Starting phenix.real_space_refine on Wed Mar 4 21:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.map" model { file = "/net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8alz_15521/03_2026/8alz_15521.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 Zn 2 6.06 5 S 79 5.16 5 C 10500 2.51 5 N 2849 2.21 5 O 2979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16409 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 14355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1783, 14355 Classifications: {'peptide': 1783} Link IDs: {'PTRANS': 81, 'TRANS': 1701} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34 SG CYS A 171 17.878 96.009 107.523 1.00148.97 S ATOM 48 SG CYS A 173 19.881 96.409 104.173 1.00118.44 S ATOM 193 SG CYS A 192 20.019 99.152 106.867 1.00134.45 S ATOM 135 SG CYS A 184 32.026 103.846 111.718 1.00122.03 S ATOM 157 SG CYS A 187 32.316 101.135 114.342 1.00110.73 S ATOM 247 SG CYS A 200 29.014 103.168 114.010 1.00143.50 S ATOM 272 SG CYS A 203 32.081 104.696 115.443 1.00132.54 S Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16409 At special positions: 0 Unit cell: (103.168, 133.952, 169.728, 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) Zn 2 29.99 S 79 16.00 O 2979 8.00 N 2849 7.00 C 10500 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: 1.36 Conformation dependent library (CDL) restraints added in 720.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 178 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 192 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 171 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 173 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 203 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 187 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 184 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 200 " Number of angles added : 9 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 47.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 209 through 219 removed outlier: 4.627A pdb=" N ILE A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.684A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.934A pdb=" N GLN A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 429' Processing helix chain 'A' and resid 440 through 449 removed outlier: 4.098A pdb=" N LEU A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 4.240A pdb=" N VAL A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.619A pdb=" N SER A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 580 removed outlier: 3.754A pdb=" N ALA A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 478 through 489 removed outlier: 5.099A pdb=" N GLU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 removed outlier: 3.928A pdb=" N ASN B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'B' and resid 584 through 594 Processing helix chain 'B' and resid 614 through 619 removed outlier: 4.091A pdb=" N GLU B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 692 through 715 Processing helix chain 'B' and resid 724 through 741 removed outlier: 3.969A pdb=" N VAL B 729 " --> pdb=" O ARG B 725 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 730 " --> pdb=" O ASN B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 removed outlier: 6.116A pdb=" N ILE B 745 " --> pdb=" O CYS B 742 " (cutoff:3.500A) Proline residue: B 746 - end of helix No H-bonds generated for 'chain 'B' and resid 742 through 748' Processing helix chain 'B' and resid 753 through 766 removed outlier: 3.552A pdb=" N SER B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 775 Processing helix chain 'B' and resid 787 through 801 removed outlier: 3.724A pdb=" N ARG B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 842 through 852 removed outlier: 3.627A pdb=" N ARG B 852 " --> pdb=" O GLN B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 878 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 909 through 920 Processing helix chain 'B' and resid 920 through 929 removed outlier: 3.859A pdb=" N VAL B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 928 " --> pdb=" O VAL B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 934 Processing helix chain 'B' and resid 936 through 943 Processing helix chain 'B' and resid 946 through 963 Processing helix chain 'B' and resid 979 through 988 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1009 through 1017 removed outlier: 3.550A pdb=" N ALA B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1022 Processing helix chain 'B' and resid 1027 through 1041 removed outlier: 4.513A pdb=" N GLU B1032 " --> pdb=" O GLU B1028 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 3.594A pdb=" N SER B1066 " --> pdb=" O GLN B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1101 Processing helix chain 'B' and resid 1102 through 1119 removed outlier: 3.953A pdb=" N ARG B1108 " --> pdb=" O THR B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.651A pdb=" N GLN B1129 " --> pdb=" O PRO B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1144 Processing helix chain 'B' and resid 1147 through 1154 Processing helix chain 'B' and resid 1155 through 1164 Processing helix chain 'B' and resid 1165 through 1177 Processing helix chain 'B' and resid 1209 through 1214 Processing helix chain 'B' and resid 1241 through 1248 Processing helix chain 'B' and resid 1309 through 1314 removed outlier: 3.542A pdb=" N GLY B1314 " --> pdb=" O THR B1311 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1320 Processing helix chain 'B' and resid 1328 through 1338 removed outlier: 5.224A pdb=" N HIS B1336 " --> pdb=" O THR B1332 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B1337 " --> pdb=" O GLN B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1354 through 1370 removed outlier: 3.788A pdb=" N ALA B1358 " --> pdb=" O GLY B1354 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1396 Processing helix chain 'B' and resid 1410 through 1420 removed outlier: 3.728A pdb=" N LYS B1416 " --> pdb=" O THR B1412 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B1420 " --> pdb=" O LYS B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1427 through 1435 Processing helix chain 'B' and resid 1443 through 1447 removed outlier: 4.170A pdb=" N GLN B1446 " --> pdb=" O TYR B1443 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1459 Processing helix chain 'B' and resid 1464 through 1481 removed outlier: 3.658A pdb=" N VAL B1468 " --> pdb=" O PRO B1464 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1503 removed outlier: 3.795A pdb=" N LEU B1499 " --> pdb=" O ASN B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1553 removed outlier: 3.930A pdb=" N MET B1538 " --> pdb=" O TYR B1534 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA B1539 " --> pdb=" O CYS B1535 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B1543 " --> pdb=" O ALA B1539 " (cutoff:3.500A) Proline residue: B1544 - end of helix removed outlier: 4.285A pdb=" N GLN B1547 " --> pdb=" O LYS B1543 " (cutoff:3.500A) Processing helix chain 'B' and resid 1566 through 1579 removed outlier: 4.371A pdb=" N LEU B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1592 through 1603 removed outlier: 4.308A pdb=" N MET B1596 " --> pdb=" O ASP B1592 " (cutoff:3.500A) Processing helix chain 'B' and resid 1622 through 1625 Processing helix chain 'B' and resid 1626 through 1637 removed outlier: 3.954A pdb=" N ASN B1637 " --> pdb=" O GLU B1633 " (cutoff:3.500A) Processing helix chain 'B' and resid 1679 through 1688 Processing helix chain 'B' and resid 1706 through 1719 removed outlier: 3.977A pdb=" N ASP B1711 " --> pdb=" O ASP B1707 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B1712 " --> pdb=" O ILE B1708 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B1718 " --> pdb=" O LYS B1714 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1729 No H-bonds generated for 'chain 'B' and resid 1727 through 1729' Processing helix chain 'B' and resid 1730 through 1741 removed outlier: 3.531A pdb=" N ALA B1737 " --> pdb=" O ASP B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1746 through 1754 removed outlier: 3.569A pdb=" N ALA B1750 " --> pdb=" O SER B1746 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B1754 " --> pdb=" O ALA B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1757 through 1766 removed outlier: 3.551A pdb=" N ARG B1761 " --> pdb=" O THR B1757 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B1764 " --> pdb=" O PHE B1760 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B1765 " --> pdb=" O ARG B1761 " (cutoff:3.500A) Processing helix chain 'B' and resid 1767 through 1771 Processing helix chain 'B' and resid 1776 through 1798 Processing helix chain 'B' and resid 1813 through 1822 Processing helix chain 'B' and resid 1825 through 1835 removed outlier: 3.713A pdb=" N MET B1831 " --> pdb=" O GLN B1827 " (cutoff:3.500A) Processing helix chain 'B' and resid 1841 through 1851 removed outlier: 3.522A pdb=" N ASP B1851 " --> pdb=" O SER B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1863 through 1872 removed outlier: 4.166A pdb=" N MET B1867 " --> pdb=" O ASN B1863 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1869 " --> pdb=" O ASP B1865 " (cutoff:3.500A) Processing helix chain 'B' and resid 1880 through 1884 removed outlier: 4.168A pdb=" N PHE B1884 " --> pdb=" O PRO B1881 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1900 Processing helix chain 'B' and resid 1906 through 1935 removed outlier: 4.246A pdb=" N ASP B1910 " --> pdb=" O CYS B1906 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B1911 " --> pdb=" O PRO B1907 " (cutoff:3.500A) Processing helix chain 'B' and resid 1937 through 1953 Processing helix chain 'B' and resid 1959 through 1964 Processing helix chain 'B' and resid 1968 through 1970 No H-bonds generated for 'chain 'B' and resid 1968 through 1970' Processing helix chain 'B' and resid 1971 through 1977 Processing helix chain 'B' and resid 1995 through 2004 Processing helix chain 'B' and resid 2010 through 2015 removed outlier: 3.603A pdb=" N VAL B2014 " --> pdb=" O PHE B2010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2016 through 2019 Processing helix chain 'B' and resid 2022 through 2033 removed outlier: 3.618A pdb=" N ALA B2026 " --> pdb=" O LYS B2022 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.534A pdb=" N PHE A 537 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 538 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS A 516 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 540 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TRP A 435 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 580 through 583 removed outlier: 6.467A pdb=" N ILE B 533 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR B 583 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR B 535 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 534 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 608 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 647 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B 670 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 498 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 779 through 781 removed outlier: 6.613A pdb=" N SER B 780 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 823 " --> pdb=" O ILE B 865 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AA5, first strand: chain 'B' and resid 967 through 970 Processing sheet with id=AA6, first strand: chain 'B' and resid 1182 through 1187 Processing sheet with id=AA7, first strand: chain 'B' and resid 1233 through 1240 removed outlier: 5.917A pdb=" N HIS B1234 " --> pdb=" O VAL B1224 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B1224 " --> pdb=" O HIS B1234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B1285 " --> pdb=" O TYR B1267 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B1269 " --> pdb=" O CYS B1283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1405 through 1406 removed outlier: 7.538A pdb=" N ILE B1405 " --> pdb=" O VAL B1425 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B1376 " --> pdb=" O ILE B1449 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B1450 " --> pdb=" O VAL B1487 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B1489 " --> pdb=" O LEU B1450 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B1452 " --> pdb=" O LEU B1489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1522 through 1525 Processing sheet with id=AB1, first strand: chain 'B' and resid 1559 through 1561 removed outlier: 6.462A pdb=" N ILE B1560 " --> pdb=" O ALA B1645 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B1619 " --> pdb=" O ILE B1644 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1666 through 1668 Processing sheet with id=AB3, first strand: chain 'B' and resid 1801 through 1802 Processing sheet with id=AB4, first strand: chain 'B' and resid 2056 through 2058 removed outlier: 4.093A pdb=" N ILE B2040 " --> pdb=" O VAL B2058 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2126 through 2133 removed outlier: 6.675A pdb=" N LEU B2119 " --> pdb=" O ILE B2128 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B2130 " --> pdb=" O LEU B2117 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B2117 " --> pdb=" O LEU B2130 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG B2132 " --> pdb=" O TRP B2115 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TRP B2115 " --> pdb=" O ARG B2132 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1917 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: 3.60 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4334 1.33 - 1.46: 3251 1.46 - 1.58: 9084 1.58 - 1.70: 2 1.70 - 1.82: 125 Bond restraints: 16796 Sorted by residual: bond pdb=" CB PRO B 665 " pdb=" CG PRO B 665 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.85e+00 bond pdb=" CA LYS B2097 " pdb=" CB LYS B2097 " ideal model delta sigma weight residual 1.522 1.535 -0.013 7.00e-03 2.04e+04 3.21e+00 bond pdb=" CB PRO B 944 " pdb=" CG PRO B 944 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.08e+00 bond pdb=" N THR B 809 " pdb=" CA THR B 809 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.08e+00 bond pdb=" CG PRO B 944 " pdb=" CD PRO B 944 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.68e+00 ... (remaining 16791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 22410 2.46 - 4.92: 277 4.92 - 7.38: 57 7.38 - 9.84: 16 9.84 - 12.30: 4 Bond angle restraints: 22764 Sorted by residual: angle pdb=" CA PRO B 665 " pdb=" N PRO B 665 " pdb=" CD PRO B 665 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.41e+01 angle pdb=" CA PRO B 944 " pdb=" N PRO B 944 " pdb=" CD PRO B 944 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" CA ARG B 788 " pdb=" CB ARG B 788 " pdb=" CG ARG B 788 " ideal model delta sigma weight residual 114.10 123.41 -9.31 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CB MET B1765 " pdb=" CG MET B1765 " pdb=" SD MET B1765 " ideal model delta sigma weight residual 112.70 125.00 -12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" CA MET B 700 " pdb=" CB MET B 700 " pdb=" CG MET B 700 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 ... (remaining 22759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8629 17.94 - 35.87: 1179 35.87 - 53.81: 257 53.81 - 71.74: 41 71.74 - 89.68: 14 Dihedral angle restraints: 10120 sinusoidal: 4154 harmonic: 5966 Sorted by residual: dihedral pdb=" CA GLN B 857 " pdb=" C GLN B 857 " pdb=" N PHE B 858 " pdb=" CA PHE B 858 " ideal model delta harmonic sigma weight residual 180.00 154.94 25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA THR B1426 " pdb=" C THR B1426 " pdb=" N THR B1427 " pdb=" CA THR B1427 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN B 717 " pdb=" C GLN B 717 " pdb=" N VAL B 718 " pdb=" CA VAL B 718 " ideal model delta harmonic sigma weight residual 180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 10117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2094 0.058 - 0.115: 392 0.115 - 0.173: 43 0.173 - 0.230: 3 0.230 - 0.288: 2 Chirality restraints: 2534 Sorted by residual: chirality pdb=" CB ILE B 849 " pdb=" CA ILE B 849 " pdb=" CG1 ILE B 849 " pdb=" CG2 ILE B 849 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB VAL B1394 " pdb=" CA VAL B1394 " pdb=" CG1 VAL B1394 " pdb=" CG2 VAL B1394 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B1560 " pdb=" N ILE B1560 " pdb=" C ILE B1560 " pdb=" CB ILE B1560 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 2531 not shown) Planarity restraints: 2915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 664 " -0.091 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO B 665 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 943 " -0.086 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO B 944 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO B 944 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 944 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 676 " 0.026 2.00e-02 2.50e+03 2.14e-02 8.04e+00 pdb=" CG PHE B 676 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 676 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 676 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 676 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 676 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 676 " 0.007 2.00e-02 2.50e+03 ... (remaining 2912 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1591 2.74 - 3.28: 17812 3.28 - 3.82: 29057 3.82 - 4.36: 32830 4.36 - 4.90: 53751 Nonbonded interactions: 135041 Sorted by model distance: nonbonded pdb=" O ASP B1865 " pdb=" OG SER B1869 " model vdw 2.204 3.040 nonbonded pdb=" N GLU B1595 " pdb=" OE1 GLU B1595 " model vdw 2.235 3.120 nonbonded pdb=" ND2 ASN B1328 " pdb=" OE1 GLN B1331 " model vdw 2.236 3.120 nonbonded pdb=" OG SER B1247 " pdb=" OE1 GLU B1249 " model vdw 2.243 3.040 nonbonded pdb=" N GLU A 429 " pdb=" OE1 GLU A 429 " model vdw 2.247 3.120 ... (remaining 135036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 16804 Z= 0.130 Angle : 0.719 12.298 22773 Z= 0.362 Chirality : 0.044 0.288 2534 Planarity : 0.005 0.133 2915 Dihedral : 16.775 89.675 6260 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 0.39 % Allowed : 27.19 % Favored : 72.43 % 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 are not related in a simple way. whole: -0.91 (0.19), residues: 2035 helix: 0.25 (0.18), residues: 827 sheet: -0.78 (0.31), residues: 280 loop : -1.29 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.009 0.001 TYR B 535 PHE 0.049 0.001 PHE B 676 TRP 0.015 0.001 TRP B 814 HIS 0.007 0.001 HIS B 744 Details of bonding type rmsd covalent geometry : bond 0.00292 (16796) covalent geometry : angle 0.71779 (22764) hydrogen bonds : bond 0.15320 ( 675) hydrogen bonds : angle 6.46496 ( 1917) metal coordination : bond 0.00698 ( 8) metal coordination : angle 2.38890 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 TRP cc_start: 0.6570 (p90) cc_final: 0.6347 (p90) REVERT: B 413 MET cc_start: 0.4183 (pmm) cc_final: 0.3537 (pmm) REVERT: B 669 LEU cc_start: 0.8591 (mm) cc_final: 0.8235 (mm) outliers start: 7 outliers final: 5 residues processed: 198 average time/residue: 0.1404 time to fit residues: 42.2493 Evaluate side-chains 185 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 672 PHE Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 1254 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN B 468 GLN ** B1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1880 ASN ** B1948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1970 HIS ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.084737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063007 restraints weight = 71465.629| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.99 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16804 Z= 0.127 Angle : 0.639 9.226 22773 Z= 0.323 Chirality : 0.044 0.186 2534 Planarity : 0.005 0.076 2915 Dihedral : 4.533 32.057 2222 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 2.10 % Allowed : 23.64 % Favored : 74.25 % 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 are not related in a simple way. whole: -0.90 (0.19), residues: 2035 helix: 0.27 (0.18), residues: 861 sheet: -0.84 (0.30), residues: 285 loop : -1.32 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 479 TYR 0.014 0.001 TYR B1443 PHE 0.024 0.001 PHE B 676 TRP 0.013 0.001 TRP B1431 HIS 0.004 0.001 HIS B 744 Details of bonding type rmsd covalent geometry : bond 0.00274 (16796) covalent geometry : angle 0.63666 (22764) hydrogen bonds : bond 0.04495 ( 675) hydrogen bonds : angle 5.21133 ( 1917) metal coordination : bond 0.00911 ( 8) metal coordination : angle 2.73160 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4848 (pmm) cc_final: 0.3048 (ptp) REVERT: B 669 LEU cc_start: 0.8836 (mm) cc_final: 0.8123 (mt) REVERT: B 816 VAL cc_start: 0.9211 (t) cc_final: 0.9010 (m) REVERT: B 1183 MET cc_start: 0.8273 (mmp) cc_final: 0.7963 (mmp) REVERT: B 1441 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7831 (mtm-85) REVERT: B 2115 TRP cc_start: 0.7466 (m100) cc_final: 0.7096 (m100) outliers start: 38 outliers final: 16 residues processed: 225 average time/residue: 0.1268 time to fit residues: 43.7705 Evaluate side-chains 192 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1441 ARG Chi-restraints excluded: chain B residue 1493 LEU Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1705 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 201 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN B 764 GLN ** B1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 ASN B1439 GLN B1781 ASN ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.081730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059670 restraints weight = 71959.240| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.85 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16804 Z= 0.200 Angle : 0.667 9.134 22773 Z= 0.339 Chirality : 0.045 0.186 2534 Planarity : 0.005 0.073 2915 Dihedral : 4.515 32.218 2215 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 3.65 % Allowed : 23.37 % Favored : 72.98 % 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 are not related in a simple way. whole: -0.98 (0.18), residues: 2035 helix: 0.27 (0.18), residues: 862 sheet: -0.95 (0.30), residues: 291 loop : -1.41 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 552 TYR 0.015 0.002 TYR B1443 PHE 0.019 0.002 PHE B 676 TRP 0.016 0.002 TRP B1431 HIS 0.008 0.001 HIS B1234 Details of bonding type rmsd covalent geometry : bond 0.00441 (16796) covalent geometry : angle 0.66618 (22764) hydrogen bonds : bond 0.04459 ( 675) hydrogen bonds : angle 5.19261 ( 1917) metal coordination : bond 0.01525 ( 8) metal coordination : angle 2.18308 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ARG cc_start: 0.8984 (mmt90) cc_final: 0.8771 (mmt90) REVERT: B 413 MET cc_start: 0.4891 (pmm) cc_final: 0.3193 (ptt) REVERT: B 669 LEU cc_start: 0.8885 (mm) cc_final: 0.8305 (mm) REVERT: B 694 MET cc_start: 0.9143 (mmp) cc_final: 0.8869 (tmm) REVERT: B 919 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: B 1099 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8480 (ttm170) REVERT: B 1143 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.9012 (pt0) REVERT: B 1183 MET cc_start: 0.8415 (mmp) cc_final: 0.8070 (mmp) outliers start: 66 outliers final: 41 residues processed: 237 average time/residue: 0.1187 time to fit residues: 43.7576 Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 919 TYR Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1099 ARG Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1311 THR Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1441 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1493 LEU Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1662 ILE Chi-restraints excluded: chain B residue 1676 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 50 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 764 GLN ** B 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** B1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1328 ASN B1331 GLN B1439 GLN ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2139 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.078864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056486 restraints weight = 72181.467| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.75 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 16804 Z= 0.316 Angle : 0.758 11.949 22773 Z= 0.390 Chirality : 0.047 0.196 2534 Planarity : 0.005 0.064 2915 Dihedral : 4.928 28.513 2215 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 5.09 % Allowed : 23.75 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2035 helix: -0.10 (0.17), residues: 870 sheet: -1.38 (0.28), residues: 294 loop : -1.60 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 552 TYR 0.024 0.002 TYR B 705 PHE 0.029 0.002 PHE B2029 TRP 0.018 0.002 TRP B2115 HIS 0.010 0.002 HIS B1706 Details of bonding type rmsd covalent geometry : bond 0.00693 (16796) covalent geometry : angle 0.75671 (22764) hydrogen bonds : bond 0.04920 ( 675) hydrogen bonds : angle 5.55284 ( 1917) metal coordination : bond 0.02240 ( 8) metal coordination : angle 2.71921 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 173 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7370 (mmpt) cc_final: 0.7084 (mmmt) REVERT: B 413 MET cc_start: 0.4861 (pmm) cc_final: 0.3398 (ptt) REVERT: B 546 MET cc_start: 0.9320 (mmm) cc_final: 0.9116 (mmm) REVERT: B 669 LEU cc_start: 0.8959 (mm) cc_final: 0.8454 (mm) REVERT: B 733 MET cc_start: 0.9565 (mpp) cc_final: 0.9297 (mpp) REVERT: B 919 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: B 1143 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8998 (pt0) REVERT: B 1183 MET cc_start: 0.8456 (mmp) cc_final: 0.8119 (mmp) REVERT: B 1441 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8329 (mtm-85) REVERT: B 1443 TYR cc_start: 0.7528 (p90) cc_final: 0.7190 (p90) REVERT: B 1594 ARG cc_start: 0.9214 (tmm160) cc_final: 0.8944 (tmm160) outliers start: 92 outliers final: 53 residues processed: 239 average time/residue: 0.1255 time to fit residues: 46.4661 Evaluate side-chains 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 919 TYR Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1207 THR Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1311 THR Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1346 LEU Chi-restraints excluded: chain B residue 1366 VAL Chi-restraints excluded: chain B residue 1405 ILE Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1441 ARG Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1659 LEU Chi-restraints excluded: chain B residue 1662 ILE Chi-restraints excluded: chain B residue 1676 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2058 VAL Chi-restraints excluded: chain B residue 2060 THR Chi-restraints excluded: chain B residue 2094 HIS Chi-restraints excluded: chain B residue 2112 ASP Chi-restraints excluded: chain B residue 2117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 39 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 181 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN B1368 ASN B1698 GLN ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.081533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059643 restraints weight = 70500.824| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.80 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16804 Z= 0.128 Angle : 0.665 10.050 22773 Z= 0.334 Chirality : 0.045 0.180 2534 Planarity : 0.004 0.060 2915 Dihedral : 4.607 22.151 2213 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 3.32 % Allowed : 25.97 % Favored : 70.71 % 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 are not related in a simple way. whole: -1.07 (0.18), residues: 2035 helix: 0.32 (0.18), residues: 848 sheet: -1.11 (0.30), residues: 271 loop : -1.54 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 972 TYR 0.037 0.001 TYR B 402 PHE 0.029 0.001 PHE B 676 TRP 0.014 0.001 TRP B1431 HIS 0.006 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00279 (16796) covalent geometry : angle 0.66306 (22764) hydrogen bonds : bond 0.04143 ( 675) hydrogen bonds : angle 5.07213 ( 1917) metal coordination : bond 0.01289 ( 8) metal coordination : angle 2.84123 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 PHE cc_start: 0.5686 (t80) cc_final: 0.4942 (t80) REVERT: A 579 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6937 (mmmt) REVERT: B 413 MET cc_start: 0.4748 (pmm) cc_final: 0.3182 (ptt) REVERT: B 669 LEU cc_start: 0.8885 (mm) cc_final: 0.8318 (mm) REVERT: B 733 MET cc_start: 0.9582 (mpp) cc_final: 0.9320 (mpp) REVERT: B 1143 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8953 (pt0) REVERT: B 1183 MET cc_start: 0.8317 (mmp) cc_final: 0.7985 (mmp) REVERT: B 1441 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8194 (mtm-85) REVERT: B 1443 TYR cc_start: 0.7506 (p90) cc_final: 0.7088 (p90) REVERT: B 2079 GLU cc_start: 0.6892 (tt0) cc_final: 0.6531 (tm-30) outliers start: 60 outliers final: 40 residues processed: 235 average time/residue: 0.1223 time to fit residues: 44.9608 Evaluate side-chains 220 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1376 VAL Chi-restraints excluded: chain B residue 1405 ILE Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1441 ARG Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1683 VAL Chi-restraints excluded: chain B residue 1702 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2061 LEU Chi-restraints excluded: chain B residue 2094 HIS Chi-restraints excluded: chain B residue 2112 ASP Chi-restraints excluded: chain B residue 2175 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 149 optimal weight: 0.0670 chunk 174 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 97 optimal weight: 0.0070 chunk 143 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1607 ASN ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.082610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060773 restraints weight = 71066.843| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.85 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16804 Z= 0.119 Angle : 0.659 10.301 22773 Z= 0.326 Chirality : 0.045 0.217 2534 Planarity : 0.004 0.057 2915 Dihedral : 4.461 24.058 2213 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 3.60 % Allowed : 26.02 % Favored : 70.38 % 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 are not related in a simple way. whole: -1.01 (0.18), residues: 2035 helix: 0.38 (0.18), residues: 846 sheet: -1.07 (0.31), residues: 261 loop : -1.51 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.016 0.001 TYR B1203 PHE 0.024 0.001 PHE B 676 TRP 0.015 0.001 TRP B2115 HIS 0.007 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00261 (16796) covalent geometry : angle 0.65724 (22764) hydrogen bonds : bond 0.03901 ( 675) hydrogen bonds : angle 4.90363 ( 1917) metal coordination : bond 0.01121 ( 8) metal coordination : angle 2.55313 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7365 (mmpt) cc_final: 0.7065 (mmmt) REVERT: B 413 MET cc_start: 0.4725 (pmm) cc_final: 0.3218 (ptt) REVERT: B 510 MET cc_start: 0.8807 (ptp) cc_final: 0.8547 (ptt) REVERT: B 669 LEU cc_start: 0.8981 (mm) cc_final: 0.8414 (mm) REVERT: B 975 TYR cc_start: 0.8198 (m-80) cc_final: 0.7867 (m-80) REVERT: B 1143 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8978 (pt0) REVERT: B 1183 MET cc_start: 0.8316 (mmp) cc_final: 0.7997 (mmp) REVERT: B 1441 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7071 (mtm-85) REVERT: B 1765 MET cc_start: 0.8996 (mmm) cc_final: 0.8796 (mmm) outliers start: 65 outliers final: 43 residues processed: 246 average time/residue: 0.1307 time to fit residues: 49.7329 Evaluate side-chains 227 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1311 THR Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1376 VAL Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1441 ARG Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1683 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2094 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 ASN ** B1826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.080922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058760 restraints weight = 72544.923| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.87 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16804 Z= 0.184 Angle : 0.682 11.104 22773 Z= 0.340 Chirality : 0.045 0.183 2534 Planarity : 0.004 0.055 2915 Dihedral : 4.548 24.036 2213 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 3.65 % Allowed : 26.74 % Favored : 69.60 % 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 are not related in a simple way. whole: -1.03 (0.18), residues: 2035 helix: 0.38 (0.18), residues: 849 sheet: -1.20 (0.31), residues: 264 loop : -1.52 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 552 TYR 0.030 0.002 TYR B 402 PHE 0.023 0.001 PHE B 676 TRP 0.016 0.001 TRP B2115 HIS 0.007 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00413 (16796) covalent geometry : angle 0.67811 (22764) hydrogen bonds : bond 0.04025 ( 675) hydrogen bonds : angle 5.03046 ( 1917) metal coordination : bond 0.01664 ( 8) metal coordination : angle 3.52720 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 PHE cc_start: 0.5852 (t80) cc_final: 0.5107 (t80) REVERT: A 579 LYS cc_start: 0.7361 (mmpt) cc_final: 0.7033 (mmmt) REVERT: B 413 MET cc_start: 0.4751 (pmm) cc_final: 0.3178 (ptt) REVERT: B 669 LEU cc_start: 0.9009 (mm) cc_final: 0.8488 (mm) REVERT: B 975 TYR cc_start: 0.8141 (m-80) cc_final: 0.7828 (m-80) REVERT: B 1143 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8990 (pt0) REVERT: B 1183 MET cc_start: 0.8292 (mmp) cc_final: 0.7992 (mmp) REVERT: B 2079 GLU cc_start: 0.7180 (tt0) cc_final: 0.6554 (tm-30) outliers start: 66 outliers final: 47 residues processed: 229 average time/residue: 0.1287 time to fit residues: 45.9131 Evaluate side-chains 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1311 THR Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1415 MET Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1683 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2040 ILE Chi-restraints excluded: chain B residue 2060 THR Chi-restraints excluded: chain B residue 2061 LEU Chi-restraints excluded: chain B residue 2094 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 52 optimal weight: 0.9980 chunk 185 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN ** B1826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1971 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 = 0.3872 r_free = 0.3872 target = 0.081532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059400 restraints weight = 72111.872| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.91 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16804 Z= 0.139 Angle : 0.682 11.443 22773 Z= 0.336 Chirality : 0.045 0.182 2534 Planarity : 0.004 0.054 2915 Dihedral : 4.507 23.749 2213 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 3.77 % Allowed : 26.91 % Favored : 69.32 % 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 are not related in a simple way. whole: -1.01 (0.18), residues: 2035 helix: 0.41 (0.18), residues: 849 sheet: -1.17 (0.31), residues: 264 loop : -1.52 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 788 TYR 0.012 0.001 TYR B 933 PHE 0.023 0.001 PHE B 676 TRP 0.016 0.001 TRP B2115 HIS 0.007 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00310 (16796) covalent geometry : angle 0.67895 (22764) hydrogen bonds : bond 0.03919 ( 675) hydrogen bonds : angle 4.94224 ( 1917) metal coordination : bond 0.01411 ( 8) metal coordination : angle 3.07800 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 187 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 PHE cc_start: 0.5736 (t80) cc_final: 0.4947 (t80) REVERT: A 579 LYS cc_start: 0.7374 (mmpt) cc_final: 0.7053 (mmmt) REVERT: B 413 MET cc_start: 0.4649 (pmm) cc_final: 0.3041 (ptt) REVERT: B 552 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8364 (tmm160) REVERT: B 580 MET cc_start: 0.3279 (ttt) cc_final: 0.3075 (tmm) REVERT: B 669 LEU cc_start: 0.8996 (mm) cc_final: 0.8468 (mm) REVERT: B 975 TYR cc_start: 0.8149 (m-80) cc_final: 0.7839 (m-80) REVERT: B 1143 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8965 (pt0) REVERT: B 1183 MET cc_start: 0.8246 (mmp) cc_final: 0.7937 (mmp) REVERT: B 1439 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8611 (tp40) REVERT: B 1655 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7635 (p90) REVERT: B 2079 GLU cc_start: 0.7094 (tt0) cc_final: 0.6520 (tm-30) outliers start: 68 outliers final: 52 residues processed: 234 average time/residue: 0.1284 time to fit residues: 46.6344 Evaluate side-chains 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1311 THR Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1344 ASN Chi-restraints excluded: chain B residue 1376 VAL Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1405 ILE Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1415 MET Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1439 GLN Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1655 PHE Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1683 VAL Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1928 LEU Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2040 ILE Chi-restraints excluded: chain B residue 2060 THR Chi-restraints excluded: chain B residue 2061 LEU Chi-restraints excluded: chain B residue 2094 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 24 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 chunk 128 optimal weight: 0.5980 chunk 29 optimal weight: 0.0000 chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 ASN ** B1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1971 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 = 0.3902 r_free = 0.3902 target = 0.082892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060895 restraints weight = 71887.061| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.93 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16804 Z= 0.122 Angle : 0.706 11.965 22773 Z= 0.345 Chirality : 0.046 0.183 2534 Planarity : 0.004 0.054 2915 Dihedral : 4.484 24.351 2213 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 3.05 % Allowed : 27.80 % Favored : 69.16 % 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 are not related in a simple way. whole: -1.00 (0.18), residues: 2035 helix: 0.42 (0.18), residues: 851 sheet: -1.01 (0.32), residues: 250 loop : -1.56 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 788 TYR 0.032 0.001 TYR B 402 PHE 0.021 0.001 PHE B 676 TRP 0.016 0.001 TRP B1955 HIS 0.008 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00264 (16796) covalent geometry : angle 0.70397 (22764) hydrogen bonds : bond 0.03783 ( 675) hydrogen bonds : angle 4.87282 ( 1917) metal coordination : bond 0.01063 ( 8) metal coordination : angle 2.99933 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7313 (mmpt) cc_final: 0.6996 (mmmt) REVERT: B 413 MET cc_start: 0.4602 (pmm) cc_final: 0.2918 (ptt) REVERT: B 669 LEU cc_start: 0.8945 (mm) cc_final: 0.8476 (mm) REVERT: B 975 TYR cc_start: 0.8121 (m-80) cc_final: 0.7776 (m-80) REVERT: B 1099 ARG cc_start: 0.9056 (tpp80) cc_final: 0.8377 (tpp80) REVERT: B 1183 MET cc_start: 0.8239 (mmp) cc_final: 0.7941 (mmp) REVERT: B 1439 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8592 (tp40) REVERT: B 1655 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7620 (p90) outliers start: 55 outliers final: 41 residues processed: 237 average time/residue: 0.1272 time to fit residues: 46.8106 Evaluate side-chains 228 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1344 ASN Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1439 GLN Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1655 PHE Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2013 MET Chi-restraints excluded: chain B residue 2040 ILE Chi-restraints excluded: chain B residue 2060 THR Chi-restraints excluded: chain B residue 2061 LEU Chi-restraints excluded: chain B residue 2094 HIS Chi-restraints excluded: chain B residue 2175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 191 optimal weight: 5.9990 chunk 45 optimal weight: 0.0670 chunk 165 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1971 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 = 0.3867 r_free = 0.3867 target = 0.081189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059107 restraints weight = 70517.728| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.76 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16804 Z= 0.168 Angle : 0.734 17.238 22773 Z= 0.362 Chirality : 0.046 0.239 2534 Planarity : 0.004 0.054 2915 Dihedral : 4.544 24.042 2213 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 2.55 % Allowed : 27.85 % Favored : 69.60 % 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 are not related in a simple way. whole: -1.01 (0.18), residues: 2035 helix: 0.39 (0.18), residues: 853 sheet: -1.08 (0.30), residues: 287 loop : -1.54 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 552 TYR 0.018 0.001 TYR B 940 PHE 0.019 0.001 PHE B 676 TRP 0.016 0.001 TRP B1955 HIS 0.028 0.001 HIS B1533 Details of bonding type rmsd covalent geometry : bond 0.00377 (16796) covalent geometry : angle 0.73183 (22764) hydrogen bonds : bond 0.04003 ( 675) hydrogen bonds : angle 4.96055 ( 1917) metal coordination : bond 0.01560 ( 8) metal coordination : angle 3.15580 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 PHE cc_start: 0.5948 (t80) cc_final: 0.5415 (t80) REVERT: B 413 MET cc_start: 0.4658 (pmm) cc_final: 0.3013 (ptt) REVERT: B 552 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8602 (tmm160) REVERT: B 669 LEU cc_start: 0.9014 (mm) cc_final: 0.8496 (mm) REVERT: B 975 TYR cc_start: 0.8109 (m-80) cc_final: 0.7766 (m-80) REVERT: B 1183 MET cc_start: 0.8230 (mmp) cc_final: 0.7937 (mmp) REVERT: B 1415 MET cc_start: 0.7923 (mmp) cc_final: 0.7505 (mmm) REVERT: B 1439 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8641 (tp40) REVERT: B 1655 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7631 (p90) REVERT: B 2079 GLU cc_start: 0.7054 (tt0) cc_final: 0.6457 (tm-30) outliers start: 46 outliers final: 41 residues processed: 224 average time/residue: 0.1356 time to fit residues: 46.6568 Evaluate side-chains 224 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1161 HIS Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1254 VAL Chi-restraints excluded: chain B residue 1296 HIS Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1376 VAL Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1427 THR Chi-restraints excluded: chain B residue 1439 GLN Chi-restraints excluded: chain B residue 1561 PHE Chi-restraints excluded: chain B residue 1568 THR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1655 PHE Chi-restraints excluded: chain B residue 1661 ILE Chi-restraints excluded: chain B residue 1705 VAL Chi-restraints excluded: chain B residue 1716 PHE Chi-restraints excluded: chain B residue 1757 THR Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1937 LEU Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2040 ILE Chi-restraints excluded: chain B residue 2060 THR Chi-restraints excluded: chain B residue 2061 LEU Chi-restraints excluded: chain B residue 2094 HIS Chi-restraints excluded: chain B residue 2175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 99 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 170 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1971 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 = 0.3885 r_free = 0.3885 target = 0.082077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.059979 restraints weight = 72161.774| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.90 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16804 Z= 0.133 Angle : 0.727 15.094 22773 Z= 0.357 Chirality : 0.046 0.219 2534 Planarity : 0.004 0.053 2915 Dihedral : 4.545 24.170 2213 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 2.44 % Allowed : 28.24 % Favored : 69.32 % 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 are not related in a simple way. whole: -1.02 (0.18), residues: 2035 helix: 0.38 (0.18), residues: 853 sheet: -1.03 (0.30), residues: 280 loop : -1.55 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 552 TYR 0.035 0.001 TYR B 402 PHE 0.023 0.001 PHE B 749 TRP 0.015 0.001 TRP B1955 HIS 0.032 0.001 HIS B1533 Details of bonding type rmsd covalent geometry : bond 0.00296 (16796) covalent geometry : angle 0.72526 (22764) hydrogen bonds : bond 0.03858 ( 675) hydrogen bonds : angle 4.91058 ( 1917) metal coordination : bond 0.01270 ( 8) metal coordination : angle 2.89032 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.19 seconds wall clock time: 59 minutes 0.83 seconds (3540.83 seconds total)