Starting phenix.real_space_refine on Sat Aug 23 05:24:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fth_29426/08_2025/8fth_29426.map" } resolution = 3.17 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= 0.044 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 2 5.49 5 S 62 5.16 5 C 6200 2.51 5 N 1697 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9780 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9753 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 51, 'TRANS': 1211} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 6, 'GLN:plan1': 9, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 8, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9780 At special positions: 0 Unit cell: (71.1808, 89.1904, 180.954, 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 62 16.00 P 2 15.00 O 1819 8.00 N 1697 7.00 C 6200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 279.9 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 5 sheets defined 63.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.775A pdb=" N LEU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.777A pdb=" N ALA A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.754A pdb=" N LEU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 451 Processing helix chain 'A' and resid 458 through 474 removed outlier: 3.833A pdb=" N ILE A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.548A pdb=" N ILE A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 521 removed outlier: 3.851A pdb=" N ALA A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.740A pdb=" N PHE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 565 Processing helix chain 'A' and resid 581 through 605 removed outlier: 3.507A pdb=" N LEU A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 624 through 634 removed outlier: 4.222A pdb=" N ILE A 628 " --> pdb=" O THR A 624 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 652 removed outlier: 3.693A pdb=" N THR A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.724A pdb=" N PHE A 671 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 710 removed outlier: 4.029A pdb=" N LEU A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 701 " --> pdb=" O PRO A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 719 removed outlier: 3.721A pdb=" N ARG A 719 " --> pdb=" O GLN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 747 removed outlier: 3.548A pdb=" N ALA A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 756 through 776 removed outlier: 3.631A pdb=" N MET A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.035A pdb=" N MET A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 800 removed outlier: 3.712A pdb=" N LYS A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 808 removed outlier: 3.588A pdb=" N ARG A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 808' Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.677A pdb=" N ASP A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 815 " --> pdb=" O LEU A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.747A pdb=" N GLY A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 876 through 887 removed outlier: 3.783A pdb=" N ARG A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1116 removed outlier: 4.029A pdb=" N HIS A1111 " --> pdb=" O MET A1107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A1112 " --> pdb=" O ASP A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1150 Processing helix chain 'A' and resid 1150 through 1167 removed outlier: 3.630A pdb=" N GLU A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1167 " --> pdb=" O THR A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1202 Processing helix chain 'A' and resid 1271 through 1283 Processing helix chain 'A' and resid 1284 through 1287 Processing helix chain 'A' and resid 1289 through 1295 Processing helix chain 'A' and resid 1307 through 1317 removed outlier: 3.591A pdb=" N ASN A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1332 removed outlier: 3.895A pdb=" N ARG A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1326 " --> pdb=" O GLN A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1358 Processing helix chain 'A' and resid 1395 through 1409 removed outlier: 3.654A pdb=" N VAL A1399 " --> pdb=" O SER A1395 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1438 removed outlier: 3.592A pdb=" N ASP A1437 " --> pdb=" O ALA A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1449 removed outlier: 3.723A pdb=" N ARG A1447 " --> pdb=" O LEU A1443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1448 " --> pdb=" O VAL A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1483 removed outlier: 3.628A pdb=" N ALA A1473 " --> pdb=" O GLY A1469 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A1475 " --> pdb=" O ILE A1471 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A1476 " --> pdb=" O LYS A1472 " (cutoff:3.500A) Proline residue: A1480 - end of helix Processing helix chain 'A' and resid 1495 through 1521 removed outlier: 3.987A pdb=" N LYS A1505 " --> pdb=" O PHE A1501 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A1506 " --> pdb=" O ASP A1502 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1507 " --> pdb=" O GLU A1503 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A1508 " --> pdb=" O LEU A1504 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1519 " --> pdb=" O ILE A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1544 removed outlier: 3.693A pdb=" N GLU A1530 " --> pdb=" O ALA A1526 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A1532 " --> pdb=" O GLU A1528 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A1538 " --> pdb=" O ARG A1534 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A1542 " --> pdb=" O GLN A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1560 removed outlier: 3.646A pdb=" N HIS A1556 " --> pdb=" O GLY A1553 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A1557 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET A1558 " --> pdb=" O GLY A1555 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A1559 " --> pdb=" O HIS A1556 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A1560 " --> pdb=" O GLU A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 removed outlier: 3.652A pdb=" N SER A1608 " --> pdb=" O PRO A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1628 removed outlier: 3.536A pdb=" N MET A1624 " --> pdb=" O LEU A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1654 removed outlier: 3.561A pdb=" N LYS A1651 " --> pdb=" O ARG A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1668 removed outlier: 3.537A pdb=" N LEU A1667 " --> pdb=" O ASP A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1675 removed outlier: 3.766A pdb=" N HIS A1673 " --> pdb=" O GLN A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1718 removed outlier: 3.713A pdb=" N VAL A1705 " --> pdb=" O ASN A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1750 Processing helix chain 'A' and resid 1752 through 1757 Processing helix chain 'A' and resid 1788 through 1800 removed outlier: 3.796A pdb=" N THR A1800 " --> pdb=" O ASN A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1830 Processing helix chain 'A' and resid 1838 through 1844 removed outlier: 3.826A pdb=" N SER A1844 " --> pdb=" O MET A1840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1182 through 1183 removed outlier: 3.647A pdb=" N VAL A1183 " --> pdb=" O PHE A1186 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1186 " --> pdb=" O VAL A1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1189 through 1193 removed outlier: 3.617A pdb=" N LYS A1232 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A1245 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A1230 " --> pdb=" O ARG A1245 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP A1207 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A1208 " --> pdb=" O ILE A1268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1422 through 1424 removed outlier: 6.737A pdb=" N LEU A1423 " --> pdb=" O CYS A1548 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A1389 " --> pdb=" O LEU A1547 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA A1549 " --> pdb=" O LEU A1389 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL A1391 " --> pdb=" O ALA A1549 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR A1336 " --> pdb=" O LEU A1595 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLY A1597 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A1338 " --> pdb=" O GLY A1597 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A1337 " --> pdb=" O HIS A1633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1410 through 1411 removed outlier: 3.827A pdb=" N VAL A1410 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1758 through 1760 removed outlier: 3.521A pdb=" N GLU A1758 " --> pdb=" O ILE A1728 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A1760 " --> pdb=" O ILE A1730 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A1771 " --> pdb=" O SER A1805 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N TRP A1807 " --> pdb=" O GLU A1771 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A1773 " --> pdb=" O TRP A1807 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU A1809 " --> pdb=" O ILE A1773 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A1775 " --> pdb=" O LEU A1809 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A1682 " --> pdb=" O LEU A1806 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N THR A1835 " --> pdb=" O TYR A1681 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE A1683 " --> pdb=" O THR A1835 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1491 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: 1.42 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1650 1.32 - 1.44: 2468 1.44 - 1.57: 5721 1.57 - 1.69: 3 1.69 - 1.82: 105 Bond restraints: 9947 Sorted by residual: bond pdb=" CA SER A 713 " pdb=" CB SER A 713 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.69e-02 3.50e+03 1.76e+01 bond pdb=" C ILE A1584 " pdb=" N PRO A1585 " ideal model delta sigma weight residual 1.334 1.412 -0.078 2.34e-02 1.83e+03 1.11e+01 bond pdb=" C PRO A 712 " pdb=" O PRO A 712 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" N LYS A1829 " pdb=" CA LYS A1829 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.52e+00 bond pdb=" N ARG A1831 " pdb=" CA ARG A1831 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.38e+00 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 13215 3.29 - 6.58: 206 6.58 - 9.87: 26 9.87 - 13.16: 6 13.16 - 16.45: 1 Bond angle restraints: 13454 Sorted by residual: angle pdb=" N PRO A 712 " pdb=" CA PRO A 712 " pdb=" CB PRO A 712 " ideal model delta sigma weight residual 103.25 94.80 8.45 1.05e+00 9.07e-01 6.48e+01 angle pdb=" N VAL A1746 " pdb=" CA VAL A1746 " pdb=" C VAL A1746 " ideal model delta sigma weight residual 111.05 105.17 5.88 1.25e+00 6.40e-01 2.22e+01 angle pdb=" CA LEU A 566 " pdb=" CB LEU A 566 " pdb=" CG LEU A 566 " ideal model delta sigma weight residual 116.30 132.75 -16.45 3.50e+00 8.16e-02 2.21e+01 angle pdb=" C PRO A1671 " pdb=" CA PRO A1671 " pdb=" CB PRO A1671 " ideal model delta sigma weight residual 111.56 104.46 7.10 1.65e+00 3.67e-01 1.85e+01 angle pdb=" C ALA A 886 " pdb=" N LEU A 887 " pdb=" CA LEU A 887 " ideal model delta sigma weight residual 120.58 113.82 6.76 1.71e+00 3.42e-01 1.56e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 5477 24.77 - 49.54: 505 49.54 - 74.31: 70 74.31 - 99.08: 6 99.08 - 123.85: 1 Dihedral angle restraints: 6059 sinusoidal: 2388 harmonic: 3671 Sorted by residual: dihedral pdb=" O1B ADP A2101 " pdb=" O3A ADP A2101 " pdb=" PB ADP A2101 " pdb=" PA ADP A2101 " ideal model delta sinusoidal sigma weight residual -60.00 63.85 -123.85 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA THR A 411 " pdb=" C THR A 411 " pdb=" N SER A 412 " pdb=" CA SER A 412 " ideal model delta harmonic sigma weight residual -180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TYR A1654 " pdb=" C TYR A1654 " pdb=" N GLU A1655 " pdb=" CA GLU A1655 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 6056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1187 0.054 - 0.108: 275 0.108 - 0.161: 74 0.161 - 0.215: 10 0.215 - 0.269: 4 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA PHE A1648 " pdb=" N PHE A1648 " pdb=" C PHE A1648 " pdb=" CB PHE A1648 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB THR A1269 " pdb=" CA THR A1269 " pdb=" OG1 THR A1269 " pdb=" CG2 THR A1269 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLN A1670 " pdb=" N GLN A1670 " pdb=" C GLN A1670 " pdb=" CB GLN A1670 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1547 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 524 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C LYS A 524 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS A 524 " 0.035 2.00e-02 2.50e+03 pdb=" N PRO A 525 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 609 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 610 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 840 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLU A 840 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU A 840 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 841 " -0.024 2.00e-02 2.50e+03 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2795 2.82 - 3.34: 8550 3.34 - 3.86: 15464 3.86 - 4.38: 17496 4.38 - 4.90: 30754 Nonbonded interactions: 75059 Sorted by model distance: nonbonded pdb=" OD1 ASN A 772 " pdb=" OG1 THR A 830 " model vdw 2.298 3.040 nonbonded pdb=" O ALA A1279 " pdb=" OG SER A1283 " model vdw 2.305 3.040 nonbonded pdb=" O GLU A1156 " pdb=" OG SER A1160 " model vdw 2.310 3.040 nonbonded pdb=" O SER A1554 " pdb=" OH TYR A1588 " model vdw 2.315 3.040 nonbonded pdb=" O ALA A1164 " pdb=" OG1 THR A1168 " model vdw 2.320 3.040 ... (remaining 75054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.006 0.078 9947 Z= 0.276 Angle : 1.008 16.453 13454 Z= 0.534 Chirality : 0.052 0.269 1550 Planarity : 0.008 0.114 1717 Dihedral : 18.199 123.854 3663 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.28 % Favored : 94.23 % Rotamer: Outliers : 1.28 % Allowed : 26.59 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.58 (0.21), residues: 1231 helix: -1.39 (0.16), residues: 733 sheet: -0.91 (0.55), residues: 106 loop : -2.28 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1640 TYR 0.016 0.002 TYR A1681 PHE 0.026 0.003 PHE A1304 TRP 0.014 0.002 TRP A1672 HIS 0.009 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9947) covalent geometry : angle 1.00827 (13454) hydrogen bonds : bond 0.16677 ( 505) hydrogen bonds : angle 6.25323 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.7741 (mmm) cc_final: 0.7046 (mtp) REVERT: A 843 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6985 (mtp) REVERT: A 1290 MET cc_start: 0.6608 (tpp) cc_final: 0.6363 (mmt) REVERT: A 1317 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6683 (pt0) REVERT: A 1714 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6481 (ttt180) REVERT: A 1830 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7333 (tp-100) outliers start: 13 outliers final: 5 residues processed: 146 average time/residue: 0.0951 time to fit residues: 18.8070 Evaluate side-chains 147 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 712 PRO Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172411 restraints weight = 12211.305| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.92 r_work: 0.3939 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9947 Z= 0.138 Angle : 0.603 10.562 13454 Z= 0.303 Chirality : 0.040 0.201 1550 Planarity : 0.005 0.076 1717 Dihedral : 6.700 109.789 1375 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.36 % Allowed : 25.71 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.23), residues: 1231 helix: 0.04 (0.18), residues: 764 sheet: -0.81 (0.55), residues: 104 loop : -2.13 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.013 0.001 TYR A1145 PHE 0.022 0.001 PHE A1648 TRP 0.010 0.001 TRP A 734 HIS 0.009 0.001 HIS A1673 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9947) covalent geometry : angle 0.60329 (13454) hydrogen bonds : bond 0.05259 ( 505) hydrogen bonds : angle 4.30798 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.361 Fit side-chains REVERT: A 327 MET cc_start: 0.7912 (mmm) cc_final: 0.7698 (mmm) REVERT: A 366 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7132 (mtp180) REVERT: A 663 MET cc_start: 0.8258 (mmm) cc_final: 0.8042 (mmt) REVERT: A 1353 MET cc_start: 0.6542 (tpp) cc_final: 0.6318 (tpp) REVERT: A 1714 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6681 (ttt180) REVERT: A 1830 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7486 (tm-30) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.0988 time to fit residues: 22.1583 Evaluate side-chains 154 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.200477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.171270 restraints weight = 12140.366| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.91 r_work: 0.3926 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9947 Z= 0.130 Angle : 0.576 9.644 13454 Z= 0.286 Chirality : 0.040 0.170 1550 Planarity : 0.005 0.061 1717 Dihedral : 6.072 103.935 1361 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.45 % Allowed : 26.69 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1231 helix: 0.83 (0.19), residues: 764 sheet: -0.64 (0.57), residues: 106 loop : -2.00 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1647 TYR 0.013 0.001 TYR A1145 PHE 0.020 0.001 PHE A1648 TRP 0.010 0.001 TRP A 734 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9947) covalent geometry : angle 0.57617 (13454) hydrogen bonds : bond 0.04559 ( 505) hydrogen bonds : angle 3.94117 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.252 Fit side-chains REVERT: A 366 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7132 (mtp180) REVERT: A 1714 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6599 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7546 (tm-30) outliers start: 25 outliers final: 15 residues processed: 162 average time/residue: 0.1052 time to fit residues: 22.8919 Evaluate side-chains 156 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.197238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.167546 restraints weight = 12351.152| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.92 r_work: 0.3886 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9947 Z= 0.157 Angle : 0.605 9.665 13454 Z= 0.301 Chirality : 0.041 0.188 1550 Planarity : 0.005 0.057 1717 Dihedral : 6.201 110.301 1361 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.34 % Allowed : 26.10 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1231 helix: 1.10 (0.20), residues: 759 sheet: -0.71 (0.56), residues: 107 loop : -1.94 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1647 TYR 0.015 0.001 TYR A1145 PHE 0.021 0.002 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9947) covalent geometry : angle 0.60506 (13454) hydrogen bonds : bond 0.04907 ( 505) hydrogen bonds : angle 3.95450 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.262 Fit side-chains REVERT: A 366 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.6889 (ttt-90) REVERT: A 1714 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6700 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 34 outliers final: 22 residues processed: 172 average time/residue: 0.0892 time to fit residues: 21.2382 Evaluate side-chains 162 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1714 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.199422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169996 restraints weight = 12255.488| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.92 r_work: 0.3913 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9947 Z= 0.122 Angle : 0.567 8.687 13454 Z= 0.279 Chirality : 0.039 0.160 1550 Planarity : 0.004 0.053 1717 Dihedral : 5.618 105.055 1358 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.85 % Allowed : 27.09 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.25), residues: 1231 helix: 1.31 (0.20), residues: 765 sheet: -0.62 (0.58), residues: 106 loop : -1.92 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.012 0.001 TYR A1145 PHE 0.019 0.001 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9947) covalent geometry : angle 0.56685 (13454) hydrogen bonds : bond 0.04274 ( 505) hydrogen bonds : angle 3.83461 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 682 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7728 (tt) REVERT: A 1560 LYS cc_start: 0.6406 (tppt) cc_final: 0.6103 (tppt) REVERT: A 1714 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6587 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 29 outliers final: 22 residues processed: 169 average time/residue: 0.0878 time to fit residues: 20.7975 Evaluate side-chains 163 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.198566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169010 restraints weight = 12270.187| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.93 r_work: 0.3902 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9947 Z= 0.135 Angle : 0.576 8.411 13454 Z= 0.285 Chirality : 0.040 0.157 1550 Planarity : 0.005 0.052 1717 Dihedral : 5.648 106.602 1358 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.32 % Allowed : 25.61 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1231 helix: 1.32 (0.20), residues: 767 sheet: -0.57 (0.57), residues: 107 loop : -1.92 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.013 0.001 TYR A1145 PHE 0.019 0.001 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.018 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9947) covalent geometry : angle 0.57618 (13454) hydrogen bonds : bond 0.04382 ( 505) hydrogen bonds : angle 3.82733 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.265 Fit side-chains REVERT: A 682 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 796 LYS cc_start: 0.7489 (mmmt) cc_final: 0.6633 (mptt) REVERT: A 1551 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 1560 LYS cc_start: 0.6451 (tppt) cc_final: 0.6136 (tppt) REVERT: A 1714 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6632 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7500 (tm-30) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.1007 time to fit residues: 24.5658 Evaluate side-chains 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.198713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169194 restraints weight = 12256.586| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.92 r_work: 0.3904 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9947 Z= 0.133 Angle : 0.579 8.208 13454 Z= 0.285 Chirality : 0.040 0.214 1550 Planarity : 0.004 0.051 1717 Dihedral : 5.492 106.606 1356 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.32 % Allowed : 26.10 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.25), residues: 1231 helix: 1.34 (0.20), residues: 768 sheet: -0.53 (0.58), residues: 107 loop : -1.90 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1647 TYR 0.013 0.001 TYR A1145 PHE 0.019 0.001 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9947) covalent geometry : angle 0.57851 (13454) hydrogen bonds : bond 0.04290 ( 505) hydrogen bonds : angle 3.81710 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.286 Fit side-chains REVERT: A 682 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7767 (tt) REVERT: A 1551 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 1560 LYS cc_start: 0.6452 (tppt) cc_final: 0.6129 (tppt) REVERT: A 1714 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6640 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7515 (tm-30) outliers start: 44 outliers final: 36 residues processed: 177 average time/residue: 0.0840 time to fit residues: 20.8844 Evaluate side-chains 178 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.197284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167684 restraints weight = 12215.125| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.90 r_work: 0.3889 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9947 Z= 0.153 Angle : 0.608 9.624 13454 Z= 0.301 Chirality : 0.041 0.225 1550 Planarity : 0.005 0.051 1717 Dihedral : 5.622 110.508 1356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.02 % Allowed : 26.10 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.31 (0.25), residues: 1231 helix: 1.28 (0.20), residues: 769 sheet: -0.51 (0.58), residues: 107 loop : -1.96 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.014 0.001 TYR A1145 PHE 0.019 0.001 PHE A1648 TRP 0.010 0.001 TRP A 734 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9947) covalent geometry : angle 0.60833 (13454) hydrogen bonds : bond 0.04596 ( 505) hydrogen bonds : angle 3.89881 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.259 Fit side-chains REVERT: A 682 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7790 (tt) REVERT: A 796 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6655 (mptt) REVERT: A 1551 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8496 (mm) REVERT: A 1560 LYS cc_start: 0.6489 (tppt) cc_final: 0.6150 (tppt) REVERT: A 1647 ARG cc_start: 0.6231 (ptt180) cc_final: 0.5988 (ptt180) REVERT: A 1714 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6664 (ttt-90) REVERT: A 1737 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6034 (tt0) REVERT: A 1826 GLU cc_start: 0.6254 (pp20) cc_final: 0.5825 (pp20) REVERT: A 1830 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 41 outliers final: 34 residues processed: 172 average time/residue: 0.0929 time to fit residues: 22.2002 Evaluate side-chains 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1737 GLN Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 20.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.198151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168586 restraints weight = 12256.958| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.90 r_work: 0.3897 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9947 Z= 0.138 Angle : 0.598 10.316 13454 Z= 0.295 Chirality : 0.040 0.216 1550 Planarity : 0.005 0.050 1717 Dihedral : 5.559 108.818 1356 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.02 % Allowed : 26.10 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.25), residues: 1231 helix: 1.35 (0.20), residues: 766 sheet: -0.53 (0.58), residues: 107 loop : -1.97 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1647 TYR 0.013 0.001 TYR A1145 PHE 0.022 0.001 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9947) covalent geometry : angle 0.59840 (13454) hydrogen bonds : bond 0.04362 ( 505) hydrogen bonds : angle 3.87010 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.231 Fit side-chains REVERT: A 682 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (tt) REVERT: A 1551 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 1560 LYS cc_start: 0.6706 (tppt) cc_final: 0.6366 (tppt) REVERT: A 1670 GLN cc_start: 0.7176 (mt0) cc_final: 0.6528 (mp10) REVERT: A 1714 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6580 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6398 (pp20) cc_final: 0.5956 (pp20) REVERT: A 1830 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7509 (tm-30) outliers start: 41 outliers final: 35 residues processed: 176 average time/residue: 0.0935 time to fit residues: 22.7283 Evaluate side-chains 183 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 61 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.199281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169980 restraints weight = 12094.956| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.88 r_work: 0.3911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9947 Z= 0.125 Angle : 0.581 9.917 13454 Z= 0.286 Chirality : 0.040 0.216 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.458 106.414 1356 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.63 % Allowed : 26.50 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.46 (0.25), residues: 1231 helix: 1.42 (0.20), residues: 765 sheet: -0.52 (0.58), residues: 107 loop : -1.90 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.012 0.001 TYR A1145 PHE 0.020 0.001 PHE A1648 TRP 0.012 0.001 TRP A 734 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9947) covalent geometry : angle 0.58084 (13454) hydrogen bonds : bond 0.04104 ( 505) hydrogen bonds : angle 3.81892 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.385 Fit side-chains REVERT: A 682 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 796 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6468 (mptt) REVERT: A 1330 LYS cc_start: 0.6981 (tttt) cc_final: 0.6580 (ttmt) REVERT: A 1551 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8486 (mm) REVERT: A 1560 LYS cc_start: 0.6701 (tppt) cc_final: 0.5990 (ttpt) REVERT: A 1654 TYR cc_start: 0.7480 (m-80) cc_final: 0.7163 (m-80) REVERT: A 1714 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6575 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6367 (pp20) cc_final: 0.6022 (pp20) REVERT: A 1830 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7508 (tm-30) outliers start: 37 outliers final: 31 residues processed: 173 average time/residue: 0.1014 time to fit residues: 24.0872 Evaluate side-chains 175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 751 TRP Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1596 VAL Chi-restraints excluded: chain A residue 1655 GLU Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.199166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169648 restraints weight = 12249.537| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.91 r_work: 0.3910 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9947 Z= 0.130 Angle : 0.589 9.557 13454 Z= 0.290 Chirality : 0.040 0.260 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.463 106.747 1356 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.63 % Allowed : 26.30 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1231 helix: 1.36 (0.20), residues: 773 sheet: -0.53 (0.58), residues: 107 loop : -1.86 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1102 TYR 0.024 0.001 TYR A1749 PHE 0.020 0.001 PHE A1648 TRP 0.011 0.001 TRP A 734 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9947) covalent geometry : angle 0.58912 (13454) hydrogen bonds : bond 0.04125 ( 505) hydrogen bonds : angle 3.83340 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.03 seconds wall clock time: 38 minutes 13.01 seconds (2293.01 seconds total)