Starting phenix.real_space_refine on Wed Jun 11 18:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_32237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_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/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_32237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_32237.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_32237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0b_32237/06_2025/7w0b_32237.cif" } resolution = 3.33 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= 0.004 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 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. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.60, 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 - 3.00 Amino acid : True - 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 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: 2.22 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: 5.63 Time building geometry restraints manager: 3.69 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: 0.00 - 2.29: 17735 2.29 - 4.58: 193 4.58 - 6.86: 18 6.86 - 9.15: 6 9.15 - 11.44: 2 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 3.040 nonbonded pdb=" O ASN A1409 " pdb=" OH TYR A1624 " model vdw 2.126 3.040 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 963 " model vdw 2.158 3.040 nonbonded pdb=" O TYR A1145 " pdb=" NE ARG A1148 " model vdw 2.188 3.120 nonbonded pdb=" OD2 ASP A1125 " pdb=" NZ LYS A1129 " model vdw 2.215 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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= 0.138 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 % Allowed : 0.14 % Favored : 99.86 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A 102 HIS 0.006 0.001 HIS A1712 PHE 0.025 0.001 PHE A 818 TYR 0.026 0.001 TYR A1553 ARG 0.007 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.17097 ( 572) hydrogen bonds : angle 6.15116 ( 1626) covalent geometry : bond 0.00292 (13276) covalent geometry : angle 0.60148 (17954) *********************** 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 to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.651 Fit side-chains REVERT: A 208 MET cc_start: 0.7611 (mmp) cc_final: 0.7350 (mmm) REVERT: A 222 MET cc_start: 0.6912 (pmm) cc_final: 0.6596 (pmm) REVERT: A 382 ASP cc_start: 0.6763 (p0) cc_final: 0.6376 (p0) REVERT: A 967 MET cc_start: 0.7231 (tmm) cc_final: 0.6938 (tmm) REVERT: A 1681 MET cc_start: 0.4436 (mmt) cc_final: 0.3883 (ptp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2408 time to fit residues: 38.3959 Evaluate side-chains 78 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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: 0.0970 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.0040 chunk 144 optimal weight: 0.0970 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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** A1712 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.134771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092338 restraints weight = 38981.560| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.98 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13276 Z= 0.115 Angle : 0.545 7.009 17954 Z= 0.287 Chirality : 0.040 0.162 2004 Planarity : 0.004 0.038 2305 Dihedral : 4.114 26.593 1744 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.49 % Allowed : 6.18 % Favored : 93.33 % 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: 0.19 (0.22), residues: 1592 helix: 0.87 (0.20), residues: 723 sheet: -1.34 (0.41), residues: 164 loop : -0.16 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 102 HIS 0.005 0.001 HIS A1138 PHE 0.016 0.001 PHE A 391 TYR 0.015 0.001 TYR A 127 ARG 0.004 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 572) hydrogen bonds : angle 4.98948 ( 1626) covalent geometry : bond 0.00246 (13276) covalent geometry : angle 0.54476 (17954) *********************** 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 92 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 922 MET cc_start: 0.7379 (mmm) cc_final: 0.7035 (mmm) REVERT: A 1681 MET cc_start: 0.3794 (mmt) cc_final: 0.3486 (ttp) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 0.2353 time to fit residues: 32.9028 Evaluate side-chains 76 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1534 GLU Chi-restraints excluded: chain A residue 1692 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 61 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** A1712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.133947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091192 restraints weight = 38628.103| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.91 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13276 Z= 0.127 Angle : 0.532 9.840 17954 Z= 0.277 Chirality : 0.040 0.156 2004 Planarity : 0.003 0.036 2305 Dihedral : 4.120 27.352 1744 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 0.90 % Allowed : 8.40 % Favored : 90.69 % 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: 0.93 (0.20), residues: 722 sheet: -1.49 (0.41), residues: 163 loop : -0.24 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1634 HIS 0.005 0.001 HIS A1712 PHE 0.017 0.001 PHE A1686 TYR 0.010 0.001 TYR A1328 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 572) hydrogen bonds : angle 4.79099 ( 1626) covalent geometry : bond 0.00286 (13276) covalent geometry : angle 0.53224 (17954) *********************** 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 94 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 ASP cc_start: 0.6760 (p0) cc_final: 0.6397 (p0) REVERT: A 424 MET cc_start: 0.0741 (mmt) cc_final: 0.0353 (mmt) REVERT: A 1681 MET cc_start: 0.3882 (mmt) cc_final: 0.3463 (ttp) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 0.2253 time to fit residues: 33.6966 Evaluate side-chains 76 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 TRP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1333 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1147 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 GLN A1712 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.131350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088747 restraints weight = 38251.733| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.72 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13276 Z= 0.187 Angle : 0.598 13.205 17954 Z= 0.306 Chirality : 0.042 0.152 2004 Planarity : 0.004 0.039 2305 Dihedral : 4.327 28.661 1744 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.15 % Favored : 95.79 % Rotamer: Outliers : 1.32 % Allowed : 10.42 % Favored : 88.26 % 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: -0.01 (0.21), residues: 1592 helix: 0.78 (0.19), residues: 733 sheet: -1.30 (0.40), residues: 170 loop : -0.40 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 986 HIS 0.006 0.001 HIS A1456 PHE 0.019 0.002 PHE A1686 TYR 0.015 0.001 TYR A1328 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 572) hydrogen bonds : angle 4.81437 ( 1626) covalent geometry : bond 0.00429 (13276) covalent geometry : angle 0.59808 (17954) *********************** 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 95 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.7415 (mmm) cc_final: 0.6871 (mmm) REVERT: A 382 ASP cc_start: 0.6759 (p0) cc_final: 0.6456 (p0) REVERT: A 922 MET cc_start: 0.7434 (mmm) cc_final: 0.6962 (mmm) REVERT: A 1134 LYS cc_start: 0.6676 (mttt) cc_final: 0.6340 (tttt) REVERT: A 1681 MET cc_start: 0.3969 (mmt) cc_final: 0.3613 (ttp) REVERT: A 1689 MET cc_start: 0.6988 (tmm) cc_final: 0.6670 (ttm) outliers start: 19 outliers final: 10 residues processed: 94 average time/residue: 0.2213 time to fit residues: 33.3863 Evaluate side-chains 82 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1506 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 103 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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** A1143 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.132953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092348 restraints weight = 37584.542| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.47 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13276 Z= 0.107 Angle : 0.525 9.120 17954 Z= 0.269 Chirality : 0.040 0.152 2004 Planarity : 0.003 0.036 2305 Dihedral : 4.112 27.231 1744 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.25 % Allowed : 11.60 % Favored : 87.15 % 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: 0.18 (0.22), residues: 1592 helix: 1.00 (0.20), residues: 727 sheet: -1.31 (0.41), residues: 160 loop : -0.35 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 986 HIS 0.007 0.001 HIS A1138 PHE 0.020 0.001 PHE A1686 TYR 0.010 0.001 TYR A 291 ARG 0.003 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 572) hydrogen bonds : angle 4.61381 ( 1626) covalent geometry : bond 0.00237 (13276) covalent geometry : angle 0.52494 (17954) *********************** 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 97 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.2990 (tmm) cc_final: 0.2620 (tmm) REVERT: A 382 ASP cc_start: 0.6746 (p0) cc_final: 0.6386 (p0) REVERT: A 424 MET cc_start: 0.0637 (mmt) cc_final: 0.0108 (mmt) REVERT: A 922 MET cc_start: 0.7369 (mmm) cc_final: 0.7066 (mmm) REVERT: A 1681 MET cc_start: 0.4002 (mmt) cc_final: 0.3641 (ttp) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.2375 time to fit residues: 34.7231 Evaluate side-chains 79 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 71 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 354 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** 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** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN A1406 GLN A1712 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090422 restraints weight = 39326.483| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 5.01 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13276 Z= 0.194 Angle : 0.606 11.136 17954 Z= 0.310 Chirality : 0.042 0.172 2004 Planarity : 0.004 0.033 2305 Dihedral : 4.339 27.013 1744 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 1.04 % Allowed : 12.57 % Favored : 86.39 % 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: 0.01 (0.21), residues: 1592 helix: 0.84 (0.19), residues: 734 sheet: -1.18 (0.39), residues: 172 loop : -0.48 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1634 HIS 0.006 0.001 HIS A1456 PHE 0.018 0.002 PHE A1686 TYR 0.013 0.001 TYR A1328 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 572) hydrogen bonds : angle 4.76557 ( 1626) covalent geometry : bond 0.00449 (13276) covalent geometry : angle 0.60611 (17954) *********************** 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 90 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7787 (mp10) cc_final: 0.6845 (tm-30) REVERT: A 382 ASP cc_start: 0.6485 (p0) cc_final: 0.6249 (p0) REVERT: A 424 MET cc_start: 0.0269 (mmt) cc_final: -0.0342 (mmt) REVERT: A 922 MET cc_start: 0.7951 (mmm) cc_final: 0.7644 (mmm) REVERT: A 1681 MET cc_start: 0.4000 (mmt) cc_final: 0.3611 (ttp) REVERT: A 1689 MET cc_start: 0.6800 (tmm) cc_final: 0.6395 (ttm) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.2828 time to fit residues: 38.6322 Evaluate side-chains 78 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1506 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 0.3980 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 486 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.132191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092314 restraints weight = 38720.232| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.74 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2252 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= 0.113 Angle : 0.559 10.437 17954 Z= 0.286 Chirality : 0.041 0.150 2004 Planarity : 0.003 0.046 2305 Dihedral : 4.192 26.580 1744 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.04 % Allowed : 13.47 % Favored : 85.49 % 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: 0.12 (0.21), residues: 1592 helix: 0.95 (0.19), residues: 733 sheet: -1.20 (0.41), residues: 162 loop : -0.43 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 986 HIS 0.010 0.001 HIS A1138 PHE 0.022 0.001 PHE A1686 TYR 0.009 0.001 TYR A 686 ARG 0.002 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 572) hydrogen bonds : angle 4.65716 ( 1626) covalent geometry : bond 0.00255 (13276) covalent geometry : angle 0.55918 (17954) *********************** 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 96 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7776 (mp10) cc_final: 0.6837 (tm-30) REVERT: A 344 MET cc_start: 0.1749 (tmm) cc_final: 0.1263 (tmm) REVERT: A 382 ASP cc_start: 0.6517 (p0) cc_final: 0.6277 (p0) REVERT: A 424 MET cc_start: 0.0123 (mmt) cc_final: -0.0260 (mmt) REVERT: A 893 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: A 964 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8097 (mmtt) REVERT: A 1681 MET cc_start: 0.3809 (mmt) cc_final: 0.3379 (ttp) REVERT: A 1689 MET cc_start: 0.6986 (tmm) cc_final: 0.6518 (ttm) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.3574 time to fit residues: 49.3188 Evaluate side-chains 83 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1506 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.131489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092694 restraints weight = 38154.142| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.45 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13276 Z= 0.130 Angle : 0.562 9.689 17954 Z= 0.284 Chirality : 0.040 0.161 2004 Planarity : 0.003 0.035 2305 Dihedral : 4.154 26.460 1744 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 1.25 % Allowed : 13.26 % Favored : 85.49 % 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: 0.18 (0.21), residues: 1592 helix: 0.97 (0.19), residues: 732 sheet: -1.18 (0.42), residues: 157 loop : -0.37 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.014 0.001 HIS A1138 PHE 0.019 0.001 PHE A1686 TYR 0.009 0.001 TYR A 686 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 572) hydrogen bonds : angle 4.64087 ( 1626) covalent geometry : bond 0.00299 (13276) covalent geometry : angle 0.56158 (17954) *********************** 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 94 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7802 (mp10) cc_final: 0.6926 (tm-30) REVERT: A 344 MET cc_start: 0.1751 (tmm) cc_final: 0.1256 (tmm) REVERT: A 382 ASP cc_start: 0.6610 (p0) cc_final: 0.6396 (p0) REVERT: A 625 MET cc_start: 0.7423 (ppp) cc_final: 0.7123 (ppp) REVERT: A 893 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (mmm) REVERT: A 908 MET cc_start: 0.7052 (mmp) cc_final: 0.6654 (mmp) REVERT: A 922 MET cc_start: 0.7536 (mmm) cc_final: 0.7069 (mmm) REVERT: A 964 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8203 (mmtt) REVERT: A 1209 MET cc_start: 0.8628 (ppp) cc_final: 0.8340 (ptt) REVERT: A 1681 MET cc_start: 0.3758 (mmt) cc_final: 0.3309 (ttp) REVERT: A 1689 MET cc_start: 0.7008 (tmm) cc_final: 0.6786 (tmm) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.2404 time to fit residues: 34.2145 Evaluate side-chains 89 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1652 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 122 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 0.0370 chunk 121 optimal weight: 0.7980 overall best weight: 0.5074 ------------------------------------------------------------------------------- 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 486 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.132978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093549 restraints weight = 38777.665| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.84 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2470 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= 0.102 Angle : 0.555 10.206 17954 Z= 0.278 Chirality : 0.040 0.179 2004 Planarity : 0.003 0.037 2305 Dihedral : 4.069 26.383 1744 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.97 % Allowed : 13.47 % Favored : 85.56 % 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: 0.25 (0.22), residues: 1592 helix: 1.04 (0.19), residues: 733 sheet: -0.94 (0.42), residues: 157 loop : -0.40 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 986 HIS 0.010 0.001 HIS A1138 PHE 0.011 0.001 PHE A1023 TYR 0.008 0.001 TYR A 291 ARG 0.006 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 572) hydrogen bonds : angle 4.58507 ( 1626) covalent geometry : bond 0.00225 (13276) covalent geometry : angle 0.55516 (17954) *********************** 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 97 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7911 (mp10) cc_final: 0.7015 (tm-30) REVERT: A 344 MET cc_start: 0.1869 (tmm) cc_final: 0.1417 (tmm) REVERT: A 382 ASP cc_start: 0.6581 (p0) cc_final: 0.6378 (p0) REVERT: A 908 MET cc_start: 0.6940 (mmp) cc_final: 0.6510 (mmp) REVERT: A 922 MET cc_start: 0.7558 (mmm) cc_final: 0.7141 (mmm) REVERT: A 1209 MET cc_start: 0.8524 (ppp) cc_final: 0.8025 (ptp) REVERT: A 1681 MET cc_start: 0.3894 (mmt) cc_final: 0.3459 (ttp) REVERT: A 1689 MET cc_start: 0.6949 (tmm) cc_final: 0.6404 (ttm) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.2324 time to fit residues: 33.8325 Evaluate side-chains 87 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1652 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.132130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092440 restraints weight = 38826.724| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.64 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13276 Z= 0.124 Angle : 0.578 9.358 17954 Z= 0.289 Chirality : 0.041 0.167 2004 Planarity : 0.003 0.035 2305 Dihedral : 4.097 26.468 1744 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.97 % Allowed : 13.68 % Favored : 85.35 % 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: 0.25 (0.21), residues: 1592 helix: 1.03 (0.19), residues: 733 sheet: -0.88 (0.43), residues: 157 loop : -0.42 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1634 HIS 0.008 0.001 HIS A1712 PHE 0.011 0.001 PHE A1542 TYR 0.009 0.001 TYR A1328 ARG 0.007 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 572) hydrogen bonds : angle 4.60364 ( 1626) covalent geometry : bond 0.00285 (13276) covalent geometry : angle 0.57785 (17954) ********************** 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 93 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7500 (mp10) cc_final: 0.6820 (tm-30) REVERT: A 344 MET cc_start: 0.1927 (tmm) cc_final: 0.1491 (tmm) REVERT: A 382 ASP cc_start: 0.6573 (p0) cc_final: 0.6296 (p0) REVERT: A 908 MET cc_start: 0.6962 (mmp) cc_final: 0.6526 (mmp) REVERT: A 922 MET cc_start: 0.7575 (mmm) cc_final: 0.7154 (mmm) REVERT: A 964 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8171 (mmtt) REVERT: A 1209 MET cc_start: 0.8584 (ppp) cc_final: 0.8229 (ptt) REVERT: A 1320 LYS cc_start: 0.8585 (mttt) cc_final: 0.8203 (tppt) REVERT: A 1681 MET cc_start: 0.3920 (mmt) cc_final: 0.3484 (ttp) REVERT: A 1689 MET cc_start: 0.6919 (tmm) cc_final: 0.6375 (ttm) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.2501 time to fit residues: 34.7865 Evaluate side-chains 90 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1333 GLU Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1652 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 127 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.132524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092808 restraints weight = 38535.182| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 4.86 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13276 Z= 0.113 Angle : 0.573 11.780 17954 Z= 0.284 Chirality : 0.040 0.154 2004 Planarity : 0.003 0.037 2305 Dihedral : 4.073 26.745 1744 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 14.24 % Favored : 84.93 % 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 (0.21), residues: 1592 helix: 1.09 (0.19), residues: 732 sheet: -0.75 (0.44), residues: 145 loop : -0.44 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 442 HIS 0.009 0.001 HIS A1712 PHE 0.011 0.001 PHE A1023 TYR 0.009 0.001 TYR A 745 ARG 0.007 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 572) hydrogen bonds : angle 4.56769 ( 1626) covalent geometry : bond 0.00257 (13276) covalent geometry : angle 0.57310 (17954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6166.63 seconds wall clock time: 109 minutes 38.20 seconds (6578.20 seconds total)