Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:41:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0b_32237/02_2023/7w0b_32237.pdb" } resolution = 3.33 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= 0.004 sd= 0.039 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 GLU 105": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ASP 702": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1347": "OD1" <-> "OD2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A GLU 1411": "OE1" <-> "OE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1614": "OD1" <-> "OD2" Residue "A PHE 1686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12997 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1586, 12853 Classifications: {'peptide': 1586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1521} Chain breaks: 3 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Time building chain proxies: 7.49, per 1000 atoms: 0.58 Number of scatterers: 12997 At special positions: 0 Unit cell: (96.3425, 117.992, 163.457, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 2382 8.00 N 2218 7.00 C 8326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3062 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 55.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.721A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.662A pdb=" N GLN A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.535A pdb=" N GLU A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.509A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.651A pdb=" N THR A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.683A pdb=" N SER A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 291 removed outlier: 5.445A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 314 Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.946A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 4.652A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.968A pdb=" N ASP A 385 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.514A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.579A pdb=" N ASN A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.936A pdb=" N GLU A 466 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 467 " --> pdb=" O LEU A 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 467' Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 507 through 512 removed outlier: 4.122A pdb=" N GLU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 534 removed outlier: 4.241A pdb=" N ASP A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.558A pdb=" N TYR A 545 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 548 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.859A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.639A pdb=" N ASP A 698 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.715A pdb=" N LEU A 748 " --> pdb=" O MET A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.586A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.610A pdb=" N MET A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.858A pdb=" N ARG A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 916 through 925 Processing helix chain 'A' and resid 959 through 968 removed outlier: 3.810A pdb=" N MET A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.522A pdb=" N CYS A 976 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.646A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 4.012A pdb=" N ASP A1027 " --> pdb=" O ASN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1134 removed outlier: 3.705A pdb=" N ASP A1125 " --> pdb=" O MET A1121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A1130 " --> pdb=" O PHE A1126 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR A1131 " --> pdb=" O GLU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.872A pdb=" N ARG A1148 " --> pdb=" O TYR A1145 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A1149 " --> pdb=" O GLY A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 removed outlier: 3.654A pdb=" N VAL A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1186 removed outlier: 3.504A pdb=" N ILE A1186 " --> pdb=" O LYS A1183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1183 through 1186' Processing helix chain 'A' and resid 1190 through 1199 removed outlier: 3.557A pdb=" N PHE A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.559A pdb=" N GLU A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.717A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.748A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1293 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.553A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1336 removed outlier: 3.728A pdb=" N ARG A1336 " --> pdb=" O VAL A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1363 through 1382 removed outlier: 3.794A pdb=" N ALA A1367 " --> pdb=" O ASN A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 4.273A pdb=" N LEU A1407 " --> pdb=" O PRO A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1411 No H-bonds generated for 'chain 'A' and resid 1409 through 1411' Processing helix chain 'A' and resid 1416 through 1420 removed outlier: 3.785A pdb=" N ASN A1420 " --> pdb=" O MET A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 4.290A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.619A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.801A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1508 removed outlier: 3.641A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1521 through 1525 removed outlier: 3.665A pdb=" N PHE A1524 " --> pdb=" O LEU A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 3.705A pdb=" N GLN A1546 " --> pdb=" O PHE A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1559 Processing helix chain 'A' and resid 1560 through 1562 No H-bonds generated for 'chain 'A' and resid 1560 through 1562' Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 3.760A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A1617 " --> pdb=" O GLY A1613 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix removed outlier: 3.548A pdb=" N THR A1649 " --> pdb=" O LEU A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1663 removed outlier: 4.168A pdb=" N HIS A1663 " --> pdb=" O GLN A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1666 No H-bonds generated for 'chain 'A' and resid 1664 through 1666' Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 4.049A pdb=" N ALA A1705 " --> pdb=" O ASN A1701 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 6.343A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 167 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY A 24 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR A 172 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 26 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 460 removed outlier: 8.998A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 389 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 357 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 618 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 removed outlier: 3.547A pdb=" N ARG A 703 " --> pdb=" O ILE A1361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 removed outlier: 5.171A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 970 through 971 removed outlier: 6.435A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1674 through 1675 580 hydrogen bonds defined for protein. 1626 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: 5.61 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2716 1.33 - 1.45: 2973 1.45 - 1.57: 7475 1.57 - 1.69: 0 1.69 - 1.82: 112 Bond restraints: 13276 Sorted by residual: bond pdb=" CG GLN A 520 " pdb=" CD GLN A 520 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CD GLN A 520 " pdb=" OE1 GLN A 520 " ideal model delta sigma weight residual 1.231 1.207 0.024 1.90e-02 2.77e+03 1.58e+00 bond pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" C GLU A 732 " pdb=" N PRO A 733 " ideal model delta sigma weight residual 1.335 1.325 0.010 8.70e-03 1.32e+04 1.35e+00 bond pdb=" CA GLN A 520 " pdb=" CB GLN A 520 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.66e-02 3.63e+03 9.24e-01 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 95.24 - 102.99: 84 102.99 - 110.74: 4223 110.74 - 118.50: 6123 118.50 - 126.25: 7363 126.25 - 134.01: 161 Bond angle restraints: 17954 Sorted by residual: angle pdb=" N GLN A 520 " pdb=" CA GLN A 520 " pdb=" CB GLN A 520 " ideal model delta sigma weight residual 110.28 116.80 -6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 967 " pdb=" CG MET A 967 " pdb=" SD MET A 967 " ideal model delta sigma weight residual 112.70 122.52 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA GLN A 520 " pdb=" CB GLN A 520 " pdb=" CG GLN A 520 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C ASN A 927 " pdb=" N ARG A 928 " pdb=" CA ARG A 928 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 ... (remaining 17949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7208 17.89 - 35.78: 699 35.78 - 53.67: 108 53.67 - 71.55: 17 71.55 - 89.44: 15 Dihedral angle restraints: 8047 sinusoidal: 3326 harmonic: 4721 Sorted by residual: dihedral pdb=" CA THR A 126 " pdb=" C THR A 126 " pdb=" N TYR A 127 " pdb=" CA TYR A 127 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR A1553 " pdb=" C TYR A1553 " pdb=" N VAL A1554 " pdb=" CA VAL A1554 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU A 207 " pdb=" C GLU A 207 " pdb=" N MET A 208 " pdb=" CA MET A 208 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1173 0.028 - 0.057: 534 0.057 - 0.085: 182 0.085 - 0.113: 93 0.113 - 0.141: 22 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA GLU A1534 " pdb=" N GLU A1534 " pdb=" C GLU A1534 " pdb=" CB GLU A1534 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 970 " pdb=" N ILE A 970 " pdb=" C ILE A 970 " pdb=" CB ILE A 970 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CB VAL A1421 " pdb=" CA VAL A1421 " pdb=" CG1 VAL A1421 " pdb=" CG2 VAL A1421 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 2001 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 102 " -0.027 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP A 102 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A 102 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 102 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 102 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 102 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 102 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1667 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A1668 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1668 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1668 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 442 " -0.012 2.00e-02 2.50e+03 1.01e-02 2.57e+00 pdb=" CG TRP A 442 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 442 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 442 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 442 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 442 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 442 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 442 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 442 " -0.001 2.00e-02 2.50e+03 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 159 2.62 - 3.19: 11979 3.19 - 3.76: 20401 3.76 - 4.33: 27094 4.33 - 4.90: 43773 Nonbonded interactions: 103406 Sorted by model distance: nonbonded pdb=" OH TYR A 88 " pdb=" OE2 GLU A 105 " model vdw 2.049 2.440 nonbonded pdb=" O ASN A1409 " pdb=" OH TYR A1624 " model vdw 2.126 2.440 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 963 " model vdw 2.158 2.440 nonbonded pdb=" O TYR A1145 " pdb=" NE ARG A1148 " model vdw 2.188 2.520 nonbonded pdb=" OD2 ASP A1125 " pdb=" NZ LYS A1129 " model vdw 2.215 2.520 ... (remaining 103401 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: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 8326 2.51 5 N 2218 2.21 5 O 2382 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.180 Process input model: 38.420 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.003 0.034 13276 Z= 0.191 Angle : 0.601 11.440 17954 Z= 0.320 Chirality : 0.040 0.141 2004 Planarity : 0.004 0.040 2305 Dihedral : 14.321 89.442 4985 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.14 (0.22), residues: 1592 helix: 0.81 (0.20), residues: 720 sheet: -1.50 (0.39), residues: 168 loop : -0.08 (0.25), residues: 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2397 time to fit residues: 37.8469 Evaluate side-chains 78 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13276 Z= 0.172 Angle : 0.540 6.911 17954 Z= 0.284 Chirality : 0.040 0.174 2004 Planarity : 0.003 0.036 2305 Dihedral : 4.156 27.003 1744 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.22), residues: 1592 helix: 0.95 (0.20), residues: 717 sheet: -1.42 (0.41), residues: 164 loop : -0.19 (0.25), residues: 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.614 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 87 average time/residue: 0.2319 time to fit residues: 32.2883 Evaluate side-chains 74 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1164 time to fit residues: 2.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13276 Z= 0.204 Angle : 0.530 8.549 17954 Z= 0.275 Chirality : 0.040 0.162 2004 Planarity : 0.003 0.035 2305 Dihedral : 4.191 26.905 1744 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.41 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.15 (0.22), residues: 1592 helix: 0.97 (0.20), residues: 720 sheet: -1.44 (0.40), residues: 171 loop : -0.30 (0.24), residues: 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.619 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 0.2374 time to fit residues: 33.4142 Evaluate side-chains 75 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1474 time to fit residues: 3.5595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1147 ASN A1287 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 13276 Z= 0.263 Angle : 0.570 8.674 17954 Z= 0.293 Chirality : 0.041 0.193 2004 Planarity : 0.004 0.034 2305 Dihedral : 4.297 28.377 1744 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.06 (0.22), residues: 1592 helix: 0.91 (0.20), residues: 727 sheet: -1.25 (0.39), residues: 174 loop : -0.44 (0.24), residues: 691 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.730 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.2524 time to fit residues: 32.2312 Evaluate side-chains 72 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1428 time to fit residues: 4.1612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1306 ASN ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 ASN A1543 GLN A1712 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13276 Z= 0.219 Angle : 0.549 7.939 17954 Z= 0.282 Chirality : 0.041 0.183 2004 Planarity : 0.003 0.033 2305 Dihedral : 4.274 29.065 1744 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.10 (0.22), residues: 1592 helix: 0.96 (0.20), residues: 734 sheet: -1.30 (0.41), residues: 160 loop : -0.46 (0.24), residues: 698 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 83 average time/residue: 0.2356 time to fit residues: 30.9886 Evaluate side-chains 71 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1383 time to fit residues: 3.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13276 Z= 0.156 Angle : 0.544 9.849 17954 Z= 0.277 Chirality : 0.040 0.182 2004 Planarity : 0.003 0.044 2305 Dihedral : 4.159 28.932 1744 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.60 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.22 (0.22), residues: 1592 helix: 1.07 (0.20), residues: 721 sheet: -1.21 (0.41), residues: 162 loop : -0.38 (0.24), residues: 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 80 average time/residue: 0.2453 time to fit residues: 31.0021 Evaluate side-chains 69 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1219 time to fit residues: 2.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 95 optimal weight: 0.0040 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN A1543 GLN A1712 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13276 Z= 0.147 Angle : 0.537 9.288 17954 Z= 0.271 Chirality : 0.040 0.174 2004 Planarity : 0.003 0.033 2305 Dihedral : 4.053 28.287 1744 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.31 (0.22), residues: 1592 helix: 1.13 (0.20), residues: 723 sheet: -1.12 (0.41), residues: 162 loop : -0.34 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 79 average time/residue: 0.2450 time to fit residues: 30.8567 Evaluate side-chains 69 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1660 time to fit residues: 3.2240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13276 Z= 0.280 Angle : 0.604 9.794 17954 Z= 0.306 Chirality : 0.042 0.170 2004 Planarity : 0.004 0.032 2305 Dihedral : 4.331 28.044 1744 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.29 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.11 (0.22), residues: 1592 helix: 0.95 (0.20), residues: 734 sheet: -0.95 (0.39), residues: 176 loop : -0.51 (0.25), residues: 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.2793 time to fit residues: 31.7051 Evaluate side-chains 69 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3292 time to fit residues: 3.5932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 146 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN A1543 GLN A1712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13276 Z= 0.150 Angle : 0.555 9.911 17954 Z= 0.279 Chirality : 0.040 0.185 2004 Planarity : 0.003 0.033 2305 Dihedral : 4.158 28.395 1744 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.29 (0.22), residues: 1592 helix: 1.10 (0.20), residues: 728 sheet: -0.92 (0.42), residues: 160 loop : -0.41 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.627 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2669 time to fit residues: 30.8945 Evaluate side-chains 70 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1379 time to fit residues: 3.0336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13276 Z= 0.165 Angle : 0.570 10.666 17954 Z= 0.283 Chirality : 0.040 0.196 2004 Planarity : 0.003 0.033 2305 Dihedral : 4.145 28.041 1744 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.41 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.30 (0.22), residues: 1592 helix: 1.12 (0.20), residues: 725 sheet: -0.90 (0.42), residues: 160 loop : -0.40 (0.24), residues: 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.765 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.2579 time to fit residues: 29.3586 Evaluate side-chains 70 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1351 time to fit residues: 2.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1712 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.132584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092683 restraints weight = 38328.734| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.88 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13276 Z= 0.170 Angle : 0.587 10.928 17954 Z= 0.289 Chirality : 0.040 0.187 2004 Planarity : 0.003 0.033 2305 Dihedral : 4.206 27.808 1744 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.34 (0.22), residues: 1592 helix: 1.16 (0.20), residues: 725 sheet: -0.87 (0.40), residues: 172 loop : -0.39 (0.25), residues: 695 =============================================================================== Job complete usr+sys time: 2350.29 seconds wall clock time: 43 minutes 56.04 seconds (2636.04 seconds total)