Starting phenix.real_space_refine on Fri Mar 6 11:46:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ozi_71059/03_2026/9ozi_71059.map" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 9469 2.51 5 N 2376 2.21 5 O 2884 1.98 5 H 13874 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28661 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1788, 28188 Classifications: {'peptide': 1788} Link IDs: {'PCIS': 1, 'PTRANS': 94, 'TRANS': 1692} Chain breaks: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 350 Unusual residues: {'NAG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 4.69, per 1000 atoms: 0.16 Number of scatterers: 28661 At special positions: 0 Unit cell: (115.64, 204.14, 299.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 O 2884 8.00 N 2376 7.00 C 9469 6.00 H 13874 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 868 " distance=2.03 Simple disulfide: pdb=" SG CYS A 984 " - pdb=" SG CYS A1000 " distance=2.03 Simple disulfide: pdb=" SG CYS A1336 " - pdb=" SG CYS A1378 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1380 " distance=2.03 Simple disulfide: pdb=" SG CYS A1453 " - pdb=" SG CYS A1486 " distance=2.03 Simple disulfide: pdb=" SG CYS A1721 " - pdb=" SG CYS A1729 " distance=2.03 Simple disulfide: pdb=" SG CYS A1825 " - pdb=" SG CYS A1829 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2401 " - " ASN A 123 " " NAG A2402 " - " ASN A 132 " " NAG A2403 " - " ASN A 333 " " NAG A2404 " - " ASN A 405 " " NAG A2405 " - " ASN A 607 " " NAG A2406 " - " ASN A 628 " " NAG A2407 " - " ASN A 971 " " NAG A2408 " - " ASN A 49 " " NAG A2409 " - " ASN A 65 " " NAG A2410 " - " ASN A 265 " " NAG A2411 " - " ASN A 287 " " NAG A2412 " - " ASN A 377 " " NAG A2413 " - " ASN A 714 " " NAG A2414 " - " ASN A1110 " " NAG A2415 " - " ASN A1233 " " NAG A2416 " - " ASN A1255 " " NAG A2417 " - " ASN A1282 " " NAG A2418 " - " ASN A1696 " " NAG A2419 " - " ASN A1730 " " NAG A2420 " - " ASN A1795 " " NAG A2421 " - " ASN A1822 " " NAG A2422 " - " ASN A1588 " " NAG A2423 " - " ASN A1628 " " NAG A2424 " - " ASN A1316 " " NAG A2425 " - " ASN A 962 " " NAG B 1 " - " ASN A 480 " " NAG C 1 " - " ASN A1180 " " NAG D 1 " - " ASN A1470 " " NAG E 1 " - " ASN A1682 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 767.2 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 42 sheets defined 6.5% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 49 through 64 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.855A pdb=" N LYS A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 76 " --> pdb=" O CYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.663A pdb=" N ILE A 329 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 1228 through 1232 Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1328 through 1333 removed outlier: 4.179A pdb=" N ARG A1333 " --> pdb=" O GLU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1345 Processing helix chain 'A' and resid 1442 through 1446 Processing helix chain 'A' and resid 1450 through 1455 removed outlier: 3.771A pdb=" N LEU A1454 " --> pdb=" O ASP A1450 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.918A pdb=" N GLU A 41 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA A 784 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 770 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 753 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.649A pdb=" N THR A 125 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 119 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.523A pdb=" N TRP A 142 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 137 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.523A pdb=" N TRP A 142 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 137 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 213 removed outlier: 5.398A pdb=" N ILE A 209 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 225 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP A 211 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A 223 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 247 through 252 removed outlier: 3.828A pdb=" N VAL A 273 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA A 274 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A 276 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.817A pdb=" N TRP A 301 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 562 " --> pdb=" O TRP A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 340 removed outlier: 3.831A pdb=" N GLY A 336 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 354 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 384 removed outlier: 3.941A pdb=" N SER A 380 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 422 through 426 removed outlier: 3.799A pdb=" N LYS A 422 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 440 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 510 through 514 removed outlier: 3.715A pdb=" N GLU A 514 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE A 518 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 526 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 576 through 579 removed outlier: 5.704A pdb=" N LEU A 577 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 592 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 587 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 623 through 629 removed outlier: 3.816A pdb=" N ASN A 628 " --> pdb=" O TYR A 610 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 610 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 623 through 629 removed outlier: 3.816A pdb=" N ASN A 628 " --> pdb=" O TYR A 610 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 610 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 698 through 701 removed outlier: 5.893A pdb=" N PHE A 699 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS A 688 " --> pdb=" O PHE A 699 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A 701 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 710 through 711 removed outlier: 3.691A pdb=" N TRP A 719 " --> pdb=" O GLN A 727 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 790 through 796 removed outlier: 3.924A pdb=" N THR A 809 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 810 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 832 through 840 removed outlier: 5.601A pdb=" N VAL A 834 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 851 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 836 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A 856 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 878 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC3, first strand: chain 'A' and resid 958 through 961 Processing sheet with id=AC4, first strand: chain 'A' and resid 982 through 983 Processing sheet with id=AC5, first strand: chain 'A' and resid 1021 through 1026 Processing sheet with id=AC6, first strand: chain 'A' and resid 1056 through 1061 removed outlier: 6.190A pdb=" N VAL A1073 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG A1124 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A1075 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER A1122 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1087 through 1098 removed outlier: 3.930A pdb=" N GLN A1089 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A1135 " --> pdb=" O TYR A1093 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1181 through 1187 removed outlier: 3.576A pdb=" N HIS A1181 " --> pdb=" O ASP A1176 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A1174 " --> pdb=" O ILE A1183 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU A1185 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A1172 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1195 through 1198 removed outlier: 3.598A pdb=" N TYR A1206 " --> pdb=" O PHE A1213 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A1212 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1234 through 1239 removed outlier: 3.815A pdb=" N ALA A1236 " --> pdb=" O ALA A1249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1284 through 1291 removed outlier: 5.565A pdb=" N ILE A1285 " --> pdb=" O GLU A1302 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU A1302 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A1287 " --> pdb=" O ILE A1300 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET A1309 " --> pdb=" O ILE A1322 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A1311 " --> pdb=" O TYR A1320 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A1318 " --> pdb=" O ASP A1313 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1350 through 1352 removed outlier: 5.813A pdb=" N ALA A1372 " --> pdb=" O ARG A1382 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG A1382 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1393 through 1399 removed outlier: 6.418A pdb=" N ILE A1394 " --> pdb=" O GLU A1409 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A1409 " --> pdb=" O ILE A1394 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1396 " --> pdb=" O THR A1407 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR A1414 " --> pdb=" O LYS A1431 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS A1431 " --> pdb=" O THR A1414 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A1416 " --> pdb=" O GLN A1429 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1456 through 1458 Processing sheet with id=AD6, first strand: chain 'A' and resid 1464 through 1468 removed outlier: 4.014A pdb=" N THR A1464 " --> pdb=" O SER A1476 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A1474 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR A1468 " --> pdb=" O SER A1472 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER A1472 " --> pdb=" O THR A1468 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A1531 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1520 through 1524 removed outlier: 3.652A pdb=" N LYS A1547 " --> pdb=" O THR A1495 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1577 through 1583 removed outlier: 6.566A pdb=" N THR A1586 " --> pdb=" O LEU A1582 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1621 through 1622 removed outlier: 3.959A pdb=" N ARG A1605 " --> pdb=" O PHE A1651 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TRP A1657 " --> pdb=" O HIS A1652 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1621 through 1622 removed outlier: 3.959A pdb=" N ARG A1605 " --> pdb=" O PHE A1651 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1676 through 1680 removed outlier: 5.429A pdb=" N ASN A1677 " --> pdb=" O GLU A1688 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A1688 " --> pdb=" O ASN A1677 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A1686 " --> pdb=" O ILE A1679 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A1730 " --> pdb=" O THR A1720 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A1720 " --> pdb=" O ASN A1730 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1695 through 1706 removed outlier: 6.538A pdb=" N VAL A1747 " --> pdb=" O ASN A1696 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N THR A1698 " --> pdb=" O THR A1745 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR A1745 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N PHE A1700 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG A1743 " --> pdb=" O PHE A1700 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N PHE A1702 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N LEU A1741 " --> pdb=" O PHE A1702 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N LEU A1704 " --> pdb=" O ASN A1739 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N ASN A1739 " --> pdb=" O LEU A1704 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1695 through 1706 removed outlier: 6.538A pdb=" N VAL A1747 " --> pdb=" O ASN A1696 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N THR A1698 " --> pdb=" O THR A1745 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR A1745 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N PHE A1700 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG A1743 " --> pdb=" O PHE A1700 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N PHE A1702 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N LEU A1741 " --> pdb=" O PHE A1702 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N LEU A1704 " --> pdb=" O ASN A1739 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N ASN A1739 " --> pdb=" O LEU A1704 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1775 through 1777 removed outlier: 3.645A pdb=" N SER A1783 " --> pdb=" O ALA A1777 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A1786 " --> pdb=" O CYS A1829 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A1829 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1818 through 1823 removed outlier: 5.271A pdb=" N VAL A1819 " --> pdb=" O SER A1803 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER A1803 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A1821 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR A1798 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA A1844 " --> pdb=" O TYR A1855 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A1855 " --> pdb=" O ALA A1844 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA A1846 " --> pdb=" O GLY A1853 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1191 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: 7.91 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13869 1.03 - 1.23: 55 1.23 - 1.42: 6554 1.42 - 1.62: 8492 1.62 - 1.82: 81 Bond restraints: 29051 Sorted by residual: bond pdb=" N CYS A 24 " pdb=" CA CYS A 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N CYS A 24 " pdb=" H CYS A 24 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N ASN A 768 " pdb=" CA ASN A 768 " ideal model delta sigma weight residual 1.466 1.448 0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C TYR A 677 " pdb=" N ILE A 678 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.29e-02 6.01e+03 1.56e+00 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 9.81e-01 ... (remaining 29046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 49454 1.07 - 2.14: 2520 2.14 - 3.21: 133 3.21 - 4.28: 49 4.28 - 5.35: 5 Bond angle restraints: 52161 Sorted by residual: angle pdb=" N ARG A 750 " pdb=" CA ARG A 750 " pdb=" C ARG A 750 " ideal model delta sigma weight residual 112.13 107.76 4.37 1.37e+00 5.33e-01 1.02e+01 angle pdb=" C ALA A 767 " pdb=" CA ALA A 767 " pdb=" CB ALA A 767 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.22e+00 angle pdb=" CA ASN A1339 " pdb=" C ASN A1339 " pdb=" O ASN A1339 " ideal model delta sigma weight residual 121.20 118.44 2.76 1.04e+00 9.25e-01 7.06e+00 angle pdb=" N GLY A1033 " pdb=" CA GLY A1033 " pdb=" C GLY A1033 " ideal model delta sigma weight residual 110.18 113.87 -3.69 1.56e+00 4.11e-01 5.61e+00 angle pdb=" N ALA A 767 " pdb=" CA ALA A 767 " pdb=" C ALA A 767 " ideal model delta sigma weight residual 110.80 106.29 4.51 2.13e+00 2.20e-01 4.49e+00 ... (remaining 52156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 13678 17.53 - 35.07: 499 35.07 - 52.60: 152 52.60 - 70.14: 44 70.14 - 87.67: 9 Dihedral angle restraints: 14382 sinusoidal: 7930 harmonic: 6452 Sorted by residual: dihedral pdb=" CA ASN A1255 " pdb=" C ASN A1255 " pdb=" N GLU A1256 " pdb=" CA GLU A1256 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB CYS A 72 " pdb=" SG CYS A 72 " pdb=" SG CYS A 93 " pdb=" CB CYS A 93 " ideal model delta sinusoidal sigma weight residual 93.00 122.75 -29.75 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CA VAL A 743 " pdb=" C VAL A 743 " pdb=" N PRO A 744 " pdb=" CA PRO A 744 " ideal model delta harmonic sigma weight residual 180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 14379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2069 0.053 - 0.106: 223 0.106 - 0.159: 110 0.159 - 0.212: 0 0.212 - 0.266: 2 Chirality restraints: 2404 Sorted by residual: chirality pdb=" C1 NAG A2418 " pdb=" ND2 ASN A1696 " pdb=" C2 NAG A2418 " pdb=" O5 NAG A2418 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG A2414 " pdb=" ND2 ASN A1110 " pdb=" C2 NAG A2414 " pdb=" O5 NAG A2414 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A1123 " pdb=" N ILE A1123 " pdb=" C ILE A1123 " pdb=" CB ILE A1123 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2401 not shown) Planarity restraints: 4291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1159 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A1160 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1160 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1160 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1127 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A1128 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1128 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1128 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 574 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 575 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 575 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 575 " 0.018 5.00e-02 4.00e+02 ... (remaining 4288 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 16527 2.44 - 2.98: 63914 2.98 - 3.52: 71651 3.52 - 4.06: 100979 4.06 - 4.60: 144469 Nonbonded interactions: 397540 Sorted by model distance: nonbonded pdb=" H THR A1566 " pdb=" HG1 THR A1566 " model vdw 1.904 2.100 nonbonded pdb=" H THR A 643 " pdb=" HG1 THR A 668 " model vdw 1.915 2.100 nonbonded pdb=" H THR A 171 " pdb=" HG1 THR A 197 " model vdw 1.925 2.100 nonbonded pdb=" HD3 ARG A 475 " pdb="HH11 ARG A 475 " model vdw 1.930 2.270 nonbonded pdb=" H THR A 35 " pdb=" HG1 THR A 35 " model vdw 1.938 2.100 ... (remaining 397535 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } 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: 5.550 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: 0.150 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.400 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.032 15226 Z= 0.123 Angle : 0.547 7.140 20826 Z= 0.309 Chirality : 0.043 0.266 2404 Planarity : 0.003 0.036 2578 Dihedral : 8.815 85.186 5964 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.25 % Allowed : 1.99 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1770 helix: 3.38 (0.66), residues: 65 sheet: -1.45 (0.21), residues: 611 loop : -0.35 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.007 0.001 TYR A 701 PHE 0.008 0.001 PHE A1310 TRP 0.006 0.001 TRP A 848 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00230 (15177) covalent geometry : angle 0.52929 (20694) SS BOND : bond 0.00169 ( 15) SS BOND : angle 0.66142 ( 30) hydrogen bonds : bond 0.22552 ( 445) hydrogen bonds : angle 11.26170 ( 1191) link_BETA1-4 : bond 0.00607 ( 5) link_BETA1-4 : angle 1.72134 ( 15) link_NAG-ASN : bond 0.00325 ( 29) link_NAG-ASN : angle 2.06660 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.8242 (tpp) cc_final: 0.7780 (tpp) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2538 time to fit residues: 20.0663 Evaluate side-chains 36 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 1134 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.080621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047214 restraints weight = 166434.176| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.45 r_work: 0.2965 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15226 Z= 0.152 Angle : 0.514 6.082 20826 Z= 0.267 Chirality : 0.044 0.229 2404 Planarity : 0.004 0.037 2578 Dihedral : 5.013 57.456 2642 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.50 % Allowed : 2.67 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1770 helix: 3.32 (0.68), residues: 65 sheet: -1.33 (0.20), residues: 657 loop : -0.35 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1333 TYR 0.010 0.001 TYR A1311 PHE 0.009 0.001 PHE A1090 TRP 0.013 0.001 TRP A1701 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00337 (15177) covalent geometry : angle 0.49863 (20694) SS BOND : bond 0.00178 ( 15) SS BOND : angle 1.01612 ( 30) hydrogen bonds : bond 0.05276 ( 445) hydrogen bonds : angle 7.80064 ( 1191) link_BETA1-4 : bond 0.00337 ( 5) link_BETA1-4 : angle 1.28635 ( 15) link_NAG-ASN : bond 0.00282 ( 29) link_NAG-ASN : angle 1.89021 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.8670 (tpp) cc_final: 0.8093 (tpp) REVERT: A 1319 MET cc_start: 0.8374 (tmm) cc_final: 0.8061 (tmm) REVERT: A 1752 MET cc_start: 0.7626 (mmm) cc_final: 0.7399 (mmm) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.2423 time to fit residues: 16.6537 Evaluate side-chains 39 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1338 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 3.9990 chunk 165 optimal weight: 0.0770 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.079852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047614 restraints weight = 166566.920| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.87 r_work: 0.2922 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15226 Z= 0.252 Angle : 0.542 6.665 20826 Z= 0.279 Chirality : 0.044 0.219 2404 Planarity : 0.004 0.041 2578 Dihedral : 5.285 56.366 2642 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.50 % Allowed : 3.42 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1770 helix: 2.46 (0.66), residues: 71 sheet: -1.44 (0.20), residues: 678 loop : -0.56 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.013 0.001 TYR A1311 PHE 0.014 0.001 PHE A 918 TRP 0.012 0.001 TRP A 848 HIS 0.005 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00561 (15177) covalent geometry : angle 0.52524 (20694) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.98089 ( 30) hydrogen bonds : bond 0.04135 ( 445) hydrogen bonds : angle 7.00282 ( 1191) link_BETA1-4 : bond 0.00275 ( 5) link_BETA1-4 : angle 1.35820 ( 15) link_NAG-ASN : bond 0.00340 ( 29) link_NAG-ASN : angle 1.99973 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8353 (tpt) cc_final: 0.8110 (tpt) REVERT: A 1319 MET cc_start: 0.8449 (tmm) cc_final: 0.8189 (tmm) REVERT: A 1752 MET cc_start: 0.8206 (mmm) cc_final: 0.7936 (mmm) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.2471 time to fit residues: 16.4077 Evaluate side-chains 40 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1338 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 34 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.080686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047430 restraints weight = 165179.091| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.42 r_work: 0.2971 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15226 Z= 0.116 Angle : 0.487 7.028 20826 Z= 0.248 Chirality : 0.044 0.221 2404 Planarity : 0.003 0.039 2578 Dihedral : 5.093 55.971 2642 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.44 % Allowed : 3.85 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1770 helix: 2.69 (0.67), residues: 71 sheet: -1.27 (0.20), residues: 658 loop : -0.49 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.012 0.001 TYR A1311 PHE 0.009 0.001 PHE A1230 TRP 0.013 0.001 TRP A1701 HIS 0.002 0.001 HIS A1652 Details of bonding type rmsd covalent geometry : bond 0.00262 (15177) covalent geometry : angle 0.47259 (20694) SS BOND : bond 0.00185 ( 15) SS BOND : angle 0.81291 ( 30) hydrogen bonds : bond 0.03419 ( 445) hydrogen bonds : angle 6.50566 ( 1191) link_BETA1-4 : bond 0.00344 ( 5) link_BETA1-4 : angle 1.16015 ( 15) link_NAG-ASN : bond 0.00266 ( 29) link_NAG-ASN : angle 1.79214 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 1319 MET cc_start: 0.8597 (tmm) cc_final: 0.8110 (tmm) REVERT: A 1752 MET cc_start: 0.8165 (mmm) cc_final: 0.7804 (mmm) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.2601 time to fit residues: 17.2624 Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1338 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.080264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047026 restraints weight = 166600.063| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.39 r_work: 0.2961 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15226 Z= 0.172 Angle : 0.493 6.078 20826 Z= 0.252 Chirality : 0.044 0.216 2404 Planarity : 0.003 0.040 2578 Dihedral : 5.115 55.802 2642 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.44 % Allowed : 4.10 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1770 helix: 2.63 (0.66), residues: 71 sheet: -1.33 (0.19), residues: 682 loop : -0.49 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 475 TYR 0.013 0.001 TYR A1311 PHE 0.011 0.001 PHE A 918 TRP 0.012 0.001 TRP A1701 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00387 (15177) covalent geometry : angle 0.47925 (20694) SS BOND : bond 0.00186 ( 15) SS BOND : angle 0.81271 ( 30) hydrogen bonds : bond 0.03284 ( 445) hydrogen bonds : angle 6.30953 ( 1191) link_BETA1-4 : bond 0.00280 ( 5) link_BETA1-4 : angle 1.23478 ( 15) link_NAG-ASN : bond 0.00263 ( 29) link_NAG-ASN : angle 1.72795 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7056 (t80) REVERT: A 1319 MET cc_start: 0.8625 (tmm) cc_final: 0.8306 (tmm) REVERT: A 1752 MET cc_start: 0.8289 (mmm) cc_final: 0.7895 (mmm) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.2391 time to fit residues: 16.2563 Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1338 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 0.0020 chunk 153 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 172 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.080656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048642 restraints weight = 165480.101| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.83 r_work: 0.2958 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15226 Z= 0.113 Angle : 0.474 6.168 20826 Z= 0.241 Chirality : 0.044 0.217 2404 Planarity : 0.003 0.040 2578 Dihedral : 4.991 55.821 2642 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.44 % Allowed : 4.35 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1770 helix: 2.76 (0.67), residues: 71 sheet: -1.18 (0.20), residues: 660 loop : -0.49 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.013 0.001 TYR A1311 PHE 0.011 0.001 PHE A1230 TRP 0.013 0.001 TRP A1701 HIS 0.002 0.000 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00256 (15177) covalent geometry : angle 0.46133 (20694) SS BOND : bond 0.00178 ( 15) SS BOND : angle 0.74964 ( 30) hydrogen bonds : bond 0.03081 ( 445) hydrogen bonds : angle 6.08900 ( 1191) link_BETA1-4 : bond 0.00312 ( 5) link_BETA1-4 : angle 1.16001 ( 15) link_NAG-ASN : bond 0.00257 ( 29) link_NAG-ASN : angle 1.65336 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.6984 (t80) REVERT: A 1319 MET cc_start: 0.8687 (tmm) cc_final: 0.8382 (tmm) REVERT: A 1752 MET cc_start: 0.8403 (mmm) cc_final: 0.8109 (mmm) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.2633 time to fit residues: 17.8091 Evaluate side-chains 40 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.080201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.048002 restraints weight = 166165.524| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.95 r_work: 0.2930 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15226 Z= 0.182 Angle : 0.489 5.801 20826 Z= 0.249 Chirality : 0.043 0.211 2404 Planarity : 0.003 0.041 2578 Dihedral : 5.040 56.112 2642 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.75 % Allowed : 4.16 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1770 helix: 2.80 (0.66), residues: 70 sheet: -1.24 (0.19), residues: 684 loop : -0.50 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.013 0.001 TYR A1311 PHE 0.012 0.001 PHE A 918 TRP 0.013 0.001 TRP A1701 HIS 0.003 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00411 (15177) covalent geometry : angle 0.47545 (20694) SS BOND : bond 0.00187 ( 15) SS BOND : angle 0.80263 ( 30) hydrogen bonds : bond 0.03110 ( 445) hydrogen bonds : angle 6.03377 ( 1191) link_BETA1-4 : bond 0.00255 ( 5) link_BETA1-4 : angle 1.22612 ( 15) link_NAG-ASN : bond 0.00266 ( 29) link_NAG-ASN : angle 1.69639 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7165 (t80) REVERT: A 1319 MET cc_start: 0.8668 (tmm) cc_final: 0.8356 (tmm) REVERT: A 1646 PHE cc_start: 0.8435 (m-80) cc_final: 0.7756 (m-80) REVERT: A 1752 MET cc_start: 0.8383 (mmm) cc_final: 0.8090 (mmm) outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 0.2382 time to fit residues: 17.9401 Evaluate side-chains 42 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 8 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.0970 chunk 65 optimal weight: 0.2980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.080215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047066 restraints weight = 166143.684| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.38 r_work: 0.2961 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15226 Z= 0.170 Angle : 0.489 6.536 20826 Z= 0.249 Chirality : 0.044 0.210 2404 Planarity : 0.003 0.042 2578 Dihedral : 5.049 55.913 2642 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.75 % Allowed : 4.54 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1770 helix: 2.77 (0.66), residues: 70 sheet: -1.21 (0.19), residues: 684 loop : -0.50 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.013 0.001 TYR A1311 PHE 0.015 0.001 PHE A1230 TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00382 (15177) covalent geometry : angle 0.47595 (20694) SS BOND : bond 0.00191 ( 15) SS BOND : angle 0.75340 ( 30) hydrogen bonds : bond 0.03066 ( 445) hydrogen bonds : angle 5.94303 ( 1191) link_BETA1-4 : bond 0.00263 ( 5) link_BETA1-4 : angle 1.20844 ( 15) link_NAG-ASN : bond 0.00248 ( 29) link_NAG-ASN : angle 1.70376 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 1319 MET cc_start: 0.8581 (tmm) cc_final: 0.8247 (tmm) REVERT: A 1646 PHE cc_start: 0.8365 (m-80) cc_final: 0.7683 (m-80) REVERT: A 1752 MET cc_start: 0.8379 (mmm) cc_final: 0.8061 (mmm) outliers start: 12 outliers final: 10 residues processed: 43 average time/residue: 0.2382 time to fit residues: 17.2879 Evaluate side-chains 44 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 chunk 125 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.080297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047146 restraints weight = 165729.571| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.41 r_work: 0.2963 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15226 Z= 0.152 Angle : 0.477 5.527 20826 Z= 0.242 Chirality : 0.043 0.208 2404 Planarity : 0.003 0.041 2578 Dihedral : 4.998 56.243 2642 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.62 % Allowed : 4.60 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1770 helix: 2.87 (0.66), residues: 70 sheet: -1.16 (0.19), residues: 690 loop : -0.49 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.014 0.001 TYR A1311 PHE 0.010 0.001 PHE A 918 TRP 0.017 0.001 TRP A1701 HIS 0.002 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00341 (15177) covalent geometry : angle 0.46449 (20694) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.75778 ( 30) hydrogen bonds : bond 0.02971 ( 445) hydrogen bonds : angle 5.82543 ( 1191) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 1.21026 ( 15) link_NAG-ASN : bond 0.00246 ( 29) link_NAG-ASN : angle 1.63120 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7050 (t80) REVERT: A 1319 MET cc_start: 0.8615 (tmm) cc_final: 0.8282 (tmm) REVERT: A 1646 PHE cc_start: 0.8361 (m-80) cc_final: 0.7679 (m-80) REVERT: A 1752 MET cc_start: 0.8396 (mmm) cc_final: 0.8078 (mmm) outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.2255 time to fit residues: 15.5651 Evaluate side-chains 43 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 117 optimal weight: 9.9990 chunk 20 optimal weight: 0.0670 chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.080581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.047609 restraints weight = 164884.505| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.38 r_work: 0.2981 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15226 Z= 0.102 Angle : 0.467 8.643 20826 Z= 0.235 Chirality : 0.044 0.208 2404 Planarity : 0.003 0.039 2578 Dihedral : 4.856 56.190 2642 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.50 % Allowed : 4.79 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1770 helix: 3.01 (0.67), residues: 70 sheet: -1.05 (0.20), residues: 681 loop : -0.41 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.013 0.001 TYR A1311 PHE 0.007 0.001 PHE A 918 TRP 0.020 0.001 TRP A1701 HIS 0.002 0.001 HIS A1652 Details of bonding type rmsd covalent geometry : bond 0.00231 (15177) covalent geometry : angle 0.45541 (20694) SS BOND : bond 0.00177 ( 15) SS BOND : angle 0.70322 ( 30) hydrogen bonds : bond 0.02849 ( 445) hydrogen bonds : angle 5.69178 ( 1191) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 1.14743 ( 15) link_NAG-ASN : bond 0.00247 ( 29) link_NAG-ASN : angle 1.55461 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 1319 MET cc_start: 0.8637 (tmm) cc_final: 0.8295 (tmm) REVERT: A 1646 PHE cc_start: 0.8375 (m-80) cc_final: 0.7721 (m-80) REVERT: A 1752 MET cc_start: 0.8383 (mmm) cc_final: 0.8062 (mmm) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.2717 time to fit residues: 17.9213 Evaluate side-chains 42 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 1000 CYS Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 158 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.080380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047358 restraints weight = 166241.125| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.40 r_work: 0.2972 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15226 Z= 0.131 Angle : 0.469 8.031 20826 Z= 0.237 Chirality : 0.043 0.206 2404 Planarity : 0.003 0.039 2578 Dihedral : 4.823 56.079 2642 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.62 % Allowed : 4.54 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1770 helix: 3.02 (0.67), residues: 70 sheet: -1.07 (0.20), residues: 681 loop : -0.44 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.013 0.001 TYR A1311 PHE 0.009 0.001 PHE A 918 TRP 0.018 0.001 TRP A1701 HIS 0.002 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00297 (15177) covalent geometry : angle 0.45715 (20694) SS BOND : bond 0.00179 ( 15) SS BOND : angle 0.70548 ( 30) hydrogen bonds : bond 0.02850 ( 445) hydrogen bonds : angle 5.64055 ( 1191) link_BETA1-4 : bond 0.00270 ( 5) link_BETA1-4 : angle 1.19884 ( 15) link_NAG-ASN : bond 0.00237 ( 29) link_NAG-ASN : angle 1.56535 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9078.25 seconds wall clock time: 154 minutes 27.52 seconds (9267.52 seconds total)