Starting phenix.real_space_refine on Thu Nov 16 19:36:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/11_2023/3jbr_6475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/11_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_6475/11_2023/3jbr_6475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/11_2023/3jbr_6475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/11_2023/3jbr_6475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/11_2023/3jbr_6475_updated.pdb" } resolution = 4.2 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= -0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 chiralities: 17 Time building chain proxies: 9.85, per 1000 atoms: 0.60 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: 7.19 Conformation dependent library (CDL) restraints added in 3.0 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: 4.42 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: 5.04 Time building geometry restraints manager: 7.73 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 - 16.35: 9488 16.35 - 32.69: 147 32.69 - 49.04: 40 49.04 - 65.38: 5 65.38 - 81.73: 5 Dihedral angle restraints: 9685 sinusoidal: 2397 harmonic: 7288 Sorted by residual: 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 dihedral pdb=" CA LEU F1034 " pdb=" C LEU F1034 " pdb=" N ILE F1035 " pdb=" CA ILE F1035 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR A 621 " pdb=" C TYR A 621 " pdb=" N ASN A 622 " pdb=" CA ASN A 622 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2341 0.066 - 0.132: 448 0.132 - 0.199: 37 0.199 - 0.265: 20 0.265 - 0.331: 11 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 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.470 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 47.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.009 0.072 16662 Z= 0.568 Angle : 1.313 15.528 22799 Z= 0.912 Chirality : 0.056 0.331 2857 Planarity : 0.005 0.062 3000 Dihedral : 8.318 81.729 4918 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 % Allowed : 0.83 % Favored : 98.81 % 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 : 1.851 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: 0.2688 time to fit residues: 136.0053 Evaluate side-chains 222 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1327 time to fit residues: 2.6155 ------------------------------------------------------------------------------- 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** ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16662 Z= 0.295 Angle : 0.779 10.868 22799 Z= 0.415 Chirality : 0.041 0.220 2857 Planarity : 0.005 0.045 3000 Dihedral : 6.249 34.295 2590 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 3.09 % Allowed : 10.37 % Favored : 86.54 % Rotamer: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.87 % 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: -2.18 (0.17), residues: 2103 helix: -0.52 (0.13), residues: 1152 sheet: -3.70 (0.33), residues: 165 loop : -2.20 (0.24), residues: 786 *********************** 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 275 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 272 time to evaluate : 1.831 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: 3 outliers final: 0 residues processed: 275 average time/residue: 0.2685 time to fit residues: 115.4781 Evaluate side-chains 211 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3398 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 160 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 16662 Z= 0.556 Angle : 0.988 15.176 22799 Z= 0.519 Chirality : 0.048 0.225 2857 Planarity : 0.006 0.130 3000 Dihedral : 6.788 37.554 2590 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 2.85 % Allowed : 13.69 % Favored : 83.45 % Rotamer: Outliers : 0.46 % Allowed : 6.15 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.65 (0.17), residues: 2103 helix: -0.68 (0.14), residues: 1156 sheet: -3.72 (0.32), residues: 175 loop : -2.85 (0.22), residues: 772 *********************** 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 233 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 233 average time/residue: 0.2347 time to fit residues: 88.0491 Evaluate side-chains 187 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2844 ------------------------------------------------------------------------------- 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: 0.4980 chunk 111 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 617 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN A1374 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16662 Z= 0.213 Angle : 0.693 9.624 22799 Z= 0.360 Chirality : 0.040 0.199 2857 Planarity : 0.004 0.040 3000 Dihedral : 5.871 30.712 2590 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 2.76 % Allowed : 10.32 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -1.72 (0.18), residues: 2103 helix: 0.22 (0.15), residues: 1152 sheet: -3.32 (0.35), residues: 160 loop : -2.74 (0.22), residues: 791 *********************** 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 254 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2463 time to fit residues: 99.2091 Evaluate side-chains 196 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2312 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 141 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 617 ASN A 958 ASN ** 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 299 ASN F 316 ASN ** F 379 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16662 Z= 0.301 Angle : 0.722 10.811 22799 Z= 0.379 Chirality : 0.041 0.187 2857 Planarity : 0.004 0.043 3000 Dihedral : 5.755 31.006 2590 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 2.52 % Allowed : 12.74 % Favored : 84.74 % Rotamer: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % 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: -1.61 (0.18), residues: 2103 helix: 0.36 (0.15), residues: 1146 sheet: -3.21 (0.36), residues: 158 loop : -2.76 (0.22), residues: 799 *********************** 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 239 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2374 time to fit residues: 91.4422 Evaluate side-chains 190 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4783 ------------------------------------------------------------------------------- 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: 2.9990 chunk 141 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 0.0060 chunk 157 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 A1131 ASN A1154 ASN B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN F 297 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16662 Z= 0.172 Angle : 0.640 8.361 22799 Z= 0.331 Chirality : 0.039 0.172 2857 Planarity : 0.003 0.037 3000 Dihedral : 5.317 30.882 2590 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 2.43 % Allowed : 9.99 % Favored : 87.59 % Rotamer: Outliers : 0.28 % Allowed : 1.28 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.88 % 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: -1.14 (0.19), residues: 2103 helix: 0.78 (0.15), residues: 1149 sheet: -2.83 (0.37), residues: 155 loop : -2.67 (0.22), residues: 799 *********************** 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 258 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 256 average time/residue: 0.2368 time to fit residues: 97.5315 Evaluate side-chains 201 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1672 ------------------------------------------------------------------------------- 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: 20.0000 chunk 17 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 617 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 316 ASN F 408 ASN F 424 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16662 Z= 0.272 Angle : 0.687 9.675 22799 Z= 0.361 Chirality : 0.040 0.226 2857 Planarity : 0.004 0.043 3000 Dihedral : 5.339 30.509 2590 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 2.38 % Allowed : 11.94 % Favored : 85.69 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -1.14 (0.19), residues: 2103 helix: 0.80 (0.16), residues: 1150 sheet: -2.77 (0.38), residues: 152 loop : -2.74 (0.22), residues: 801 *********************** 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 237 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2391 time to fit residues: 92.0662 Evaluate side-chains 190 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4255 ------------------------------------------------------------------------------- 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: 20.0000 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16662 Z= 0.174 Angle : 0.637 9.342 22799 Z= 0.330 Chirality : 0.039 0.231 2857 Planarity : 0.003 0.035 3000 Dihedral : 5.112 28.379 2590 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 2.28 % Allowed : 10.27 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.92 (0.19), residues: 2103 helix: 1.00 (0.16), residues: 1158 sheet: -2.60 (0.37), residues: 155 loop : -2.72 (0.22), residues: 790 *********************** 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 252 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.669 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: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2418 time to fit residues: 98.9746 Evaluate side-chains 198 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3013 ------------------------------------------------------------------------------- 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: 1.9990 chunk 146 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 138 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** A1307 GLN B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS F 198 ASN ** F 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN ** F 470 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: 0.7220 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16662 Z= 0.399 Angle : 0.790 12.722 22799 Z= 0.415 Chirality : 0.043 0.245 2857 Planarity : 0.005 0.054 3000 Dihedral : 5.594 33.220 2590 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 2.28 % Allowed : 13.08 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -1.28 (0.19), residues: 2103 helix: 0.68 (0.16), residues: 1144 sheet: -2.58 (0.40), residues: 154 loop : -2.83 (0.22), residues: 805 *********************** 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 225 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.742 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: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2399 time to fit residues: 87.6453 Evaluate side-chains 183 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3365 ------------------------------------------------------------------------------- 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: 0.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN F 297 ASN F 408 ASN F 424 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4811 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= 0.172 Angle : 0.651 12.439 22799 Z= 0.336 Chirality : 0.040 0.245 2857 Planarity : 0.003 0.047 3000 Dihedral : 5.123 26.621 2590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 2.28 % Allowed : 10.22 % Favored : 87.49 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.54 % 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: -0.85 (0.19), residues: 2103 helix: 1.07 (0.16), residues: 1145 sheet: -2.49 (0.39), residues: 145 loop : -2.68 (0.22), residues: 813 ********************** 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 242 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.2342 time to fit residues: 93.1236 Evaluate side-chains 191 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2544 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 40.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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 617 ASN B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4153 r_free = 0.4153 target = 0.125241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.088219 restraints weight = 63298.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085320 restraints weight = 49374.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086013 restraints weight = 41583.004| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16662 Z= 0.270 Angle : 0.698 13.554 22799 Z= 0.361 Chirality : 0.041 0.225 2857 Planarity : 0.004 0.043 3000 Dihedral : 5.228 28.179 2590 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 2.14 % Allowed : 12.22 % Favored : 85.64 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.93 (0.19), residues: 2103 helix: 1.04 (0.16), residues: 1148 sheet: -2.58 (0.37), residues: 155 loop : -2.77 (0.22), residues: 800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.80 seconds wall clock time: 54 minutes 44.72 seconds (3284.72 seconds total)