Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 14:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/08_2023/7nyd_12651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/08_2023/7nyd_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_12651/08_2023/7nyd_12651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/08_2023/7nyd_12651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/08_2023/7nyd_12651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyd_12651/08_2023/7nyd_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 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 chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 18.59, per 1000 atoms: 0.48 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: 15.68 Conformation dependent library (CDL) restraints added in 5.3 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: 4.39 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: 17.38 Time building geometry restraints manager: 16.65 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 - 17.72: 21691 17.72 - 35.44: 1614 35.44 - 53.16: 279 53.16 - 70.88: 87 70.88 - 88.60: 40 Dihedral angle restraints: 23711 sinusoidal: 9392 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 23708 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.210 Check model and map are aligned: 0.570 Set scattering table: 0.300 Process input model: 97.610 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.150 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.710 ------------------------------------------------------------------------------- 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 : 13.732 88.597 14238 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 % 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 *********************** 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 : 4.164 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 outliers start: 27 outliers final: 16 residues processed: 1294 average time/residue: 0.5770 time to fit residues: 1170.0846 Evaluate side-chains 1059 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1043 time to evaluate : 4.283 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.5463 time to fit residues: 19.9461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 205 optimal weight: 50.0000 chunk 126 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 148 optimal weight: 0.0060 chunk 233 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 455 GLN E 135 GLN E 267 GLN E 423 ASN E 432 GLN E 459 GLN 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 B 625 GLN H 289 ASN H 465 ASN H 471 GLN F 21 ASN F 78 GLN F 173 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 HIS A 280 GLN A 301 ASN 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** A1092 ASN A1094 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN A1417 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 39230 Z= 0.258 Angle : 0.778 11.889 53146 Z= 0.411 Chirality : 0.048 0.415 5851 Planarity : 0.005 0.057 6944 Dihedral : 6.980 33.110 5360 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % 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: -0.85 (0.11), residues: 4890 helix: -0.43 (0.18), residues: 772 sheet: 0.12 (0.13), residues: 1457 loop : -0.96 (0.11), residues: 2661 *********************** 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 1166 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1058 time to evaluate : 4.435 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 outliers start: 108 outliers final: 63 residues processed: 1100 average time/residue: 0.5584 time to fit residues: 971.5656 Evaluate side-chains 1039 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 976 time to evaluate : 3.917 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4408 time to fit residues: 54.6960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 369 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 444 optimal weight: 0.5980 chunk 480 optimal weight: 8.9990 chunk 396 optimal weight: 1.9990 chunk 441 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 356 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN D 109 GLN D 114 GLN D 360 ASN D 437 GLN D 495 ASN E 10 GLN E 204 ASN E 423 ASN E 451 GLN ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS G 275 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN C 347 ASN B 5 HIS B 23 GLN B 177 HIS ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 173 GLN A 52 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN A 976 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 GLN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3311 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= 0.275 Angle : 0.699 11.257 53146 Z= 0.369 Chirality : 0.046 0.366 5851 Planarity : 0.005 0.049 6944 Dihedral : 6.318 32.321 5360 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 2.47 % 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: -0.78 (0.11), residues: 4890 helix: -0.17 (0.18), residues: 765 sheet: 0.08 (0.13), residues: 1428 loop : -0.93 (0.11), residues: 2697 *********************** 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 1089 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 988 time to evaluate : 4.220 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 outliers start: 101 outliers final: 46 residues processed: 1042 average time/residue: 0.5588 time to fit residues: 920.6265 Evaluate side-chains 995 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 949 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3766 time to fit residues: 37.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 212 optimal weight: 40.0000 chunk 298 optimal weight: 2.9990 chunk 446 optimal weight: 0.0980 chunk 472 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 423 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 423 ASN E 432 GLN E 459 GLN G 99 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS G 281 HIS ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN C 175 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN B 23 GLN B 280 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 631 ASN H 465 ASN H 471 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 416 ASN A 767 GLN A1005 HIS ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.204 39230 Z= 0.552 Angle : 0.821 11.697 53146 Z= 0.436 Chirality : 0.053 0.328 5851 Planarity : 0.006 0.074 6944 Dihedral : 6.596 36.213 5360 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.36 (0.11), residues: 4890 helix: -0.71 (0.17), residues: 778 sheet: -0.27 (0.13), residues: 1442 loop : -1.30 (0.11), residues: 2670 *********************** 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 1109 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 979 time to evaluate : 4.710 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 outliers start: 130 outliers final: 66 residues processed: 1033 average time/residue: 0.5732 time to fit residues: 931.4460 Evaluate side-chains 998 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 932 time to evaluate : 4.146 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3734 time to fit residues: 51.7690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 0.7980 chunk 268 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 351 optimal weight: 0.4980 chunk 195 optimal weight: 0.0770 chunk 403 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 424 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN D 437 GLN D 457 ASN E 423 ASN E 435 HIS ** 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 467 HIS ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 44 ASN C 175 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 223 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 GLN A1184 HIS A1242 ASN A1274 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 39230 Z= 0.231 Angle : 0.677 10.309 53146 Z= 0.354 Chirality : 0.045 0.306 5851 Planarity : 0.005 0.057 6944 Dihedral : 6.018 33.851 5360 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 2.66 % 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: -0.94 (0.11), residues: 4890 helix: 0.01 (0.19), residues: 752 sheet: -0.11 (0.13), residues: 1420 loop : -1.07 (0.11), residues: 2718 *********************** 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 1067 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 958 time to evaluate : 4.137 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 outliers start: 109 outliers final: 51 residues processed: 1011 average time/residue: 0.5824 time to fit residues: 922.7572 Evaluate side-chains 974 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 923 time to evaluate : 4.081 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4334 time to fit residues: 44.1622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 93 optimal weight: 0.0050 chunk 277 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 473 optimal weight: 0.8980 chunk 392 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN D 437 GLN D 457 ASN D 511 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 GLN E 423 ASN E 432 GLN E 435 HIS E 488 GLN ** G 177 ASN ** 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 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 39230 Z= 0.273 Angle : 0.680 10.773 53146 Z= 0.355 Chirality : 0.046 0.289 5851 Planarity : 0.005 0.060 6944 Dihedral : 5.854 35.875 5360 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.93 (0.12), residues: 4890 helix: 0.14 (0.19), residues: 746 sheet: -0.14 (0.13), residues: 1424 loop : -1.08 (0.11), residues: 2720 *********************** 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 1031 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 951 time to evaluate : 4.099 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 outliers start: 80 outliers final: 45 residues processed: 986 average time/residue: 0.5957 time to fit residues: 923.0869 Evaluate side-chains 956 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 911 time to evaluate : 4.125 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4066 time to fit residues: 38.9096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 345 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 398 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 471 optimal weight: 40.0000 chunk 294 optimal weight: 0.0970 chunk 287 optimal weight: 0.0770 chunk 217 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN D 433 GLN D 457 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN E 432 GLN E 435 HIS ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 312 HIS ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 ASN ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 158 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 356 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 39230 Z= 0.215 Angle : 0.661 12.279 53146 Z= 0.342 Chirality : 0.045 0.273 5851 Planarity : 0.005 0.053 6944 Dihedral : 5.595 35.609 5360 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % 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: -0.82 (0.12), residues: 4890 helix: 0.33 (0.19), residues: 744 sheet: -0.11 (0.13), residues: 1440 loop : -1.02 (0.12), residues: 2706 *********************** 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 995 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 940 time to evaluate : 4.226 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 outliers start: 55 outliers final: 23 residues processed: 965 average time/residue: 0.5960 time to fit residues: 901.9422 Evaluate side-chains 931 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 908 time to evaluate : 3.977 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4103 time to fit residues: 23.0236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 281 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 233 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 455 GLN D 457 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN E 459 GLN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN F 78 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 39230 Z= 0.263 Angle : 0.684 11.560 53146 Z= 0.354 Chirality : 0.045 0.313 5851 Planarity : 0.005 0.057 6944 Dihedral : 5.590 37.714 5360 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.22 % 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: -0.84 (0.12), residues: 4890 helix: 0.28 (0.19), residues: 744 sheet: -0.12 (0.13), residues: 1458 loop : -1.04 (0.12), residues: 2688 *********************** 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 982 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 932 time to evaluate : 4.138 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 outliers start: 50 outliers final: 26 residues processed: 950 average time/residue: 0.5801 time to fit residues: 863.9018 Evaluate side-chains 926 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 900 time to evaluate : 4.359 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4004 time to fit residues: 25.1667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 0.9990 chunk 451 optimal weight: 0.6980 chunk 411 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 396 optimal weight: 0.0980 chunk 415 optimal weight: 1.9990 chunk 437 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 457 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 49 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A1097 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 39230 Z= 0.237 Angle : 0.686 13.227 53146 Z= 0.354 Chirality : 0.045 0.255 5851 Planarity : 0.005 0.053 6944 Dihedral : 5.502 36.716 5360 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % 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: -0.81 (0.12), residues: 4890 helix: 0.31 (0.19), residues: 745 sheet: -0.13 (0.13), residues: 1464 loop : -1.00 (0.12), residues: 2681 *********************** 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 960 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 917 time to evaluate : 4.181 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 outliers start: 43 outliers final: 19 residues processed: 927 average time/residue: 0.5750 time to fit residues: 836.3466 Evaluate side-chains 909 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 890 time to evaluate : 4.026 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4339 time to fit residues: 20.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 0.9990 chunk 464 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 487 optimal weight: 40.0000 chunk 448 optimal weight: 0.9990 chunk 387 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 299 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 434 ASN D 437 GLN D 457 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 128 GLN C 276 GLN ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 HIS F 78 GLN A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 836 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.163 39230 Z= 0.396 Angle : 0.765 14.313 53146 Z= 0.399 Chirality : 0.049 0.279 5851 Planarity : 0.005 0.061 6944 Dihedral : 5.852 39.849 5360 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.13 % 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: -1.10 (0.12), residues: 4890 helix: -0.07 (0.19), residues: 750 sheet: -0.27 (0.14), residues: 1420 loop : -1.15 (0.11), residues: 2720 ********************** 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 940 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 910 time to evaluate : 4.275 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 outliers start: 30 outliers final: 18 residues processed: 920 average time/residue: 0.5969 time to fit residues: 863.2884 Evaluate side-chains 907 residues out of total 4341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 889 time to evaluate : 4.266 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4039 time to fit residues: 19.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 2.9990 chunk 413 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 357 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 398 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 437 GLN D 457 ASN D 495 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 49 GLN ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN B 23 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 173 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN ** A1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.170871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.138356 restraints weight = 60511.074| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.02 r_work: 0.3677 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 39230 Z= 0.254 Angle : 0.715 13.180 53146 Z= 0.368 Chirality : 0.046 0.249 5851 Planarity : 0.005 0.053 6944 Dihedral : 5.617 37.438 5360 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.61 % 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: -0.97 (0.12), residues: 4890 helix: 0.12 (0.19), residues: 746 sheet: -0.23 (0.14), residues: 1441 loop : -1.08 (0.12), residues: 2703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15764.75 seconds wall clock time: 279 minutes 49.88 seconds (16789.88 seconds total)