Starting phenix.real_space_refine on Wed Mar 4 12:48:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzt_66408/03_2026/9wzt_66408.map" } resolution = 3.64 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= 0.007 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 P 1 5.49 5 S 77 5.16 5 C 8544 2.51 5 N 2104 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 12952 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1526, 12473 Classifications: {'peptide': 1526} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1455} Chain breaks: 10 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: "A" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 451 Unusual residues: {'AV0': 2, 'ERG': 9, 'POV': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 2.98, per 1000 atoms: 0.23 Number of scatterers: 12952 At special positions: 0 Unit cell: (99.9, 129.5, 119.14, 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 77 16.00 P 1 15.00 O 2226 8.00 N 2104 7.00 C 8544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 688 " distance=2.02 Simple disulfide: pdb=" SG CYS A1347 " - pdb=" SG CYS A1364 " distance=2.03 Simple disulfide: pdb=" SG CYS A1698 " - pdb=" SG CYS A1701 " distance=2.04 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 C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN A1868 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 495.5 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 3 sheets defined 66.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.835A pdb=" N THR A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.633A pdb=" N LYS A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.733A pdb=" N ILE A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 3.552A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 334 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 340 through 356 removed outlier: 3.593A pdb=" N ASP A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 402 through 406 removed outlier: 4.044A pdb=" N VAL A 406 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 removed outlier: 3.840A pdb=" N LEU A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.636A pdb=" N ILE A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.504A pdb=" N ASP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.587A pdb=" N LEU A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 489 removed outlier: 3.629A pdb=" N TRP A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.679A pdb=" N PHE A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 537 removed outlier: 3.804A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 570 removed outlier: 3.598A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Proline residue: A 564 - end of helix removed outlier: 3.882A pdb=" N PHE A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 602 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 634 through 659 removed outlier: 3.826A pdb=" N TRP A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 663 through 671 removed outlier: 3.504A pdb=" N ARG A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 690 through 731 removed outlier: 3.533A pdb=" N ALA A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.402A pdb=" N TYR A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 782 removed outlier: 3.564A pdb=" N LEU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.718A pdb=" N LYS A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 817 removed outlier: 3.714A pdb=" N VAL A 816 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 845 removed outlier: 3.698A pdb=" N LEU A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 899 through 912 Processing helix chain 'A' and resid 953 through 965 Processing helix chain 'A' and resid 968 through 977 removed outlier: 3.930A pdb=" N THR A 972 " --> pdb=" O THR A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 991 removed outlier: 4.028A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.459A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1016 removed outlier: 3.716A pdb=" N GLU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1106 through 1111 removed outlier: 3.531A pdb=" N ILE A1110 " --> pdb=" O HIS A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.509A pdb=" N ALA A1139 " --> pdb=" O ARG A1135 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1199 Processing helix chain 'A' and resid 1199 through 1207 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.795A pdb=" N THR A1225 " --> pdb=" O THR A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1252 Processing helix chain 'A' and resid 1286 through 1290 removed outlier: 3.717A pdb=" N MET A1289 " --> pdb=" O GLY A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 3.662A pdb=" N TYR A1295 " --> pdb=" O SER A1291 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A1300 " --> pdb=" O TYR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1311 removed outlier: 3.684A pdb=" N THR A1308 " --> pdb=" O ASP A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1343 removed outlier: 4.151A pdb=" N HIS A1317 " --> pdb=" O HIS A1313 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1321 " --> pdb=" O HIS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1388 removed outlier: 3.502A pdb=" N TRP A1373 " --> pdb=" O PRO A1369 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A1374 " --> pdb=" O ALA A1370 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG A1375 " --> pdb=" O ILE A1371 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A1385 " --> pdb=" O ILE A1381 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A1386 " --> pdb=" O PHE A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1400 removed outlier: 3.930A pdb=" N VAL A1393 " --> pdb=" O PHE A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1411 Processing helix chain 'A' and resid 1456 through 1465 removed outlier: 3.516A pdb=" N PHE A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1486 removed outlier: 3.741A pdb=" N ARG A1474 " --> pdb=" O TYR A1470 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1475 " --> pdb=" O MET A1471 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A1486 " --> pdb=" O GLY A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1491 through 1507 removed outlier: 3.531A pdb=" N TRP A1495 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1500 " --> pdb=" O ALA A1496 " (cutoff:3.500A) Proline residue: A1505 - end of helix Processing helix chain 'A' and resid 1516 through 1530 removed outlier: 3.773A pdb=" N LEU A1520 " --> pdb=" O GLU A1516 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A1530 " --> pdb=" O ILE A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1578 through 1602 removed outlier: 3.517A pdb=" N ILE A1584 " --> pdb=" O ILE A1580 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A1585 " --> pdb=" O MET A1581 " (cutoff:3.500A) Proline residue: A1586 - end of helix removed outlier: 3.514A pdb=" N CYS A1594 " --> pdb=" O TYR A1590 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1597 " --> pdb=" O GLY A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1645 removed outlier: 3.823A pdb=" N ILE A1622 " --> pdb=" O THR A1618 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS A1624 " --> pdb=" O ARG A1620 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A1627 " --> pdb=" O ILE A1623 " (cutoff:3.500A) Proline residue: A1628 - end of helix Processing helix chain 'A' and resid 1646 through 1654 removed outlier: 4.227A pdb=" N MET A1652 " --> pdb=" O PRO A1648 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A1653 " --> pdb=" O LEU A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1684 removed outlier: 3.810A pdb=" N VAL A1660 " --> pdb=" O LYS A1656 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1671 " --> pdb=" O GLY A1667 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A1681 " --> pdb=" O PHE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1713 removed outlier: 3.567A pdb=" N ILE A1693 " --> pdb=" O VAL A1689 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A1698 " --> pdb=" O GLY A1694 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A1700 " --> pdb=" O VAL A1696 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS A1701 " --> pdb=" O THR A1697 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1703 " --> pdb=" O ILE A1699 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1711 " --> pdb=" O HIS A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1730 removed outlier: 4.208A pdb=" N ALA A1726 " --> pdb=" O HIS A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1773 removed outlier: 3.559A pdb=" N ARG A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A1757 " --> pdb=" O VAL A1753 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A1772 " --> pdb=" O VAL A1768 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A1773 " --> pdb=" O ILE A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1779 Processing helix chain 'A' and resid 1782 through 1794 Processing helix chain 'A' and resid 1805 through 1841 removed outlier: 3.542A pdb=" N LEU A1811 " --> pdb=" O LYS A1807 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A1817 " --> pdb=" O LYS A1813 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A1818 " --> pdb=" O ARG A1814 " (cutoff:3.500A) Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1852 through 1856 Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392 Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.658A pdb=" N THR A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 3.907A pdb=" N PHE A1087 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1052 " --> pdb=" O MET A1023 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 861 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A1020 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL A 863 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A1022 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 865 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A1119 " --> pdb=" O ASP A1216 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP A1216 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A1168 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A1167 " --> pdb=" O ARG A1254 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LYS A1256 " --> pdb=" O VAL A1167 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A1169 " --> pdb=" O LYS A1256 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS A1258 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY A1171 " --> pdb=" O CYS A1258 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR A1260 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG A1173 " --> pdb=" O TYR A1260 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A1262 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A1175 " --> pdb=" O GLN A1262 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY A1264 " --> pdb=" O TYR A1175 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1905 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: 2.42 Time building geometry restraints manager: 1.60 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: 2297 1.33 - 1.45: 3555 1.45 - 1.57: 7352 1.57 - 1.69: 6 1.69 - 1.82: 123 Bond restraints: 13333 Sorted by residual: bond pdb=" N LYS A1353 " pdb=" CA LYS A1353 " ideal model delta sigma weight residual 1.458 1.487 -0.030 7.40e-03 1.83e+04 1.60e+01 bond pdb=" C LYS A1353 " pdb=" O LYS A1353 " ideal model delta sigma weight residual 1.235 1.251 -0.016 4.70e-03 4.53e+04 1.23e+01 bond pdb=" N ILE A1096 " pdb=" CA ILE A1096 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.08e+01 bond pdb=" N TRP A1742 " pdb=" CA TRP A1742 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.09e+00 bond pdb=" N ILE A1355 " pdb=" CA ILE A1355 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.99e+00 ... (remaining 13328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 17579 1.98 - 3.95: 458 3.95 - 5.93: 73 5.93 - 7.90: 11 7.90 - 9.88: 7 Bond angle restraints: 18128 Sorted by residual: angle pdb=" N ILE A1699 " pdb=" CA ILE A1699 " pdb=" C ILE A1699 " ideal model delta sigma weight residual 111.05 103.78 7.27 1.25e+00 6.40e-01 3.38e+01 angle pdb=" CA GLY A 679 " pdb=" C GLY A 679 " pdb=" O GLY A 679 " ideal model delta sigma weight residual 122.33 118.21 4.12 8.10e-01 1.52e+00 2.59e+01 angle pdb=" N ASP A1352 " pdb=" CA ASP A1352 " pdb=" C ASP A1352 " ideal model delta sigma weight residual 112.93 107.66 5.27 1.12e+00 7.97e-01 2.21e+01 angle pdb=" N GLY A1363 " pdb=" CA GLY A1363 " pdb=" C GLY A1363 " ideal model delta sigma weight residual 115.72 108.96 6.76 1.51e+00 4.39e-01 2.00e+01 angle pdb=" N ARG A 744 " pdb=" CA ARG A 744 " pdb=" C ARG A 744 " ideal model delta sigma weight residual 113.18 108.07 5.11 1.21e+00 6.83e-01 1.79e+01 ... (remaining 18123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 7819 28.32 - 56.64: 500 56.64 - 84.96: 99 84.96 - 113.28: 48 113.28 - 141.61: 9 Dihedral angle restraints: 8475 sinusoidal: 4000 harmonic: 4475 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 688 " pdb=" CB CYS A 688 " ideal model delta sinusoidal sigma weight residual -86.00 -143.57 57.57 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA MET A 427 " pdb=" C MET A 427 " pdb=" N GLU A 428 " pdb=" CA GLU A 428 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" OAJ AV0 A1901 " pdb=" CBN AV0 A1901 " pdb=" CCD AV0 A1901 " pdb=" OBZ AV0 A1901 " ideal model delta sinusoidal sigma weight residual 64.90 -76.71 141.61 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 8472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1613 0.053 - 0.105: 318 0.105 - 0.158: 58 0.158 - 0.210: 15 0.210 - 0.263: 5 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CCR AV0 A1901 " pdb=" CCV AV0 A1901 " pdb=" O4 AV0 A1901 " pdb=" OBY AV0 A1901 " both_signs ideal model delta sigma weight residual False -2.24 -1.98 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ILE A1699 " pdb=" N ILE A1699 " pdb=" C ILE A1699 " pdb=" CB ILE A1699 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.36e+00 ... (remaining 2006 not shown) Planarity restraints: 2197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A1904 " -0.095 2.00e-02 2.50e+03 2.14e-01 4.56e+02 pdb=" C22 ERG A1904 " 0.286 2.00e-02 2.50e+03 pdb=" C23 ERG A1904 " -0.287 2.00e-02 2.50e+03 pdb=" C24 ERG A1904 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A1905 " 0.087 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C22 ERG A1905 " -0.245 2.00e-02 2.50e+03 pdb=" C23 ERG A1905 " 0.245 2.00e-02 2.50e+03 pdb=" C24 ERG A1905 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A1903 " -0.086 2.00e-02 2.50e+03 1.82e-01 3.33e+02 pdb=" C22 ERG A1903 " 0.243 2.00e-02 2.50e+03 pdb=" C23 ERG A1903 " -0.243 2.00e-02 2.50e+03 pdb=" C24 ERG A1903 " 0.087 2.00e-02 2.50e+03 ... (remaining 2194 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1310 2.75 - 3.28: 13184 3.28 - 3.82: 21015 3.82 - 4.36: 23742 4.36 - 4.90: 40718 Nonbonded interactions: 99969 Sorted by model distance: nonbonded pdb=" O ALA A1220 " pdb=" OG1 THR A1224 " model vdw 2.207 3.040 nonbonded pdb=" O LEU A 212 " pdb=" OG SER A 216 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 862 " pdb=" O ARG A1113 " model vdw 2.237 3.040 nonbonded pdb=" O THR A 520 " pdb=" OG SER A 523 " model vdw 2.271 3.040 nonbonded pdb=" O THR A1725 " pdb=" OG1 THR A1729 " model vdw 2.272 3.040 ... (remaining 99964 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.390 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.760 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.004 0.059 13338 Z= 0.290 Angle : 0.722 9.878 18140 Z= 0.425 Chirality : 0.046 0.263 2009 Planarity : 0.009 0.214 2196 Dihedral : 20.583 141.606 5580 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.82 % Allowed : 23.36 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.18 (0.22), residues: 1504 helix: 1.02 (0.18), residues: 872 sheet: 0.43 (0.80), residues: 46 loop : -1.27 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1747 TYR 0.021 0.001 TYR A 894 PHE 0.014 0.001 PHE A1385 TRP 0.023 0.001 TRP A 903 HIS 0.007 0.001 HIS A1313 Details of bonding type rmsd covalent geometry : bond 0.00435 (13333) covalent geometry : angle 0.72145 (18128) SS BOND : bond 0.00885 ( 3) SS BOND : angle 1.18761 ( 6) hydrogen bonds : bond 0.25779 ( 651) hydrogen bonds : angle 6.82514 ( 1905) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 1.54043 ( 3) link_NAG-ASN : bond 0.00281 ( 1) link_NAG-ASN : angle 1.09701 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1012 MET cc_start: 0.7692 (tmm) cc_final: 0.7371 (tmm) REVERT: A 1223 MET cc_start: 0.8290 (mmm) cc_final: 0.8028 (tpp) REVERT: A 1407 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6595 (tp40) REVERT: A 1590 TYR cc_start: 0.8626 (t80) cc_final: 0.8335 (t80) REVERT: A 1747 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7100 (tpt-90) outliers start: 11 outliers final: 2 residues processed: 218 average time/residue: 0.1178 time to fit residues: 36.9426 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 1670 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN A 784 HIS A 792 GLN A 899 HIS A1105 GLN A1161 GLN A1488 GLN A1767 HIS A1857 HIS A1858 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124819 restraints weight = 21897.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125690 restraints weight = 13308.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126877 restraints weight = 11360.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127357 restraints weight = 9295.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127459 restraints weight = 8922.234| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 13338 Z= 0.217 Angle : 0.754 13.578 18140 Z= 0.368 Chirality : 0.046 0.349 2009 Planarity : 0.005 0.044 2196 Dihedral : 15.332 123.496 2627 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 4.03 % Allowed : 21.79 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.38 (0.22), residues: 1504 helix: 1.26 (0.17), residues: 888 sheet: 0.45 (0.83), residues: 46 loop : -1.40 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1551 TYR 0.025 0.002 TYR A 381 PHE 0.018 0.002 PHE A 648 TRP 0.013 0.002 TRP A1495 HIS 0.008 0.001 HIS A1767 Details of bonding type rmsd covalent geometry : bond 0.00499 (13333) covalent geometry : angle 0.74758 (18128) SS BOND : bond 0.01382 ( 3) SS BOND : angle 5.61290 ( 6) hydrogen bonds : bond 0.07131 ( 651) hydrogen bonds : angle 4.98210 ( 1905) link_BETA1-4 : bond 0.00110 ( 1) link_BETA1-4 : angle 1.35252 ( 3) link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 0.46409 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 870 GLU cc_start: 0.7609 (mp0) cc_final: 0.7103 (mt-10) REVERT: A 1012 MET cc_start: 0.7696 (tmm) cc_final: 0.7283 (tmm) REVERT: A 1223 MET cc_start: 0.8144 (mmm) cc_final: 0.7822 (ttt) REVERT: A 1349 TYR cc_start: 0.8472 (t80) cc_final: 0.8208 (t80) REVERT: A 1680 MET cc_start: 0.8814 (tpp) cc_final: 0.8562 (tpp) outliers start: 54 outliers final: 34 residues processed: 228 average time/residue: 0.1063 time to fit residues: 35.9503 Evaluate side-chains 204 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 790 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1670 VAL Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1829 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.159410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127733 restraints weight = 21541.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129287 restraints weight = 13496.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130433 restraints weight = 10184.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130902 restraints weight = 8699.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131321 restraints weight = 8078.241| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13338 Z= 0.142 Angle : 0.659 12.903 18140 Z= 0.315 Chirality : 0.043 0.508 2009 Planarity : 0.004 0.042 2196 Dihedral : 12.312 114.844 2627 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 4.63 % Allowed : 22.69 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.70 (0.22), residues: 1504 helix: 1.54 (0.17), residues: 885 sheet: 0.31 (0.83), residues: 46 loop : -1.26 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1551 TYR 0.016 0.001 TYR A 381 PHE 0.013 0.001 PHE A 648 TRP 0.012 0.001 TRP A1495 HIS 0.006 0.001 HIS A1313 Details of bonding type rmsd covalent geometry : bond 0.00307 (13333) covalent geometry : angle 0.64912 (18128) SS BOND : bond 0.00481 ( 3) SS BOND : angle 6.19109 ( 6) hydrogen bonds : bond 0.05957 ( 651) hydrogen bonds : angle 4.59245 ( 1905) link_BETA1-4 : bond 0.00053 ( 1) link_BETA1-4 : angle 1.54965 ( 3) link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 0.51071 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 251 MET cc_start: 0.7431 (tpp) cc_final: 0.7062 (tpp) REVERT: A 689 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: A 759 MET cc_start: 0.6497 (mmm) cc_final: 0.6285 (mmm) REVERT: A 870 GLU cc_start: 0.7595 (mp0) cc_final: 0.7152 (mt-10) REVERT: A 1012 MET cc_start: 0.7570 (tmm) cc_final: 0.7081 (tmm) REVERT: A 1070 LEU cc_start: 0.7934 (tp) cc_final: 0.7351 (tp) REVERT: A 1223 MET cc_start: 0.8066 (mmm) cc_final: 0.7733 (ttt) REVERT: A 1349 TYR cc_start: 0.8548 (t80) cc_final: 0.8336 (t80) REVERT: A 1638 PHE cc_start: 0.7881 (t80) cc_final: 0.6740 (m-80) REVERT: A 1684 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7843 (mm-30) outliers start: 62 outliers final: 30 residues processed: 236 average time/residue: 0.1060 time to fit residues: 37.0887 Evaluate side-chains 209 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 790 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1682 VAL Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1790 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 GLN A1707 HIS A1767 HIS A1873 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.156021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123499 restraints weight = 21927.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125005 restraints weight = 13778.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126546 restraints weight = 10472.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126967 restraints weight = 8757.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127592 restraints weight = 8713.481| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 13338 Z= 0.171 Angle : 0.649 10.991 18140 Z= 0.314 Chirality : 0.044 0.515 2009 Planarity : 0.004 0.047 2196 Dihedral : 10.742 106.759 2623 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.75 % Allowed : 22.09 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.71 (0.22), residues: 1504 helix: 1.59 (0.17), residues: 883 sheet: 0.16 (0.82), residues: 46 loop : -1.30 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.012 0.001 TYR A1377 PHE 0.018 0.002 PHE A 454 TRP 0.010 0.001 TRP A 308 HIS 0.008 0.001 HIS A1767 Details of bonding type rmsd covalent geometry : bond 0.00398 (13333) covalent geometry : angle 0.64790 (18128) SS BOND : bond 0.00726 ( 3) SS BOND : angle 2.17667 ( 6) hydrogen bonds : bond 0.05796 ( 651) hydrogen bonds : angle 4.46569 ( 1905) link_BETA1-4 : bond 0.00035 ( 1) link_BETA1-4 : angle 1.92362 ( 3) link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 0.62714 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 400 GLU cc_start: 0.8170 (pm20) cc_final: 0.7864 (tm-30) REVERT: A 553 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: A 558 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8532 (ttp) REVERT: A 759 MET cc_start: 0.6483 (mmm) cc_final: 0.6247 (mmm) REVERT: A 870 GLU cc_start: 0.7628 (mp0) cc_final: 0.7136 (mt-10) REVERT: A 1012 MET cc_start: 0.7649 (tmm) cc_final: 0.7047 (tmm) REVERT: A 1070 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7627 (tp) REVERT: A 1084 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7282 (ptm-80) REVERT: A 1104 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6470 (t0) REVERT: A 1132 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 1223 MET cc_start: 0.8128 (mmm) cc_final: 0.7864 (ttt) REVERT: A 1471 MET cc_start: 0.7864 (tpp) cc_final: 0.7652 (tpp) REVERT: A 1638 PHE cc_start: 0.7959 (t80) cc_final: 0.6757 (m-80) REVERT: A 1747 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7535 (ttt180) REVERT: A 1755 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7672 (tp30) outliers start: 77 outliers final: 45 residues processed: 239 average time/residue: 0.0972 time to fit residues: 35.0558 Evaluate side-chains 228 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 790 HIS Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1084 ARG Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1682 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1755 GLU Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1828 ILE Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.158057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126274 restraints weight = 21805.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127964 restraints weight = 13488.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129457 restraints weight = 10181.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129911 restraints weight = 8444.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130575 restraints weight = 8351.772| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 13338 Z= 0.134 Angle : 0.629 10.771 18140 Z= 0.300 Chirality : 0.043 0.531 2009 Planarity : 0.004 0.060 2196 Dihedral : 10.148 104.088 2623 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.88 % Allowed : 24.33 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1504 helix: 1.68 (0.17), residues: 890 sheet: 0.16 (0.81), residues: 46 loop : -1.18 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 748 TYR 0.018 0.001 TYR A1349 PHE 0.016 0.001 PHE A 454 TRP 0.010 0.001 TRP A1495 HIS 0.006 0.001 HIS A1767 Details of bonding type rmsd covalent geometry : bond 0.00303 (13333) covalent geometry : angle 0.62770 (18128) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.50928 ( 6) hydrogen bonds : bond 0.05250 ( 651) hydrogen bonds : angle 4.30537 ( 1905) link_BETA1-4 : bond 0.00122 ( 1) link_BETA1-4 : angle 1.85249 ( 3) link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 0.50208 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8836 (mt) REVERT: A 251 MET cc_start: 0.7455 (tpp) cc_final: 0.7205 (tpp) REVERT: A 558 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8490 (ttp) REVERT: A 689 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7866 (mtpt) REVERT: A 759 MET cc_start: 0.6387 (mmm) cc_final: 0.6156 (mmm) REVERT: A 870 GLU cc_start: 0.7642 (mp0) cc_final: 0.7170 (mt-10) REVERT: A 1012 MET cc_start: 0.7664 (tmm) cc_final: 0.7022 (tmm) REVERT: A 1084 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7209 (ptm-80) REVERT: A 1132 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 1223 MET cc_start: 0.8082 (mmm) cc_final: 0.7810 (ttt) REVERT: A 1471 MET cc_start: 0.7915 (tpp) cc_final: 0.7686 (tpp) REVERT: A 1638 PHE cc_start: 0.8014 (t80) cc_final: 0.6809 (m-80) REVERT: A 1747 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7486 (ttt180) outliers start: 52 outliers final: 35 residues processed: 219 average time/residue: 0.0964 time to fit residues: 32.1422 Evaluate side-chains 218 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1084 ARG Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1828 ILE Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A1036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125641 restraints weight = 21487.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.127892 restraints weight = 13169.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129108 restraints weight = 9933.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129360 restraints weight = 8185.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129454 restraints weight = 8107.349| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 13338 Z= 0.132 Angle : 0.619 10.576 18140 Z= 0.295 Chirality : 0.043 0.473 2009 Planarity : 0.004 0.044 2196 Dihedral : 9.593 102.167 2623 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 5.07 % Allowed : 23.51 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.22), residues: 1504 helix: 1.71 (0.17), residues: 891 sheet: 0.13 (0.81), residues: 46 loop : -1.16 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1576 TYR 0.012 0.001 TYR A 485 PHE 0.013 0.001 PHE A 454 TRP 0.011 0.001 TRP A1495 HIS 0.004 0.001 HIS A1313 Details of bonding type rmsd covalent geometry : bond 0.00302 (13333) covalent geometry : angle 0.61836 (18128) SS BOND : bond 0.00473 ( 3) SS BOND : angle 1.29455 ( 6) hydrogen bonds : bond 0.04985 ( 651) hydrogen bonds : angle 4.22064 ( 1905) link_BETA1-4 : bond 0.00106 ( 1) link_BETA1-4 : angle 1.91928 ( 3) link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 0.52300 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 186 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8853 (mt) REVERT: A 251 MET cc_start: 0.7369 (tpp) cc_final: 0.7078 (tpp) REVERT: A 558 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8440 (ttp) REVERT: A 759 MET cc_start: 0.6313 (mmm) cc_final: 0.5990 (mmt) REVERT: A 870 GLU cc_start: 0.7562 (mp0) cc_final: 0.7160 (mt-10) REVERT: A 902 GLU cc_start: 0.7347 (tp30) cc_final: 0.7123 (tp30) REVERT: A 977 MET cc_start: 0.7474 (mmm) cc_final: 0.7117 (tpp) REVERT: A 1012 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: A 1132 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 1223 MET cc_start: 0.8077 (mmm) cc_final: 0.7780 (ttt) REVERT: A 1471 MET cc_start: 0.7912 (tpp) cc_final: 0.7605 (tpp) REVERT: A 1638 PHE cc_start: 0.8019 (t80) cc_final: 0.6849 (m-80) outliers start: 68 outliers final: 46 residues processed: 231 average time/residue: 0.0922 time to fit residues: 32.6565 Evaluate side-chains 225 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A1767 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127240 restraints weight = 21477.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129124 restraints weight = 13158.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130445 restraints weight = 9963.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130825 restraints weight = 8349.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130920 restraints weight = 8203.017| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 13338 Z= 0.126 Angle : 0.624 11.357 18140 Z= 0.297 Chirality : 0.042 0.294 2009 Planarity : 0.004 0.043 2196 Dihedral : 9.303 101.125 2623 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 4.33 % Allowed : 24.55 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.96 (0.22), residues: 1504 helix: 1.76 (0.17), residues: 889 sheet: 0.17 (0.80), residues: 46 loop : -1.17 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1551 TYR 0.013 0.001 TYR A 485 PHE 0.014 0.001 PHE A 454 TRP 0.009 0.001 TRP A1495 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00289 (13333) covalent geometry : angle 0.62294 (18128) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.18341 ( 6) hydrogen bonds : bond 0.04809 ( 651) hydrogen bonds : angle 4.16374 ( 1905) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.90954 ( 3) link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 0.52633 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 251 MET cc_start: 0.7336 (tpp) cc_final: 0.7035 (tpp) REVERT: A 558 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: A 759 MET cc_start: 0.6276 (mmm) cc_final: 0.5965 (mmt) REVERT: A 870 GLU cc_start: 0.7633 (mp0) cc_final: 0.7221 (mt-10) REVERT: A 902 GLU cc_start: 0.7355 (tp30) cc_final: 0.7111 (tp30) REVERT: A 977 MET cc_start: 0.7459 (mmm) cc_final: 0.7107 (tpp) REVERT: A 1012 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6963 (tmm) REVERT: A 1104 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6543 (t0) REVERT: A 1132 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 1223 MET cc_start: 0.8057 (mmm) cc_final: 0.7716 (ttt) REVERT: A 1471 MET cc_start: 0.7907 (tpp) cc_final: 0.7590 (tpp) REVERT: A 1638 PHE cc_start: 0.8019 (t80) cc_final: 0.6805 (m-80) REVERT: A 1650 LEU cc_start: 0.8808 (mp) cc_final: 0.8145 (tt) REVERT: A 1747 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7436 (ttt180) outliers start: 58 outliers final: 42 residues processed: 226 average time/residue: 0.0973 time to fit residues: 33.7462 Evaluate side-chains 225 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 115 optimal weight: 0.0370 chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129226 restraints weight = 21392.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131051 restraints weight = 12884.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132376 restraints weight = 9940.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132741 restraints weight = 8315.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132866 restraints weight = 8149.897| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 13338 Z= 0.118 Angle : 0.622 11.859 18140 Z= 0.295 Chirality : 0.041 0.266 2009 Planarity : 0.004 0.043 2196 Dihedral : 9.098 99.609 2623 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 3.21 % Allowed : 25.67 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.22), residues: 1504 helix: 1.84 (0.17), residues: 891 sheet: 0.18 (0.79), residues: 46 loop : -1.12 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.016 0.001 TYR A1525 PHE 0.015 0.001 PHE A 454 TRP 0.010 0.001 TRP A1495 HIS 0.003 0.001 HIS A1338 Details of bonding type rmsd covalent geometry : bond 0.00267 (13333) covalent geometry : angle 0.62121 (18128) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.02082 ( 6) hydrogen bonds : bond 0.04472 ( 651) hydrogen bonds : angle 4.05555 ( 1905) link_BETA1-4 : bond 0.00157 ( 1) link_BETA1-4 : angle 1.84539 ( 3) link_NAG-ASN : bond 0.00283 ( 1) link_NAG-ASN : angle 0.57244 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8415 (ttp) REVERT: A 759 MET cc_start: 0.6247 (mmm) cc_final: 0.5942 (mmt) REVERT: A 870 GLU cc_start: 0.7625 (mp0) cc_final: 0.7205 (mt-10) REVERT: A 1012 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6875 (tmm) REVERT: A 1132 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 1223 MET cc_start: 0.8089 (mmm) cc_final: 0.7677 (ttt) REVERT: A 1471 MET cc_start: 0.7876 (tpp) cc_final: 0.7566 (tpp) REVERT: A 1638 PHE cc_start: 0.8009 (t80) cc_final: 0.6780 (m-80) REVERT: A 1650 LEU cc_start: 0.8857 (mp) cc_final: 0.8187 (tt) REVERT: A 1684 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7759 (mm-30) outliers start: 43 outliers final: 33 residues processed: 222 average time/residue: 0.0974 time to fit residues: 32.6248 Evaluate side-chains 219 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 149 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1148 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.157990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127025 restraints weight = 21459.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129196 restraints weight = 12685.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130316 restraints weight = 9695.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130573 restraints weight = 8007.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130706 restraints weight = 7914.502| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 13338 Z= 0.148 Angle : 0.656 11.441 18140 Z= 0.312 Chirality : 0.042 0.286 2009 Planarity : 0.004 0.041 2196 Dihedral : 9.193 98.735 2623 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 3.81 % Allowed : 25.60 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.96 (0.22), residues: 1504 helix: 1.75 (0.17), residues: 891 sheet: 0.12 (0.78), residues: 46 loop : -1.16 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1551 TYR 0.014 0.001 TYR A 485 PHE 0.017 0.001 PHE A 454 TRP 0.008 0.001 TRP A 475 HIS 0.004 0.001 HIS A1313 Details of bonding type rmsd covalent geometry : bond 0.00350 (13333) covalent geometry : angle 0.65486 (18128) SS BOND : bond 0.00482 ( 3) SS BOND : angle 1.15160 ( 6) hydrogen bonds : bond 0.04868 ( 651) hydrogen bonds : angle 4.15872 ( 1905) link_BETA1-4 : bond 0.00024 ( 1) link_BETA1-4 : angle 2.06756 ( 3) link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 0.54035 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 251 MET cc_start: 0.7487 (tpp) cc_final: 0.7112 (tpp) REVERT: A 558 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8427 (ttp) REVERT: A 759 MET cc_start: 0.6237 (mmm) cc_final: 0.5937 (mmt) REVERT: A 870 GLU cc_start: 0.7569 (mp0) cc_final: 0.7090 (mt-10) REVERT: A 878 GLU cc_start: 0.7688 (pm20) cc_final: 0.7451 (pm20) REVERT: A 1012 MET cc_start: 0.7669 (tmm) cc_final: 0.7030 (tmm) REVERT: A 1104 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6414 (t0) REVERT: A 1132 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 1223 MET cc_start: 0.8143 (mmm) cc_final: 0.7753 (ttt) REVERT: A 1471 MET cc_start: 0.7930 (tpp) cc_final: 0.7595 (tpp) REVERT: A 1575 HIS cc_start: 0.8320 (p90) cc_final: 0.8105 (p-80) REVERT: A 1638 PHE cc_start: 0.8089 (t80) cc_final: 0.6839 (m-80) REVERT: A 1650 LEU cc_start: 0.8830 (mp) cc_final: 0.8230 (tt) outliers start: 51 outliers final: 40 residues processed: 213 average time/residue: 0.1000 time to fit residues: 31.9993 Evaluate side-chains 214 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1604 GLN Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 0.9990 chunk 142 optimal weight: 0.0970 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1148 GLN ** 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 = 0.4097 r_free = 0.4097 target = 0.159605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128356 restraints weight = 21482.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130512 restraints weight = 12769.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131772 restraints weight = 9653.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132106 restraints weight = 8076.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132244 restraints weight = 7933.021| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13338 Z= 0.125 Angle : 0.644 13.221 18140 Z= 0.304 Chirality : 0.041 0.274 2009 Planarity : 0.004 0.042 2196 Dihedral : 9.085 97.932 2623 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.21 % Allowed : 26.12 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.22), residues: 1504 helix: 1.83 (0.17), residues: 891 sheet: 0.09 (0.77), residues: 46 loop : -1.14 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1747 TYR 0.015 0.001 TYR A 485 PHE 0.013 0.001 PHE A 454 TRP 0.009 0.001 TRP A1495 HIS 0.003 0.001 HIS A1338 Details of bonding type rmsd covalent geometry : bond 0.00289 (13333) covalent geometry : angle 0.64366 (18128) SS BOND : bond 0.00486 ( 3) SS BOND : angle 1.02067 ( 6) hydrogen bonds : bond 0.04564 ( 651) hydrogen bonds : angle 4.08010 ( 1905) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 1.97486 ( 3) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 0.58446 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 251 MET cc_start: 0.7437 (tpp) cc_final: 0.7051 (tpp) REVERT: A 558 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: A 759 MET cc_start: 0.6221 (mmm) cc_final: 0.5910 (mmt) REVERT: A 870 GLU cc_start: 0.7549 (mp0) cc_final: 0.7155 (mt-10) REVERT: A 1012 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6993 (tmm) REVERT: A 1104 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6458 (t0) REVERT: A 1132 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 1223 MET cc_start: 0.8154 (mmm) cc_final: 0.7738 (ttt) REVERT: A 1471 MET cc_start: 0.7858 (tpp) cc_final: 0.7562 (tpp) REVERT: A 1575 HIS cc_start: 0.8326 (p90) cc_final: 0.8095 (p-80) REVERT: A 1638 PHE cc_start: 0.8071 (t80) cc_final: 0.6833 (m-80) REVERT: A 1650 LEU cc_start: 0.8815 (mp) cc_final: 0.8252 (tt) REVERT: A 1661 MET cc_start: 0.8708 (mmt) cc_final: 0.8448 (mmt) REVERT: A 1684 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 1747 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7615 (ttt90) outliers start: 43 outliers final: 37 residues processed: 207 average time/residue: 0.0996 time to fit residues: 30.9522 Evaluate side-chains 215 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1604 GLN Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1844 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129681 restraints weight = 21272.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132127 restraints weight = 12231.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133215 restraints weight = 9190.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133550 restraints weight = 7634.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133695 restraints weight = 7516.670| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13338 Z= 0.122 Angle : 0.639 12.333 18140 Z= 0.302 Chirality : 0.041 0.270 2009 Planarity : 0.004 0.041 2196 Dihedral : 8.986 96.469 2623 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 3.06 % Allowed : 26.12 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.22), residues: 1504 helix: 1.84 (0.17), residues: 894 sheet: 0.09 (0.77), residues: 46 loop : -1.08 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1747 TYR 0.013 0.001 TYR A 485 PHE 0.014 0.001 PHE A 454 TRP 0.009 0.001 TRP A1495 HIS 0.003 0.001 HIS A1338 Details of bonding type rmsd covalent geometry : bond 0.00284 (13333) covalent geometry : angle 0.63841 (18128) SS BOND : bond 0.00493 ( 3) SS BOND : angle 0.96628 ( 6) hydrogen bonds : bond 0.04365 ( 651) hydrogen bonds : angle 4.04217 ( 1905) link_BETA1-4 : bond 0.00137 ( 1) link_BETA1-4 : angle 1.97492 ( 3) link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 0.57328 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.82 seconds wall clock time: 35 minutes 47.38 seconds (2147.38 seconds total)