Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:22:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/02_2023/3jbr_6475_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 385": "NH1" <-> "NH2" Residue "F ARG 398": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16467 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 7601 Classifications: {'peptide': 1224} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 651} Link IDs: {'CIS': 13, 'PTRANS': 31, 'TRANS': 1179} Chain breaks: 7 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2265 Unresolved non-hydrogen angles: 2984 Unresolved non-hydrogen dihedrals: 1818 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 12, 'UNK:plan-1': 125, 'TYR:plan': 27, 'ASN:plan1': 29, 'TRP:plan': 10, 'ASP:plan': 21, 'PHE:plan': 39, 'GLU:plan': 34, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 1205 Chain: "B" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2210 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 263} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 688 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 12, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 202 Chain: "F" Number of atoms: 5735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 5735 Classifications: {'peptide': 872} Incomplete info: {'backbone_only': 18, 'truncation_to_alanine': 362} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 833} Chain breaks: 18 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1064 Unresolved non-hydrogen angles: 1490 Unresolved non-hydrogen dihedrals: 720 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 13, 'ASN:plan1': 7, 'TYR:plan': 16, 'UNK:plan-1': 242, 'TRP:plan': 1, 'ASP:plan': 17, 'ARG:plan': 6, 'PHE:plan': 5, 'GLU:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 614 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 232 Unusual residues: {'BMA': 2, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 9.50, per 1000 atoms: 0.58 Number of scatterers: 16467 At special positions: 0 Unit cell: (188.76, 163.68, 149.16, 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 1 19.99 S 52 16.00 O 3144 8.00 N 2910 7.00 C 10360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1062 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.3 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 8 sheets defined 64.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.632A pdb=" N LYS A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 45 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 82 through 106 removed outlier: 3.717A pdb=" N GLU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 90 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.056A pdb=" N GLN A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 138 removed outlier: 3.991A pdb=" N ALA A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 removed outlier: 3.969A pdb=" N VAL A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 4.358A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.679A pdb=" N LYS A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 Processing helix chain 'A' and resid 217 through 225 removed outlier: 4.093A pdb=" N LYS A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 310 through 343 removed outlier: 4.455A pdb=" N GLU A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 459 removed outlier: 3.868A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 455 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Proline residue: A 457 - end of helix Processing helix chain 'A' and resid 474 through 502 removed outlier: 3.735A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 516 Processing helix chain 'A' and resid 525 through 540 removed outlier: 4.069A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 580 removed outlier: 3.871A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.922A pdb=" N MET A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 668 removed outlier: 5.023A pdb=" N PHE A 645 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A 663 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 809 through 828 Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 832 through 836 removed outlier: 4.154A pdb=" N PHE A 835 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 862 removed outlier: 3.733A pdb=" N SER A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 873 through 886 removed outlier: 3.747A pdb=" N LEU A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 910 removed outlier: 3.802A pdb=" N VAL A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 913 through 927 removed outlier: 3.846A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 950 removed outlier: 3.794A pdb=" N LEU A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1012 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1075 removed outlier: 3.698A pdb=" N PHE A1045 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A1046 " --> pdb=" O ILE A1043 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A1055 " --> pdb=" O ILE A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N MET A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A1060 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1063 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A1071 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1116 Processing helix chain 'A' and resid 1119 through 1136 removed outlier: 3.585A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1169 Processing helix chain 'A' and resid 1181 through 1203 Processing helix chain 'A' and resid 1230 through 1248 removed outlier: 3.624A pdb=" N LEU A1237 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A1242 " --> pdb=" O ARG A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1264 Processing helix chain 'A' and resid 1266 through 1286 removed outlier: 3.814A pdb=" N TYR A1269 " --> pdb=" O ALA A1266 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A1277 " --> pdb=" O ILE A1274 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A1280 " --> pdb=" O LEU A1277 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A1282 " --> pdb=" O PHE A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 removed outlier: 3.864A pdb=" N CYS A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1358 through 1382 removed outlier: 3.523A pdb=" N MET A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1394 removed outlier: 5.146A pdb=" N ARG A1389 " --> pdb=" O ASP A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1410 Processing helix chain 'A' and resid 1417 through 1422 Processing helix chain 'A' and resid 1424 through 1433 removed outlier: 4.066A pdb=" N UNK A1432 " --> pdb=" O UNK A1428 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N UNK A1433 " --> pdb=" O UNK A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1460 through 1474 removed outlier: 3.983A pdb=" N UNK A1473 " --> pdb=" O UNK A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1483 removed outlier: 3.594A pdb=" N UNK A1483 " --> pdb=" O UNK A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1480 through 1483' Processing helix chain 'A' and resid 1488 through 1497 Processing helix chain 'A' and resid 1505 through 1519 removed outlier: 3.680A pdb=" N UNK A1511 " --> pdb=" O UNK A1508 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N UNK A1513 " --> pdb=" O UNK A1510 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N UNK A1514 " --> pdb=" O UNK A1511 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N UNK A1516 " --> pdb=" O UNK A1513 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 57 removed outlier: 3.615A pdb=" N LYS B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 240 through 256 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.553A pdb=" N ARG B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 4.204A pdb=" N LYS B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 364 through 376 Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'E' and resid 3 through 28 Proline residue: E 7 - end of helix removed outlier: 3.586A pdb=" N VAL E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 128 Processing helix chain 'E' and resid 132 through 165 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 181 through 205 Proline residue: E 205 - end of helix Processing helix chain 'F' and resid 53 through 67 removed outlier: 3.886A pdb=" N VAL F 56 " --> pdb=" O UNK F 53 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS F 57 " --> pdb=" O UNK F 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN F 58 " --> pdb=" O UNK F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 112 removed outlier: 3.596A pdb=" N ARG F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 200 removed outlier: 3.623A pdb=" N ASN F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.387A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 325 Processing helix chain 'F' and resid 335 through 347 removed outlier: 4.430A pdb=" N PHE F 343 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN F 345 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 408 removed outlier: 3.755A pdb=" N CYS F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 428 removed outlier: 3.581A pdb=" N THR F 425 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR F 428 " --> pdb=" O ASN F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 437 removed outlier: 3.631A pdb=" N ARG F 434 " --> pdb=" O VAL F 431 " (cutoff:3.500A) Proline residue: F 435 - end of helix No H-bonds generated for 'chain 'F' and resid 431 through 437' Processing helix chain 'F' and resid 485 through 490 Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 572 through 582 removed outlier: 4.030A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 652 Processing helix chain 'F' and resid 663 through 676 Processing helix chain 'F' and resid 682 through 696 Processing helix chain 'F' and resid 732 through 750 Processing helix chain 'F' and resid 753 through 764 Processing helix chain 'F' and resid 778 through 798 Processing helix chain 'F' and resid 859 through 866 Processing helix chain 'F' and resid 903 through 912 Processing helix chain 'F' and resid 931 through 937 Processing helix chain 'F' and resid 978 through 988 Processing sheet with id= A, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.864A pdb=" N ALA B 63 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 105 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.288A pdb=" N ILE B 337 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 232 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL B 339 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'E' and resid 33 through 36 Processing sheet with id= D, first strand: chain 'F' and resid 216 through 218 removed outlier: 4.100A pdb=" N TRP F 207 " --> pdb=" O LYS F 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY F 211 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 291 through 293 removed outlier: 7.656A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 594 through 596 Processing sheet with id= G, first strand: chain 'F' and resid 609 through 613 Processing sheet with id= H, first strand: chain 'F' and resid 827 through 832 removed outlier: 3.686A pdb=" N UNK F 832 " --> pdb=" O UNK F 839 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2313 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: 4.90 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3263 1.32 - 1.45: 4081 1.45 - 1.57: 9234 1.57 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 16662 Sorted by residual: bond pdb=" N PRO F 627 " pdb=" CD PRO F 627 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" CA ILE A 229 " pdb=" CB ILE A 229 " ideal model delta sigma weight residual 1.548 1.512 0.036 1.13e-02 7.83e+03 1.02e+01 bond pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 1.540 1.499 0.041 1.29e-02 6.01e+03 9.90e+00 bond pdb=" CA PRO F 171 " pdb=" CB PRO F 171 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.33e-02 5.65e+03 9.47e+00 bond pdb=" CA VAL A 203 " pdb=" CB VAL A 203 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.17e-02 7.31e+03 9.31e+00 ... (remaining 16657 not shown) Histogram of bond angle deviations from ideal: 99.32 - 107.56: 448 107.56 - 115.80: 10598 115.80 - 124.04: 11495 124.04 - 132.29: 227 132.29 - 140.53: 31 Bond angle restraints: 22799 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 102.35 110.96 -8.61 7.10e-01 1.98e+00 1.47e+02 angle pdb=" C CYS F 509 " pdb=" N PRO F 510 " pdb=" CA PRO F 510 " ideal model delta sigma weight residual 119.84 130.15 -10.31 1.25e+00 6.40e-01 6.81e+01 angle pdb=" N PRO F1059 " pdb=" CA PRO F1059 " pdb=" CB PRO F1059 " ideal model delta sigma weight residual 103.31 110.44 -7.13 8.90e-01 1.26e+00 6.43e+01 angle pdb=" N PRO F 171 " pdb=" CA PRO F 171 " pdb=" CB PRO F 171 " ideal model delta sigma weight residual 103.27 110.44 -7.17 9.00e-01 1.23e+00 6.34e+01 angle pdb=" N PRO F1044 " pdb=" CA PRO F1044 " pdb=" CB PRO F1044 " ideal model delta sigma weight residual 103.27 110.28 -7.01 9.00e-01 1.23e+00 6.07e+01 ... (remaining 22794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 9696 22.31 - 44.63: 83 44.63 - 66.94: 9 66.94 - 89.26: 5 89.26 - 111.57: 2 Dihedral angle restraints: 9795 sinusoidal: 2507 harmonic: 7288 Sorted by residual: dihedral pdb=" C1 NAG F1204 " pdb=" C5 NAG F1204 " pdb=" O5 NAG F1204 " pdb=" C4 NAG F1204 " ideal model delta sinusoidal sigma weight residual -50.00 61.57 -111.57 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" C2 NAG F1204 " pdb=" C1 NAG F1204 " pdb=" O5 NAG F1204 " pdb=" C5 NAG F1204 " ideal model delta sinusoidal sigma weight residual -50.00 57.79 -107.79 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" CA ARG F 243 " pdb=" C ARG F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2360 0.066 - 0.132: 432 0.132 - 0.199: 36 0.199 - 0.265: 19 0.265 - 0.331: 10 Chirality restraints: 2857 Sorted by residual: chirality pdb=" CA PRO A 244 " pdb=" N PRO A 244 " pdb=" C PRO A 244 " pdb=" CB PRO A 244 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" C PRO A 266 " pdb=" CB PRO A 266 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA PRO F 74 " pdb=" N PRO F 74 " pdb=" C PRO F 74 " pdb=" CB PRO F 74 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2854 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 509 " -0.042 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO F 510 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 510 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 510 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 300 " 0.014 2.00e-02 2.50e+03 1.22e-02 3.70e+00 pdb=" CG TRP A 300 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 300 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 300 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 300 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 300 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 300 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 300 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 300 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 530 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO F 531 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 531 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 531 " -0.028 5.00e-02 4.00e+02 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 5 2.12 - 2.81: 5668 2.81 - 3.51: 25013 3.51 - 4.20: 36082 4.20 - 4.90: 58295 Nonbonded interactions: 125063 Sorted by model distance: nonbonded pdb=" CD1 ILE F 499 " pdb=" CD2 LEU F 626 " model vdw 1.419 3.880 nonbonded pdb=" CG1 ILE F 499 " pdb=" CD2 LEU F 626 " model vdw 1.759 3.860 nonbonded pdb=" O LEU F 626 " pdb=" N THR F 628 " model vdw 2.021 2.520 nonbonded pdb=" OH TYR F 335 " pdb=" O GLU F 369 " model vdw 2.047 2.440 nonbonded pdb=" O GLY A 365 " pdb=" OG SER A 368 " model vdw 2.115 2.440 ... (remaining 125058 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 52 5.16 5 C 10360 2.51 5 N 2910 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.610 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: 0.010 Extract box with map and model: 4.970 Check model and map are aligned: 0.230 Process input model: 41.620 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.008 0.072 16662 Z= 0.563 Angle : 1.298 15.528 22799 Z= 0.909 Chirality : 0.055 0.331 2857 Planarity : 0.005 0.062 3000 Dihedral : 8.636 111.570 5028 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 7.04 % Allowed : 8.13 % Favored : 84.83 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.16), residues: 2103 helix: -2.39 (0.10), residues: 1137 sheet: -3.80 (0.34), residues: 161 loop : -1.39 (0.25), residues: 805 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 330 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 334 average time/residue: 0.2721 time to fit residues: 136.9878 Evaluate side-chains 222 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1430 time to fit residues: 2.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN B 49 GLN B 67 ASN B 130 GLN B 314 GLN B 324 ASN B 363 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 316 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 16662 Z= 0.296 Angle : 0.789 11.232 22799 Z= 0.418 Chirality : 0.041 0.221 2857 Planarity : 0.005 0.053 3000 Dihedral : 6.981 107.372 2700 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 3.09 % Allowed : 10.51 % Favored : 86.40 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.23 (0.17), residues: 2103 helix: -0.60 (0.13), residues: 1150 sheet: -3.71 (0.33), residues: 165 loop : -2.17 (0.24), residues: 788 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.2549 time to fit residues: 108.4167 Evaluate side-chains 209 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 0.0040 chunk 40 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 overall best weight: 3.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 123 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 16662 Z= 0.333 Angle : 0.768 14.024 22799 Z= 0.401 Chirality : 0.041 0.226 2857 Planarity : 0.004 0.070 3000 Dihedral : 6.796 107.502 2700 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 2.85 % Allowed : 12.03 % Favored : 85.12 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.90 (0.18), residues: 2103 helix: -0.09 (0.14), residues: 1154 sheet: -3.60 (0.33), residues: 165 loop : -2.45 (0.23), residues: 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2311 time to fit residues: 92.5366 Evaluate side-chains 199 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.7980 chunk 111 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 0.0770 chunk 42 optimal weight: 40.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN F 169 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1015 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.065 16662 Z= 0.167 Angle : 0.656 12.449 22799 Z= 0.335 Chirality : 0.039 0.214 2857 Planarity : 0.003 0.032 3000 Dihedral : 6.322 106.605 2700 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 2.71 % Allowed : 9.80 % Favored : 87.49 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.30 (0.19), residues: 2103 helix: 0.51 (0.15), residues: 1168 sheet: -3.12 (0.34), residues: 170 loop : -2.48 (0.23), residues: 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.2425 time to fit residues: 102.1079 Evaluate side-chains 207 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 50.0000 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 0.0060 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 39 optimal weight: 50.0000 overall best weight: 4.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 16662 Z= 0.348 Angle : 0.742 13.753 22799 Z= 0.386 Chirality : 0.041 0.234 2857 Planarity : 0.004 0.101 3000 Dihedral : 6.440 107.530 2700 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 2.33 % Allowed : 12.27 % Favored : 85.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.33 (0.19), residues: 2103 helix: 0.55 (0.15), residues: 1157 sheet: -3.09 (0.36), residues: 162 loop : -2.60 (0.23), residues: 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.666 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2422 time to fit residues: 89.4144 Evaluate side-chains 188 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 chunk 31 optimal weight: 50.0000 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A1131 ASN A1154 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN F 483 ASN ** F 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 16662 Z= 0.156 Angle : 0.645 13.399 22799 Z= 0.329 Chirality : 0.038 0.196 2857 Planarity : 0.003 0.038 3000 Dihedral : 6.140 106.521 2700 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 2.38 % Allowed : 9.46 % Favored : 88.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 2103 helix: 0.83 (0.15), residues: 1171 sheet: -2.51 (0.39), residues: 152 loop : -2.61 (0.23), residues: 780 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2485 time to fit residues: 100.3888 Evaluate side-chains 202 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 30.0000 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 198 HIS ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 311 GLN F 379 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN F 483 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16662 Z= 0.193 Angle : 0.646 12.831 22799 Z= 0.332 Chirality : 0.039 0.216 2857 Planarity : 0.003 0.036 3000 Dihedral : 6.042 106.688 2700 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 2.33 % Allowed : 10.84 % Favored : 86.83 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 2103 helix: 0.95 (0.15), residues: 1164 sheet: -2.34 (0.39), residues: 152 loop : -2.61 (0.23), residues: 787 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.2570 time to fit residues: 98.3742 Evaluate side-chains 207 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 198 HIS A 958 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 ASN B 94 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN F 483 ASN ** F 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16662 Z= 0.161 Angle : 0.626 12.233 22799 Z= 0.321 Chirality : 0.038 0.231 2857 Planarity : 0.003 0.039 3000 Dihedral : 5.957 106.497 2700 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 2.28 % Allowed : 10.18 % Favored : 87.54 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2103 helix: 1.05 (0.16), residues: 1169 sheet: -2.12 (0.40), residues: 152 loop : -2.60 (0.23), residues: 782 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.2590 time to fit residues: 103.9229 Evaluate side-chains 211 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0870 chunk 146 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 198 HIS B 94 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16662 Z= 0.201 Angle : 0.644 11.832 22799 Z= 0.330 Chirality : 0.039 0.206 2857 Planarity : 0.004 0.051 3000 Dihedral : 5.936 106.771 2700 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 2.23 % Allowed : 11.13 % Favored : 86.64 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2103 helix: 1.13 (0.16), residues: 1163 sheet: -2.11 (0.39), residues: 155 loop : -2.65 (0.23), residues: 785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2527 time to fit residues: 97.5374 Evaluate side-chains 211 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN F 570 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16662 Z= 0.170 Angle : 0.622 11.464 22799 Z= 0.320 Chirality : 0.038 0.196 2857 Planarity : 0.003 0.039 3000 Dihedral : 5.865 106.663 2700 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 2.14 % Allowed : 10.32 % Favored : 87.54 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 2103 helix: 1.25 (0.16), residues: 1152 sheet: -2.07 (0.39), residues: 155 loop : -2.60 (0.22), residues: 796 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.2429 time to fit residues: 96.6232 Evaluate side-chains 216 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0670 chunk 39 optimal weight: 50.0000 chunk 119 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 35 optimal weight: 50.0000 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 113 optimal weight: 40.0000 overall best weight: 2.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 198 HIS ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 94 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.127931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.091040 restraints weight = 64226.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088628 restraints weight = 50445.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089668 restraints weight = 42159.766| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16662 Z= 0.210 Angle : 0.645 11.477 22799 Z= 0.332 Chirality : 0.039 0.200 2857 Planarity : 0.003 0.037 3000 Dihedral : 5.895 106.939 2700 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 2.14 % Allowed : 11.13 % Favored : 86.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 2103 helix: 1.26 (0.16), residues: 1147 sheet: -2.03 (0.41), residues: 147 loop : -2.63 (0.22), residues: 809 =============================================================================== Job complete usr+sys time: 2885.95 seconds wall clock time: 52 minutes 58.21 seconds (3178.21 seconds total)