Starting phenix.real_space_refine on Sat Nov 16 00:33:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_29426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_29426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_29426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_29426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fth_29426/11_2024/8fth_29426.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 10} 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: 6.85, per 1000 atoms: 0.70 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.36 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: 3.58 Time building geometry restraints manager: 3.03 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: 2.690 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- 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= 0.366 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 : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A1672 HIS 0.009 0.002 HIS A 415 PHE 0.026 0.003 PHE A1304 TYR 0.016 0.002 TYR A1681 ARG 0.006 0.001 ARG A1640 *********************** 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 : 1.191 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: 0.2740 time to fit residues: 54.7000 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 : 1.170 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9947 Z= 0.229 Angle : 0.617 10.712 13454 Z= 0.311 Chirality : 0.040 0.179 1550 Planarity : 0.006 0.075 1717 Dihedral : 6.736 110.822 1375 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.85 % Allowed : 25.71 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1231 helix: 0.08 (0.18), residues: 765 sheet: -0.83 (0.56), residues: 104 loop : -2.16 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.008 0.001 HIS A1673 PHE 0.020 0.002 PHE A1648 TYR 0.015 0.001 TYR A1145 ARG 0.003 0.000 ARG A1102 *********************** 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 169 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.153 Fit side-chains REVERT: A 327 MET cc_start: 0.7892 (mmm) cc_final: 0.7629 (mmm) REVERT: A 366 ARG cc_start: 0.7706 (mtp-110) cc_final: 0.7111 (mtp180) REVERT: A 1714 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6711 (ttt180) REVERT: A 1830 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7417 (tm-30) outliers start: 29 outliers final: 17 residues processed: 162 average time/residue: 0.2520 time to fit residues: 56.2180 Evaluate side-chains 155 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 1272 THR Chi-restraints excluded: chain A residue 1511 ILE 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 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 63 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** A1220 GLN ** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9947 Z= 0.242 Angle : 0.614 10.689 13454 Z= 0.305 Chirality : 0.041 0.177 1550 Planarity : 0.005 0.062 1717 Dihedral : 6.269 109.477 1361 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.53 % Allowed : 26.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1231 helix: 0.75 (0.19), residues: 759 sheet: -0.78 (0.55), residues: 107 loop : -2.08 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.005 0.001 HIS A 727 PHE 0.021 0.002 PHE A1648 TYR 0.015 0.001 TYR A1145 ARG 0.004 0.000 ARG A1647 *********************** 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 180 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.129 Fit side-chains REVERT: A 366 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.6898 (ttt-90) REVERT: A 823 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7162 (tt) REVERT: A 1714 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6643 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7417 (tm-30) outliers start: 36 outliers final: 20 residues processed: 171 average time/residue: 0.2704 time to fit residues: 64.1295 Evaluate side-chains 164 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 764 CYS Chi-restraints excluded: chain A residue 823 LEU 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 1245 ARG Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1354 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 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9947 Z= 0.197 Angle : 0.573 9.589 13454 Z= 0.284 Chirality : 0.039 0.183 1550 Planarity : 0.005 0.056 1717 Dihedral : 6.055 105.580 1361 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.43 % Allowed : 26.10 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1231 helix: 1.07 (0.20), residues: 765 sheet: -0.70 (0.57), residues: 106 loop : -1.99 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.007 0.001 HIS A 415 PHE 0.018 0.001 PHE A1648 TYR 0.013 0.001 TYR A1145 ARG 0.003 0.000 ARG A1647 *********************** 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 179 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.194 Fit side-chains REVERT: A 366 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.6879 (ttt-90) REVERT: A 682 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 1560 LYS cc_start: 0.6392 (tppt) cc_final: 0.6105 (tppt) REVERT: A 1714 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6684 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7370 (tm-30) outliers start: 35 outliers final: 21 residues processed: 174 average time/residue: 0.2623 time to fit residues: 62.0940 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 : 1.185 ------------------------------------------------------------------------------- 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 682 LEU 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 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 1546 VAL 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 1728 ILE Chi-restraints excluded: chain A residue 1790 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 0.0010 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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** ** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1583 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= 0.183 Angle : 0.566 8.882 13454 Z= 0.279 Chirality : 0.039 0.169 1550 Planarity : 0.004 0.053 1717 Dihedral : 5.562 103.748 1358 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.83 % Allowed : 26.50 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1231 helix: 1.27 (0.20), residues: 765 sheet: -0.66 (0.58), residues: 106 loop : -1.92 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.010 0.001 HIS A 415 PHE 0.019 0.001 PHE A1648 TYR 0.012 0.001 TYR A1145 ARG 0.004 0.000 ARG A1647 *********************** 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 181 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.151 Fit side-chains REVERT: A 682 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7768 (tt) REVERT: A 1551 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8631 (mm) REVERT: A 1560 LYS cc_start: 0.6389 (tppt) cc_final: 0.6103 (tppt) REVERT: A 1714 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6592 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7391 (tm-30) outliers start: 39 outliers final: 25 residues processed: 174 average time/residue: 0.2441 time to fit residues: 58.3553 Evaluate side-chains 168 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 1258 THR Chi-restraints excluded: chain A residue 1266 VAL 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 1714 ARG Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1830 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 71 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.0040 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9947 Z= 0.167 Angle : 0.549 8.275 13454 Z= 0.271 Chirality : 0.039 0.161 1550 Planarity : 0.004 0.051 1717 Dihedral : 5.462 101.699 1358 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.63 % Allowed : 26.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1231 helix: 1.39 (0.20), residues: 767 sheet: -0.61 (0.58), residues: 106 loop : -1.85 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.008 0.001 HIS A 415 PHE 0.020 0.001 PHE A1648 TYR 0.011 0.001 TYR A1145 ARG 0.003 0.000 ARG A1647 *********************** 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 182 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.163 Fit side-chains REVERT: A 1551 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8616 (mm) REVERT: A 1560 LYS cc_start: 0.6400 (tppt) cc_final: 0.6103 (tppt) REVERT: A 1714 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6597 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7366 (tm-30) outliers start: 37 outliers final: 28 residues processed: 174 average time/residue: 0.2451 time to fit residues: 59.0627 Evaluate side-chains 174 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR 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 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 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 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 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 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** A1315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1748 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= 0.185 Angle : 0.576 9.376 13454 Z= 0.280 Chirality : 0.039 0.204 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.341 103.141 1356 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.43 % Allowed : 26.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1231 helix: 1.45 (0.20), residues: 764 sheet: -0.56 (0.59), residues: 106 loop : -1.87 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 734 HIS 0.009 0.001 HIS A 415 PHE 0.019 0.001 PHE A1648 TYR 0.012 0.001 TYR A1145 ARG 0.004 0.000 ARG A1647 *********************** 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 182 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.163 Fit side-chains REVERT: A 1551 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8649 (mm) REVERT: A 1560 LYS cc_start: 0.6411 (tppt) cc_final: 0.6109 (tppt) REVERT: A 1714 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6594 (ttt-90) REVERT: A 1830 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7380 (tm-30) outliers start: 35 outliers final: 29 residues processed: 174 average time/residue: 0.2474 time to fit residues: 60.3337 Evaluate side-chains 174 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR 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 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 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 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9947 Z= 0.213 Angle : 0.596 9.447 13454 Z= 0.290 Chirality : 0.040 0.230 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.439 106.251 1356 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.53 % Allowed : 26.50 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1231 helix: 1.43 (0.20), residues: 764 sheet: -0.54 (0.59), residues: 107 loop : -1.88 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 734 HIS 0.005 0.001 HIS A 727 PHE 0.019 0.001 PHE A1648 TYR 0.013 0.001 TYR A1145 ARG 0.004 0.000 ARG A 414 *********************** 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 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.226 Fit side-chains REVERT: A 1551 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 1560 LYS cc_start: 0.6451 (tppt) cc_final: 0.6146 (tppt) REVERT: A 1714 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6602 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6158 (pp20) cc_final: 0.5736 (pp20) REVERT: A 1830 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7351 (tm-30) outliers start: 36 outliers final: 31 residues processed: 170 average time/residue: 0.2462 time to fit residues: 58.1543 Evaluate side-chains 171 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR 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 1349 THR Chi-restraints excluded: chain A residue 1354 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 119 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1836 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= 0.198 Angle : 0.589 10.123 13454 Z= 0.287 Chirality : 0.040 0.232 1550 Planarity : 0.004 0.049 1717 Dihedral : 5.418 106.089 1356 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.34 % Allowed : 26.69 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1231 helix: 1.44 (0.20), residues: 764 sheet: -0.55 (0.59), residues: 107 loop : -1.85 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 734 HIS 0.004 0.001 HIS A 727 PHE 0.019 0.001 PHE A1648 TYR 0.012 0.001 TYR A1145 ARG 0.004 0.000 ARG A 414 *********************** 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 175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.159 Fit side-chains REVERT: A 1551 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 1560 LYS cc_start: 0.6447 (tppt) cc_final: 0.6143 (tppt) REVERT: A 1647 ARG cc_start: 0.6040 (ptt180) cc_final: 0.5811 (ptt180) REVERT: A 1654 TYR cc_start: 0.7399 (m-80) cc_final: 0.7072 (m-80) REVERT: A 1670 GLN cc_start: 0.7080 (mt0) cc_final: 0.6549 (mp10) REVERT: A 1701 ASN cc_start: 0.7562 (t0) cc_final: 0.7308 (t0) REVERT: A 1714 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6603 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6179 (pp20) cc_final: 0.5769 (pp20) REVERT: A 1830 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7351 (tm-30) outliers start: 34 outliers final: 28 residues processed: 166 average time/residue: 0.2566 time to fit residues: 58.6231 Evaluate side-chains 172 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR 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 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 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 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 83 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.0050 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 overall best weight: 0.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9947 Z= 0.164 Angle : 0.573 9.866 13454 Z= 0.278 Chirality : 0.039 0.213 1550 Planarity : 0.004 0.050 1717 Dihedral : 5.258 101.316 1356 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.04 % Allowed : 26.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1231 helix: 1.50 (0.20), residues: 770 sheet: -0.56 (0.59), residues: 106 loop : -1.77 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.003 0.001 HIS A 727 PHE 0.023 0.001 PHE A1648 TYR 0.010 0.001 TYR A1145 ARG 0.012 0.000 ARG A1647 ********************** 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 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.218 Fit side-chains REVERT: A 796 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6586 (mptt) REVERT: A 1560 LYS cc_start: 0.6419 (tppt) cc_final: 0.5869 (ttpt) REVERT: A 1670 GLN cc_start: 0.7017 (mt0) cc_final: 0.6489 (mp10) REVERT: A 1714 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6554 (ttt-90) REVERT: A 1826 GLU cc_start: 0.6175 (pp20) cc_final: 0.5858 (pp20) REVERT: A 1830 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7357 (tm-30) outliers start: 31 outliers final: 27 residues processed: 169 average time/residue: 0.2563 time to fit residues: 59.9156 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 : 1.136 ------------------------------------------------------------------------------- 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 614 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR 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 1353 MET Chi-restraints excluded: chain A residue 1546 VAL 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 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 30 optimal weight: 0.0270 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 102 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.202999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173909 restraints weight = 12070.758| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.91 r_work: 0.3955 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9947 Z= 0.164 Angle : 0.569 8.772 13454 Z= 0.276 Chirality : 0.039 0.211 1550 Planarity : 0.004 0.048 1717 Dihedral : 5.188 99.989 1356 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.94 % Allowed : 26.79 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1231 helix: 1.55 (0.20), residues: 765 sheet: -0.54 (0.59), residues: 106 loop : -1.71 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.008 0.001 HIS A 415 PHE 0.021 0.001 PHE A1648 TYR 0.018 0.001 TYR A1749 ARG 0.002 0.000 ARG A1647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2556.39 seconds wall clock time: 47 minutes 0.53 seconds (2820.53 seconds total)