLN cc_start: 0.8800 (mt0) cc_final: 0.8364 (tt0) REVERT: E 279 MET cc_start: 0.7920 (tpp) cc_final: 0.7707 (tpp) REVERT: E 280 LEU cc_start: 0.8133 (mm) cc_final: 0.7857 (mp) REVERT: E 435 HIS cc_start: 0.8602 (p90) cc_final: 0.8243 (p-80) REVERT: E 451 GLN cc_start: 0.8328 (mt0) cc_final: 0.8110 (mm-40) REVERT: E 479 ILE cc_start: 0.8127 (mt) cc_final: 0.7211 (tt) REVERT: E 480 LEU cc_start: 0.8433 (mt) cc_final: 0.8134 (tt) REVERT: E 509 ASP cc_start: 0.8760 (p0) cc_final: 0.8461 (p0) REVERT: E 531 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7206 (tt0) REVERT: G 30 TRP cc_start: 0.8548 (m-10) cc_final: 0.8290 (m-10) REVERT: G 40 MET cc_start: 0.7289 (mtm) cc_final: 0.7000 (ptm) REVERT: G 52 PHE cc_start: 0.7504 (m-80) cc_final: 0.7084 (m-80) REVERT: G 103 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.5326 (m-30) REVERT: G 108 SER cc_start: 0.8533 (t) cc_final: 0.8303 (m) REVERT: G 168 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8421 (p) REVERT: G 296 THR cc_start: 0.8079 (m) cc_final: 0.5977 (t) REVERT: G 428 VAL cc_start: 0.8083 (t) cc_final: 0.7244 (m) REVERT: G 480 TYR cc_start: 0.8835 (t80) cc_final: 0.8618 (t80) REVERT: C 14 TRP cc_start: 0.6675 (m100) cc_final: 0.6414 (m100) REVERT: C 42 VAL cc_start: 0.7635 (m) cc_final: 0.7382 (p) REVERT: C 44 ASN cc_start: 0.8678 (m110) cc_final: 0.8261 (t0) REVERT: C 93 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7592 (p0) REVERT: C 94 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 95 ASP cc_start: 0.7660 (m-30) cc_final: 0.7263 (m-30) REVERT: C 304 GLN cc_start: 0.8918 (mt0) cc_final: 0.8264 (tm-30) REVERT: C 414 VAL cc_start: 0.8193 (t) cc_final: 0.7751 (p) REVERT: C 426 TYR cc_start: 0.7858 (t80) cc_final: 0.7250 (t80) REVERT: C 447 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6651 (pt0) REVERT: C 487 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7507 (m-10) REVERT: C 497 ARG cc_start: 0.7663 (ptt-90) cc_final: 0.7096 (ptt-90) REVERT: C 517 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7209 (t) REVERT: C 615 MET cc_start: 0.6825 (mtm) cc_final: 0.6353 (mtm) REVERT: C 618 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 631 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 649 PHE cc_start: 0.8153 (m-10) cc_final: 0.7936 (m-10) REVERT: C 660 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.5048 (pt0) REVERT: B 23 GLN cc_start: 0.7736 (pt0) cc_final: 0.7511 (pt0) REVERT: B 27 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8163 (mtt90) REVERT: B 54 TRP cc_start: 0.8864 (p90) cc_final: 0.8507 (p90) REVERT: B 76 ILE cc_start: 0.8789 (mm) cc_final: 0.8138 (tp) REVERT: B 227 ASP cc_start: 0.8441 (t0) cc_final: 0.8075 (t0) REVERT: B 228 ASP cc_start: 0.8899 (t70) cc_final: 0.8615 (m-30) REVERT: B 243 ASN cc_start: 0.7729 (p0) cc_final: 0.7500 (t0) REVERT: B 412 PHE cc_start: 0.8910 (t80) cc_final: 0.8169 (t80) REVERT: B 437 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8535 (mm-30) REVERT: B 454 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.6211 (p) REVERT: B 492 GLU cc_start: 0.9155 (tp30) cc_final: 0.8945 (tm-30) REVERT: B 610 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8138 (mmmt) REVERT: B 611 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8499 (mp0) REVERT: B 630 GLU cc_start: 0.8067 (tt0) cc_final: 0.7702 (pm20) REVERT: B 648 GLU cc_start: 0.8276 (tt0) cc_final: 0.7907 (pm20) REVERT: B 695 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7879 (p) REVERT: H 133 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7436 (mtm110) REVERT: H 152 ASP cc_start: 0.8833 (t0) cc_final: 0.8415 (t0) REVERT: H 192 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7598 (mtp85) REVERT: H 272 MET cc_start: 0.3105 (ppp) cc_final: 0.2753 (ppp) REVERT: H 279 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8568 (tm-30) REVERT: H 291 ASP cc_start: 0.8229 (t0) cc_final: 0.7992 (t0) REVERT: H 341 LEU cc_start: 0.6796 (mt) cc_final: 0.5431 (mp) REVERT: H 484 PHE cc_start: 0.6309 (m-80) cc_final: 0.5735 (m-80) REVERT: F 23 ASP cc_start: 0.7922 (t0) cc_final: 0.7660 (p0) REVERT: F 112 TYR cc_start: 0.8228 (m-80) cc_final: 0.7834 (m-80) REVERT: F 128 VAL cc_start: 0.8042 (m) cc_final: 0.7774 (p) REVERT: F 158 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: A 193 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8109 (m) REVERT: A 196 THR cc_start: 0.8964 (m) cc_final: 0.8676 (t) REVERT: A 216 GLU cc_start: 0.8674 (tp30) cc_final: 0.8376 (pt0) REVERT: A 225 PHE cc_start: 0.8488 (t80) cc_final: 0.7812 (t80) REVERT: A 242 VAL cc_start: 0.8368 (t) cc_final: 0.7715 (p) REVERT: A 244 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8463 (tm-30) REVERT: A 249 ILE cc_start: 0.8463 (mm) cc_final: 0.7627 (tt) REVERT: A 258 LYS cc_start: 0.8857 (tptt) cc_final: 0.8584 (mmtm) REVERT: A 273 MET cc_start: 0.7965 (mtm) cc_final: 0.7700 (mmm) REVERT: A 307 ILE cc_start: 0.7802 (tt) cc_final: 0.7330 (pt) REVERT: A 357 VAL cc_start: 0.8978 (t) cc_final: 0.8576 (m) REVERT: A 373 ASN cc_start: 0.8114 (m110) cc_final: 0.7802 (m110) REVERT: A 419 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7720 (p) REVERT: A 426 GLU cc_start: 0.8281 (tt0) cc_final: 0.7856 (tp30) REVERT: A 462 GLU cc_start: 0.8706 (pt0) cc_final: 0.8464 (pt0) REVERT: A 475 ILE cc_start: 0.8434 (pt) cc_final: 0.8050 (mm) REVERT: A 524 VAL cc_start: 0.8625 (t) cc_final: 0.8355 (m) REVERT: A 542 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.7626 (t60) REVERT: A 569 THR cc_start: 0.8780 (m) cc_final: 0.8385 (t) REVERT: A 582 VAL cc_start: 0.8939 (p) cc_final: 0.8560 (t) REVERT: A 637 THR cc_start: 0.8872 (t) cc_final: 0.8592 (p) REVERT: A 755 TRP cc_start: 0.8462 (p-90) cc_final: 0.8238 (p-90) REVERT: A 764 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7951 (mtm-85) REVERT: A 779 TRP cc_start: 0.8872 (m100) cc_final: 0.8222 (m100) REVERT: A 780 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 792 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7575 (t) REVERT: A 793 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8537 (t) REVERT: A 835 MET cc_start: 0.7252 (ptt) cc_final: 0.6833 (mtt) REVERT: A 880 PHE cc_start: 0.7332 (m-80) cc_final: 0.6990 (m-80) REVERT: A 881 THR cc_start: 0.7931 (p) cc_final: 0.7639 (t) REVERT: A 892 ILE cc_start: 0.8102 (mt) cc_final: 0.7846 (mm) REVERT: A 895 SER cc_start: 0.7286 (m) cc_final: 0.7055 (p) REVERT: A 924 VAL cc_start: 0.7972 (m) cc_final: 0.7684 (p) REVERT: A 944 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8633 (mtp-110) REVERT: A 952 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8577 (mptt) REVERT: A 954 GLU cc_start: 0.8829 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 961 VAL cc_start: 0.8442 (p) cc_final: 0.7858 (t) REVERT: A 981 ILE cc_start: 0.8513 (mt) cc_final: 0.7905 (tp) REVERT: A 1008 GLU cc_start: 0.8478 (tp30) cc_final: 0.8119 (mt-10) REVERT: A 1045 ASP cc_start: 0.7817 (m-30) cc_final: 0.7390 (t70) REVERT: A 1052 LYS cc_start: 0.8142 (mttt) cc_final: 0.7804 (mppt) REVERT: A 1060 LEU cc_start: 0.8570 (tp) cc_final: 0.8202 (tp) REVERT: A 1168 PHE cc_start: 0.8526 (t80) cc_final: 0.7847 (t80) REVERT: A 1197 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8864 (tp30) REVERT: A 1287 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8362 (mmtt) REVERT: A 1295 ILE cc_start: 0.8346 (mt) cc_final: 0.7360 (tt) REVERT: A 1297 VAL cc_start: 0.8380 (p) cc_final: 0.7834 (t) outliers start: 180 outliers final: 144 residues processed: 1079 average time/residue: 0.5493 time to fit residues: 940.3924 Evaluate side-chains 1126 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 966 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 463 MET Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1127 THR Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 1.9990 chunk 451 optimal weight: 0.6980 chunk 411 optimal weight: 0.8980 chunk 439 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 344 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 396 optimal weight: 0.5980 chunk 415 optimal weight: 0.5980 chunk 437 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 457 ASN E 10 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 158 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 39230 Z= 0.229 Angle : 0.672 16.845 53146 Z= 0.344 Chirality : 0.045 0.277 5851 Planarity : 0.005 0.058 6944 Dihedral : 6.996 109.339 5769 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.03 % Allowed : 20.90 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.02 % 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: -0.88 (0.12), residues: 4890 helix: 0.26 (0.19), residues: 766 sheet: -0.14 (0.14), residues: 1411 loop : -1.06 (0.11), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 451 HIS 0.009 0.001 HIS C 280 PHE 0.026 0.002 PHE A 415 TYR 0.019 0.002 TYR E 126 ARG 0.015 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 981 time to evaluate : 4.481 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: 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: D 32 TYR cc_start: 0.8737 (p90) cc_final: 0.8410 (p90) REVERT: D 41 PHE cc_start: 0.8625 (m-10) cc_final: 0.8375 (m-10) REVERT: D 97 ASP cc_start: 0.8505 (p0) cc_final: 0.8134 (p0) REVERT: D 116 TRP cc_start: 0.8545 (m-10) cc_final: 0.8303 (m100) REVERT: D 141 TYR cc_start: 0.8604 (t80) cc_final: 0.8401 (t80) REVERT: D 253 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8104 (ttmt) REVERT: D 268 LYS cc_start: 0.8054 (mttt) cc_final: 0.7786 (mttm) REVERT: D 306 MET cc_start: 0.8847 (tmm) cc_final: 0.8248 (tmm) REVERT: D 432 ARG cc_start: 0.8548 (mtt180) cc_final: 0.8256 (mtp-110) REVERT: D 443 GLN cc_start: 0.8662 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 465 SER cc_start: 0.8642 (m) cc_final: 0.8316 (p) REVERT: E 14 TRP cc_start: 0.8319 (m100) cc_final: 0.7943 (m100) REVERT: E 54 CYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7855 (p) REVERT: E 139 ASP cc_start: 0.9029 (t0) cc_final: 0.8671 (t70) REVERT: E 182 PHE cc_start: 0.8746 (m-10) cc_final: 0.8523 (m-10) REVERT: E 279 MET cc_start: 0.7913 (tpp) cc_final: 0.7713 (tpp) REVERT: E 280 LEU cc_start: 0.8104 (mm) cc_final: 0.7825 (mp) REVERT: E 435 HIS cc_start: 0.8556 (p90) cc_final: 0.8205 (p-80) REVERT: E 451 GLN cc_start: 0.8311 (mt0) cc_final: 0.8099 (mm-40) REVERT: E 479 ILE cc_start: 0.8104 (mt) cc_final: 0.7144 (tt) REVERT: E 480 LEU cc_start: 0.8405 (mt) cc_final: 0.8123 (tt) REVERT: E 509 ASP cc_start: 0.8751 (p0) cc_final: 0.8456 (p0) REVERT: E 531 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7264 (tt0) REVERT: G 40 MET cc_start: 0.7307 (mtm) cc_final: 0.6955 (ptm) REVERT: G 103 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: G 108 SER cc_start: 0.8563 (t) cc_final: 0.7592 (m) REVERT: G 109 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.2798 (m-30) REVERT: G 163 ASP cc_start: 0.8155 (m-30) cc_final: 0.7378 (t0) REVERT: G 168 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8388 (p) REVERT: G 296 THR cc_start: 0.7916 (m) cc_final: 0.5708 (t) REVERT: G 428 VAL cc_start: 0.8097 (t) cc_final: 0.7262 (m) REVERT: G 480 TYR cc_start: 0.8819 (t80) cc_final: 0.8593 (t80) REVERT: C 14 TRP cc_start: 0.6675 (m100) cc_final: 0.6396 (m100) REVERT: C 42 VAL cc_start: 0.7591 (m) cc_final: 0.7352 (p) REVERT: C 44 ASN cc_start: 0.8639 (m110) cc_final: 0.8280 (t0) REVERT: C 55 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7691 (ptp-110) REVERT: C 93 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7591 (p0) REVERT: C 94 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 95 ASP cc_start: 0.7641 (m-30) cc_final: 0.7217 (m-30) REVERT: C 414 VAL cc_start: 0.8189 (t) cc_final: 0.7676 (p) REVERT: C 426 TYR cc_start: 0.7842 (t80) cc_final: 0.7320 (t80) REVERT: C 427 LEU cc_start: 0.8726 (mt) cc_final: 0.8368 (mp) REVERT: C 447 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6695 (pt0) REVERT: C 487 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: C 497 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.7193 (ptt-90) REVERT: C 615 MET cc_start: 0.6920 (mtm) cc_final: 0.6362 (mtm) REVERT: C 618 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8117 (mm) REVERT: C 631 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 660 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.5033 (pt0) REVERT: B 27 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8149 (mtt90) REVERT: B 54 TRP cc_start: 0.8847 (p90) cc_final: 0.8512 (p90) REVERT: B 76 ILE cc_start: 0.8759 (mm) cc_final: 0.8072 (tp) REVERT: B 122 LYS cc_start: 0.8632 (mttt) cc_final: 0.8389 (mmtm) REVERT: B 243 ASN cc_start: 0.7732 (p0) cc_final: 0.7510 (t0) REVERT: B 358 TYR cc_start: 0.8945 (t80) cc_final: 0.8628 (t80) REVERT: B 417 GLU cc_start: 0.9024 (tp30) cc_final: 0.8741 (tp30) REVERT: B 437 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8520 (mm-30) REVERT: B 454 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.6137 (p) REVERT: B 492 GLU cc_start: 0.9150 (tp30) cc_final: 0.8930 (tm-30) REVERT: B 610 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7999 (mmmt) REVERT: B 630 GLU cc_start: 0.8067 (tt0) cc_final: 0.7697 (pm20) REVERT: B 648 GLU cc_start: 0.8288 (tt0) cc_final: 0.7912 (pm20) REVERT: B 675 ASP cc_start: 0.7397 (t0) cc_final: 0.7007 (p0) REVERT: B 695 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (p) REVERT: H 133 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7443 (mtm110) REVERT: H 152 ASP cc_start: 0.8848 (t0) cc_final: 0.8467 (t0) REVERT: H 192 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7607 (mtp85) REVERT: H 272 MET cc_start: 0.2559 (ppp) cc_final: 0.2282 (ppp) REVERT: H 284 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7416 (tpt90) REVERT: H 291 ASP cc_start: 0.8255 (t0) cc_final: 0.8019 (t0) REVERT: H 341 LEU cc_start: 0.6823 (mt) cc_final: 0.5500 (mp) REVERT: H 484 PHE cc_start: 0.6223 (m-80) cc_final: 0.5630 (m-80) REVERT: F 128 VAL cc_start: 0.8048 (m) cc_final: 0.7790 (p) REVERT: F 158 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: A 193 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8170 (m) REVERT: A 196 THR cc_start: 0.8969 (m) cc_final: 0.8679 (t) REVERT: A 216 GLU cc_start: 0.8680 (tp30) cc_final: 0.8385 (pt0) REVERT: A 225 PHE cc_start: 0.8514 (t80) cc_final: 0.7746 (t80) REVERT: A 242 VAL cc_start: 0.8356 (t) cc_final: 0.7697 (p) REVERT: A 244 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8441 (tm-30) REVERT: A 249 ILE cc_start: 0.8438 (mm) cc_final: 0.7580 (tt) REVERT: A 258 LYS cc_start: 0.8853 (tptt) cc_final: 0.8613 (mmtm) REVERT: A 273 MET cc_start: 0.7960 (mtm) cc_final: 0.7693 (mmm) REVERT: A 307 ILE cc_start: 0.7754 (tt) cc_final: 0.7270 (pt) REVERT: A 357 VAL cc_start: 0.8985 (t) cc_final: 0.8616 (m) REVERT: A 373 ASN cc_start: 0.8087 (m110) cc_final: 0.7773 (m110) REVERT: A 426 GLU cc_start: 0.8365 (tt0) cc_final: 0.7995 (tp30) REVERT: A 462 GLU cc_start: 0.8697 (pt0) cc_final: 0.8439 (pt0) REVERT: A 475 ILE cc_start: 0.8439 (pt) cc_final: 0.8062 (mm) REVERT: A 524 VAL cc_start: 0.8566 (t) cc_final: 0.8289 (m) REVERT: A 542 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.7689 (t60) REVERT: A 569 THR cc_start: 0.8788 (m) cc_final: 0.8392 (t) REVERT: A 582 VAL cc_start: 0.8934 (p) cc_final: 0.8569 (t) REVERT: A 637 THR cc_start: 0.8849 (t) cc_final: 0.8625 (p) REVERT: A 647 ASN cc_start: 0.8095 (m-40) cc_final: 0.7818 (p0) REVERT: A 764 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7937 (mtm-85) REVERT: A 779 TRP cc_start: 0.8863 (m100) cc_final: 0.8219 (m100) REVERT: A 780 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8685 (mt-10) REVERT: A 793 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 835 MET cc_start: 0.7242 (ptt) cc_final: 0.6843 (mtt) REVERT: A 880 PHE cc_start: 0.7283 (m-80) cc_final: 0.6951 (m-80) REVERT: A 881 THR cc_start: 0.7886 (p) cc_final: 0.7590 (t) REVERT: A 892 ILE cc_start: 0.8086 (mt) cc_final: 0.7829 (mm) REVERT: A 895 SER cc_start: 0.7219 (m) cc_final: 0.6976 (p) REVERT: A 924 VAL cc_start: 0.7956 (m) cc_final: 0.7663 (p) REVERT: A 952 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8548 (mptt) REVERT: A 954 GLU cc_start: 0.8821 (tt0) cc_final: 0.8509 (tm-30) REVERT: A 957 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8115 (ptp90) REVERT: A 961 VAL cc_start: 0.8360 (p) cc_final: 0.7885 (t) REVERT: A 970 LEU cc_start: 0.8587 (mt) cc_final: 0.8238 (pp) REVERT: A 981 ILE cc_start: 0.8512 (mt) cc_final: 0.7897 (tp) REVERT: A 1008 GLU cc_start: 0.8439 (tp30) cc_final: 0.8126 (mt-10) REVERT: A 1042 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7942 (tmm-80) REVERT: A 1043 ASN cc_start: 0.8013 (t0) cc_final: 0.7792 (t0) REVERT: A 1045 ASP cc_start: 0.7838 (m-30) cc_final: 0.7486 (t70) REVERT: A 1052 LYS cc_start: 0.8072 (mttt) cc_final: 0.7739 (mppt) REVERT: A 1060 LEU cc_start: 0.8554 (tp) cc_final: 0.8062 (tp) REVERT: A 1168 PHE cc_start: 0.8518 (t80) cc_final: 0.7824 (t80) REVERT: A 1197 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8856 (tp30) REVERT: A 1287 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8348 (mmtt) REVERT: A 1295 ILE cc_start: 0.8318 (mt) cc_final: 0.7343 (tt) REVERT: A 1297 VAL cc_start: 0.8333 (p) cc_final: 0.7814 (t) REVERT: A 1310 MET cc_start: 0.7715 (mmm) cc_final: 0.7439 (mmm) outliers start: 165 outliers final: 132 residues processed: 1068 average time/residue: 0.5448 time to fit residues: 916.3766 Evaluate side-chains 1112 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 965 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 409 ARG Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 64 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 0.9980 chunk 464 optimal weight: 0.0870 chunk 283 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 322 optimal weight: 0.5980 chunk 487 optimal weight: 40.0000 chunk 448 optimal weight: 0.5980 chunk 387 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 299 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 403 GLN D 457 ASN E 10 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN G 177 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 73 GLN C 82 ASN C 128 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 173 GLN A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 39230 Z= 0.213 Angle : 0.669 14.785 53146 Z= 0.342 Chirality : 0.044 0.268 5851 Planarity : 0.005 0.056 6944 Dihedral : 6.791 106.214 5769 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.69 % Allowed : 22.07 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.83 (0.12), residues: 4890 helix: 0.38 (0.19), residues: 762 sheet: -0.16 (0.13), residues: 1442 loop : -1.03 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 494 HIS 0.007 0.001 HIS C 280 PHE 0.027 0.002 PHE D 442 TYR 0.024 0.002 TYR A1002 ARG 0.012 0.000 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 964 time to evaluate : 4.301 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: 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: D 41 PHE cc_start: 0.8621 (m-10) cc_final: 0.8360 (m-10) REVERT: D 97 ASP cc_start: 0.8502 (p0) cc_final: 0.8150 (p0) REVERT: D 116 TRP cc_start: 0.8527 (m-10) cc_final: 0.8290 (m100) REVERT: D 141 TYR cc_start: 0.8602 (t80) cc_final: 0.8358 (t80) REVERT: D 142 TYR cc_start: 0.8444 (m-80) cc_final: 0.8222 (m-80) REVERT: D 253 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8065 (ttmt) REVERT: D 268 LYS cc_start: 0.8025 (mttt) cc_final: 0.7737 (mttm) REVERT: D 306 MET cc_start: 0.8818 (tmm) cc_final: 0.8259 (tmm) REVERT: D 432 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8261 (mtp-110) REVERT: D 443 GLN cc_start: 0.8660 (tt0) cc_final: 0.8281 (tm-30) REVERT: D 465 SER cc_start: 0.8641 (m) cc_final: 0.8319 (p) REVERT: D 494 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.7109 (m100) REVERT: E 14 TRP cc_start: 0.8335 (m100) cc_final: 0.7977 (m100) REVERT: E 54 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7866 (p) REVERT: E 139 ASP cc_start: 0.8999 (t0) cc_final: 0.8643 (t70) REVERT: E 280 LEU cc_start: 0.8104 (mm) cc_final: 0.7836 (mp) REVERT: E 435 HIS cc_start: 0.8533 (p90) cc_final: 0.8187 (p-80) REVERT: E 451 GLN cc_start: 0.8309 (mt0) cc_final: 0.8098 (mm-40) REVERT: E 479 ILE cc_start: 0.8095 (mt) cc_final: 0.7056 (tt) REVERT: E 480 LEU cc_start: 0.8408 (mt) cc_final: 0.8143 (tt) REVERT: E 509 ASP cc_start: 0.8743 (p0) cc_final: 0.8455 (p0) REVERT: E 531 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7296 (tt0) REVERT: G 40 MET cc_start: 0.7305 (mtm) cc_final: 0.6958 (ptm) REVERT: G 103 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: G 108 SER cc_start: 0.8549 (t) cc_final: 0.8342 (m) REVERT: G 191 PHE cc_start: 0.8251 (t80) cc_final: 0.7779 (t80) REVERT: G 287 MET cc_start: 0.7487 (mmm) cc_final: 0.7127 (mmm) REVERT: G 298 PHE cc_start: 0.8514 (t80) cc_final: 0.7210 (t80) REVERT: G 428 VAL cc_start: 0.8086 (t) cc_final: 0.7235 (m) REVERT: G 480 TYR cc_start: 0.8815 (t80) cc_final: 0.8612 (t80) REVERT: C 14 TRP cc_start: 0.6636 (m100) cc_final: 0.6363 (m100) REVERT: C 42 VAL cc_start: 0.7569 (m) cc_final: 0.7325 (p) REVERT: C 44 ASN cc_start: 0.8628 (m110) cc_final: 0.8269 (t0) REVERT: C 55 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7701 (ptp-110) REVERT: C 93 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7574 (p0) REVERT: C 94 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 95 ASP cc_start: 0.7630 (m-30) cc_final: 0.7189 (m-30) REVERT: C 257 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8163 (tp30) REVERT: C 414 VAL cc_start: 0.8126 (t) cc_final: 0.7646 (p) REVERT: C 426 TYR cc_start: 0.7834 (t80) cc_final: 0.7335 (t80) REVERT: C 427 LEU cc_start: 0.8715 (mt) cc_final: 0.8394 (mp) REVERT: C 447 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6662 (pt0) REVERT: C 487 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: C 497 ARG cc_start: 0.7572 (ptt-90) cc_final: 0.7162 (ptt-90) REVERT: C 615 MET cc_start: 0.6937 (mtm) cc_final: 0.6274 (mtm) REVERT: C 618 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8157 (mm) REVERT: C 631 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 649 PHE cc_start: 0.7861 (m-10) cc_final: 0.7593 (m-10) REVERT: C 660 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.4392 (pt0) REVERT: B 27 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8170 (mtt90) REVERT: B 54 TRP cc_start: 0.8885 (p90) cc_final: 0.8510 (p90) REVERT: B 76 ILE cc_start: 0.8780 (mm) cc_final: 0.8101 (tp) REVERT: B 122 LYS cc_start: 0.8604 (mttt) cc_final: 0.8393 (mmtm) REVERT: B 243 ASN cc_start: 0.7753 (p0) cc_final: 0.7551 (t0) REVERT: B 358 TYR cc_start: 0.8927 (t80) cc_final: 0.8644 (t80) REVERT: B 417 GLU cc_start: 0.8989 (tp30) cc_final: 0.8782 (tp30) REVERT: B 437 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8495 (mm-30) REVERT: B 454 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.6130 (p) REVERT: B 610 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7948 (mmtt) REVERT: B 611 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8354 (tm-30) REVERT: B 630 GLU cc_start: 0.8080 (tt0) cc_final: 0.7711 (pm20) REVERT: B 648 GLU cc_start: 0.8283 (tt0) cc_final: 0.7908 (pm20) REVERT: B 675 ASP cc_start: 0.7400 (t0) cc_final: 0.7013 (p0) REVERT: B 695 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7927 (p) REVERT: H 133 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7448 (mtm110) REVERT: H 152 ASP cc_start: 0.8847 (t0) cc_final: 0.8467 (t0) REVERT: H 192 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7579 (mtp85) REVERT: H 272 MET cc_start: 0.2600 (ppp) cc_final: 0.2327 (ppp) REVERT: H 284 ARG cc_start: 0.7945 (tpt90) cc_final: 0.7378 (tpt90) REVERT: H 291 ASP cc_start: 0.8258 (t0) cc_final: 0.8040 (t0) REVERT: H 341 LEU cc_start: 0.6867 (mt) cc_final: 0.5492 (mp) REVERT: H 484 PHE cc_start: 0.6168 (m-80) cc_final: 0.5572 (m-80) REVERT: A 193 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8132 (m) REVERT: A 196 THR cc_start: 0.8980 (m) cc_final: 0.8667 (t) REVERT: A 216 GLU cc_start: 0.8690 (tp30) cc_final: 0.8398 (pt0) REVERT: A 225 PHE cc_start: 0.8503 (t80) cc_final: 0.8104 (t80) REVERT: A 242 VAL cc_start: 0.8337 (t) cc_final: 0.7676 (p) REVERT: A 244 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8475 (tm-30) REVERT: A 249 ILE cc_start: 0.8411 (mm) cc_final: 0.7712 (tp) REVERT: A 258 LYS cc_start: 0.8840 (tptt) cc_final: 0.8601 (mmtm) REVERT: A 273 MET cc_start: 0.7955 (mtm) cc_final: 0.7711 (mmm) REVERT: A 307 ILE cc_start: 0.7733 (tt) cc_final: 0.7247 (pt) REVERT: A 357 VAL cc_start: 0.8994 (t) cc_final: 0.8624 (m) REVERT: A 359 ASP cc_start: 0.7951 (m-30) cc_final: 0.7456 (p0) REVERT: A 373 ASN cc_start: 0.8077 (m110) cc_final: 0.7757 (m110) REVERT: A 419 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7675 (p) REVERT: A 426 GLU cc_start: 0.8364 (tt0) cc_final: 0.7988 (tp30) REVERT: A 462 GLU cc_start: 0.8722 (pt0) cc_final: 0.8503 (pt0) REVERT: A 475 ILE cc_start: 0.8427 (pt) cc_final: 0.7999 (mm) REVERT: A 524 VAL cc_start: 0.8547 (t) cc_final: 0.8267 (m) REVERT: A 542 TRP cc_start: 0.8727 (OUTLIER) cc_final: 0.7897 (t60) REVERT: A 569 THR cc_start: 0.8796 (m) cc_final: 0.8398 (t) REVERT: A 582 VAL cc_start: 0.8930 (p) cc_final: 0.8558 (t) REVERT: A 647 ASN cc_start: 0.8034 (m-40) cc_final: 0.7794 (p0) REVERT: A 755 TRP cc_start: 0.8475 (p-90) cc_final: 0.8258 (p-90) REVERT: A 764 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7919 (mtm-85) REVERT: A 779 TRP cc_start: 0.8853 (m100) cc_final: 0.8169 (m100) REVERT: A 780 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 793 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 835 MET cc_start: 0.7252 (ptt) cc_final: 0.6851 (mtt) REVERT: A 880 PHE cc_start: 0.7296 (m-80) cc_final: 0.6944 (m-80) REVERT: A 881 THR cc_start: 0.7886 (p) cc_final: 0.7588 (t) REVERT: A 892 ILE cc_start: 0.8062 (mt) cc_final: 0.7810 (mm) REVERT: A 895 SER cc_start: 0.7219 (m) cc_final: 0.6974 (p) REVERT: A 924 VAL cc_start: 0.7918 (m) cc_final: 0.7638 (p) REVERT: A 944 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8693 (mtp-110) REVERT: A 952 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8532 (mptt) REVERT: A 954 GLU cc_start: 0.8811 (tt0) cc_final: 0.8504 (tm-30) REVERT: A 961 VAL cc_start: 0.8360 (p) cc_final: 0.7897 (t) REVERT: A 970 LEU cc_start: 0.8591 (mt) cc_final: 0.8301 (pp) REVERT: A 981 ILE cc_start: 0.8506 (mt) cc_final: 0.7886 (tp) REVERT: A 1045 ASP cc_start: 0.7856 (m-30) cc_final: 0.7492 (t70) REVERT: A 1052 LYS cc_start: 0.8003 (mttt) cc_final: 0.7675 (mppt) REVERT: A 1060 LEU cc_start: 0.8546 (tp) cc_final: 0.7213 (tt) REVERT: A 1273 ILE cc_start: 0.8080 (mt) cc_final: 0.7661 (tt) REVERT: A 1287 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8351 (mmtt) REVERT: A 1295 ILE cc_start: 0.8310 (mt) cc_final: 0.7327 (tt) REVERT: A 1297 VAL cc_start: 0.8309 (p) cc_final: 0.7826 (t) REVERT: A 1310 MET cc_start: 0.7711 (mmm) cc_final: 0.7461 (mmm) outliers start: 151 outliers final: 124 residues processed: 1046 average time/residue: 0.5538 time to fit residues: 914.5569 Evaluate side-chains 1093 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 955 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 513 PHE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 487 TRP Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 547 TRP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1127 THR Chi-restraints excluded: chain A residue 1209 PHE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 0.1980 chunk 413 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 357 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 388 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 403 GLN E 10 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 158 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.172867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140441 restraints weight = 60172.637| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.04 r_work: 0.3692 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39230 Z= 0.196 Angle : 0.662 14.781 53146 Z= 0.337 Chirality : 0.044 0.279 5851 Planarity : 0.005 0.056 6944 Dihedral : 6.602 103.284 5769 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.64 % Allowed : 22.17 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.77 (0.12), residues: 4890 helix: 0.44 (0.19), residues: 769 sheet: -0.12 (0.13), residues: 1432 loop : -1.00 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 494 HIS 0.006 0.001 HIS C 280 PHE 0.025 0.002 PHE B 39 TYR 0.022 0.001 TYR A1235 ARG 0.013 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16810.09 seconds wall clock time: 296 minutes 33.60 seconds (17793.60 seconds total)