Starting phenix.real_space_refine on Tue Dec 31 21:20:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.map" model { file = "/net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7os2_13046/12_2024/7os2_13046.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 10517 2.51 5 N 2834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16485 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 13879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1726, 13879 Classifications: {'peptide': 1726} Link IDs: {'PTRANS': 79, 'TRANS': 1646} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 444 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "J" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2162 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 245} Time building chain proxies: 10.33, per 1000 atoms: 0.63 Number of scatterers: 16485 At special positions: 0 Unit cell: (107.091, 141.255, 145.197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 3051 8.00 N 2834 7.00 C 10517 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: 3.92 Conformation dependent library (CDL) restraints added in 2.1 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 16 sheets defined 50.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.723A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.553A pdb=" N LEU B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 4.122A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 4.984A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.804A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 4.280A pdb=" N PHE B 536 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.611A pdb=" N GLU B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.806A pdb=" N GLU B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 599 Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.850A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 696 through 715 removed outlier: 3.825A pdb=" N ASN B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 745 removed outlier: 3.566A pdb=" N LYS B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 745 " --> pdb=" O MET B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 754 Processing helix chain 'B' and resid 760 through 767 removed outlier: 4.418A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.605A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 803 Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.723A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 854 Processing helix chain 'B' and resid 875 through 884 removed outlier: 3.852A pdb=" N TYR B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 921 Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.581A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 937 removed outlier: 3.676A pdb=" N GLY B 937 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'B' and resid 949 through 967 Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1020 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 3.700A pdb=" N GLU B1042 " --> pdb=" O GLN B1038 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B1043 " --> pdb=" O LYS B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1074 through 1103 removed outlier: 3.803A pdb=" N GLY B1089 " --> pdb=" O THR B1085 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 removed outlier: 3.509A pdb=" N LYS B1110 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1136 through 1146 removed outlier: 3.559A pdb=" N LYS B1146 " --> pdb=" O LYS B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1155 Processing helix chain 'B' and resid 1157 through 1165 Processing helix chain 'B' and resid 1170 through 1181 Processing helix chain 'B' and resid 1211 through 1216 Processing helix chain 'B' and resid 1310 through 1312 No H-bonds generated for 'chain 'B' and resid 1310 through 1312' Processing helix chain 'B' and resid 1314 through 1323 removed outlier: 3.834A pdb=" N GLU B1318 " --> pdb=" O ASN B1314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B1319 " --> pdb=" O SER B1315 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B1323 " --> pdb=" O SER B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1342 removed outlier: 4.438A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1371 removed outlier: 3.558A pdb=" N ALA B1360 " --> pdb=" O LYS B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1398 Processing helix chain 'B' and resid 1411 through 1422 Processing helix chain 'B' and resid 1428 through 1437 Processing helix chain 'B' and resid 1442 through 1447 removed outlier: 3.785A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1461 removed outlier: 3.527A pdb=" N ILE B1459 " --> pdb=" O VAL B1456 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.894A pdb=" N LEU B1467 " --> pdb=" O ASN B1463 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B1480 " --> pdb=" O TYR B1476 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1505 removed outlier: 3.718A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1519 removed outlier: 3.799A pdb=" N ARG B1519 " --> pdb=" O PRO B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1542 Processing helix chain 'B' and resid 1542 through 1554 removed outlier: 3.539A pdb=" N VAL B1546 " --> pdb=" O MET B1542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B1547 " --> pdb=" O ALA B1543 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1583 removed outlier: 3.652A pdb=" N THR B1569 " --> pdb=" O SER B1565 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1602 removed outlier: 3.838A pdb=" N LEU B1597 " --> pdb=" O THR B1593 " (cutoff:3.500A) Proline residue: B1599 - end of helix removed outlier: 4.011A pdb=" N GLU B1602 " --> pdb=" O ILE B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1615 removed outlier: 3.660A pdb=" N ASN B1615 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1639 Processing helix chain 'B' and resid 1649 through 1652 removed outlier: 4.067A pdb=" N TRP B1652 " --> pdb=" O SER B1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1652' Processing helix chain 'B' and resid 1680 through 1689 Processing helix chain 'B' and resid 1690 through 1692 No H-bonds generated for 'chain 'B' and resid 1690 through 1692' Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 3.575A pdb=" N LYS B1715 " --> pdb=" O LYS B1711 " (cutoff:3.500A) Processing helix chain 'B' and resid 1731 through 1742 removed outlier: 4.606A pdb=" N HIS B1735 " --> pdb=" O CYS B1731 " (cutoff:3.500A) Processing helix chain 'B' and resid 1747 through 1756 Processing helix chain 'B' and resid 1758 through 1767 removed outlier: 3.614A pdb=" N ARG B1762 " --> pdb=" O THR B1758 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B1766 " --> pdb=" O ARG B1762 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1772 Processing helix chain 'B' and resid 1777 through 1799 removed outlier: 3.535A pdb=" N LEU B1793 " --> pdb=" O VAL B1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1822 removed outlier: 3.542A pdb=" N TYR B1822 " --> pdb=" O ILE B1818 " (cutoff:3.500A) Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1851 removed outlier: 3.748A pdb=" N GLU B1847 " --> pdb=" O ARG B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1863 through 1875 removed outlier: 3.973A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B1874 " --> pdb=" O GLN B1870 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1900 Processing helix chain 'B' and resid 1905 through 1934 removed outlier: 3.859A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1936 through 1952 removed outlier: 3.721A pdb=" N GLN B1951 " --> pdb=" O GLN B1947 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1963 removed outlier: 3.507A pdb=" N GLN B1962 " --> pdb=" O TYR B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1978 Processing helix chain 'B' and resid 1982 through 1987 Processing helix chain 'B' and resid 1989 through 1997 Processing helix chain 'B' and resid 2000 through 2014 removed outlier: 3.957A pdb=" N ASP B2006 " --> pdb=" O SER B2002 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 removed outlier: 3.577A pdb=" N GLU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 41 removed outlier: 3.532A pdb=" N SER C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 55 Processing helix chain 'J' and resid 2072 through 2081 removed outlier: 3.607A pdb=" N ARG J2076 " --> pdb=" O GLU J2072 " (cutoff:3.500A) Processing helix chain 'J' and resid 2085 through 2088 Processing helix chain 'J' and resid 2108 through 2117 Processing helix chain 'J' and resid 2166 through 2170 Processing helix chain 'J' and resid 2189 through 2203 Processing helix chain 'J' and resid 2231 through 2241 removed outlier: 3.743A pdb=" N GLN J2240 " --> pdb=" O GLU J2236 " (cutoff:3.500A) Processing helix chain 'J' and resid 2252 through 2254 No H-bonds generated for 'chain 'J' and resid 2252 through 2254' Processing helix chain 'J' and resid 2284 through 2288 Processing helix chain 'J' and resid 2310 through 2314 removed outlier: 3.535A pdb=" N HIS J2313 " --> pdb=" O ARG J2310 " (cutoff:3.500A) Processing helix chain 'J' and resid 2322 through 2327 removed outlier: 3.558A pdb=" N VAL J2325 " --> pdb=" O GLU J2322 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR J2326 " --> pdb=" O GLY J2323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 435 through 439 removed outlier: 3.712A pdb=" N PHE B 435 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 446 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 722 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 721 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER B 811 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 723 " --> pdb=" O SER B 811 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B 783 " --> pdb=" O VAL B 810 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.416A pdb=" N ALA B 567 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS B 537 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 611 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 499 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N SER B 652 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU B 501 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 832 through 835 Processing sheet with id=AA4, first strand: chain 'B' and resid 970 through 972 Processing sheet with id=AA5, first strand: chain 'B' and resid 1250 through 1257 removed outlier: 6.786A pdb=" N THR B1197 " --> pdb=" O ILE B1193 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B1201 " --> pdb=" O HIS B1189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1233 through 1242 removed outlier: 3.538A pdb=" N HIS B1235 " --> pdb=" O VAL B1225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1307 through 1308 removed outlier: 3.925A pdb=" N LEU B1307 " --> pdb=" O PHE B1328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1405 through 1407 removed outlier: 6.482A pdb=" N CYS B1376 " --> pdb=" O ILE B1425 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B1427 " --> pdb=" O CYS B1376 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR B1378 " --> pdb=" O SER B1427 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B1377 " --> pdb=" O VAL B1452 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B1454 " --> pdb=" O VAL B1377 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B1379 " --> pdb=" O ASP B1454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1523 through 1529 removed outlier: 6.214A pdb=" N VAL B1661 " --> pdb=" O VAL B1703 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET B1705 " --> pdb=" O VAL B1661 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B1663 " --> pdb=" O MET B1705 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1667 through 1670 Processing sheet with id=AB2, first strand: chain 'B' and resid 1802 through 1805 removed outlier: 3.597A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2017 through 2023 removed outlier: 3.809A pdb=" N GLU B2018 " --> pdb=" O GLU B2042 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2075 through 2082 removed outlier: 5.871A pdb=" N LEU B2076 " --> pdb=" O ASP B2070 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP B2070 " --> pdb=" O LEU B2076 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B2069 " --> pdb=" O THR B2105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 2090 through 2092 removed outlier: 6.179A pdb=" N GLY J2130 " --> pdb=" O PRO J2174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY J2176 " --> pdb=" O LEU J2128 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR J2103 " --> pdb=" O LYS J2140 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE J2142 " --> pdb=" O THR J2103 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE J2105 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N CYS J2144 " --> pdb=" O ILE J2105 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N VAL J2146 " --> pdb=" O PRO J2107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 2256 through 2259 removed outlier: 4.226A pdb=" N ALA J2227 " --> pdb=" O VAL J2259 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY J2130 " --> pdb=" O PRO J2174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY J2176 " --> pdb=" O LEU J2128 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N PHE J2270 " --> pdb=" O GLU J2141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG J2143 " --> pdb=" O PHE J2270 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET J2272 " --> pdb=" O ARG J2143 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE J2145 " --> pdb=" O MET J2272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 2151 through 2152 777 hydrogen bonds defined for protein. 2184 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: 8.49 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5419 1.34 - 1.46: 2886 1.46 - 1.57: 8405 1.57 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 16847 Sorted by residual: bond pdb=" CA VAL B1563 " pdb=" CB VAL B1563 " ideal model delta sigma weight residual 1.546 1.532 0.014 8.80e-03 1.29e+04 2.47e+00 bond pdb=" CB THR C 34 " pdb=" CG2 THR C 34 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CA GLY B1529 " pdb=" C GLY B1529 " ideal model delta sigma weight residual 1.520 1.511 0.009 7.30e-03 1.88e+04 1.57e+00 bond pdb=" CB THR B1891 " pdb=" CG2 THR B1891 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB ILE B1477 " pdb=" CG2 ILE B1477 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.48e-01 ... (remaining 16842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 22469 1.84 - 3.68: 315 3.68 - 5.53: 37 5.53 - 7.37: 6 7.37 - 9.21: 3 Bond angle restraints: 22830 Sorted by residual: angle pdb=" C ILE B1598 " pdb=" CA ILE B1598 " pdb=" CB ILE B1598 " ideal model delta sigma weight residual 113.70 110.44 3.26 9.50e-01 1.11e+00 1.18e+01 angle pdb=" CG ARG C 11 " pdb=" CD ARG C 11 " pdb=" NE ARG C 11 " ideal model delta sigma weight residual 112.00 118.78 -6.78 2.20e+00 2.07e-01 9.49e+00 angle pdb=" C PRO J2134 " pdb=" N ASP J2135 " pdb=" CA ASP J2135 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.79e+00 angle pdb=" CD ARG C 11 " pdb=" NE ARG C 11 " pdb=" CZ ARG C 11 " ideal model delta sigma weight residual 124.40 128.29 -3.89 1.40e+00 5.10e-01 7.70e+00 angle pdb=" C SER C 15 " pdb=" N GLU C 16 " pdb=" CA GLU C 16 " ideal model delta sigma weight residual 122.19 125.85 -3.66 1.41e+00 5.03e-01 6.74e+00 ... (remaining 22825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 9503 17.18 - 34.35: 608 34.35 - 51.53: 113 51.53 - 68.70: 26 68.70 - 85.88: 8 Dihedral angle restraints: 10258 sinusoidal: 4243 harmonic: 6015 Sorted by residual: dihedral pdb=" CG ARG C 11 " pdb=" CD ARG C 11 " pdb=" NE ARG C 11 " pdb=" CZ ARG C 11 " ideal model delta sinusoidal sigma weight residual 90.00 22.19 67.81 2 1.50e+01 4.44e-03 1.83e+01 dihedral pdb=" CA GLN B 418 " pdb=" C GLN B 418 " pdb=" N GLY B 419 " pdb=" CA GLY B 419 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ILE B1663 " pdb=" C ILE B1663 " pdb=" N MET B1664 " pdb=" CA MET B1664 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 10255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1429 0.031 - 0.061: 745 0.061 - 0.092: 228 0.092 - 0.123: 142 0.123 - 0.153: 18 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA ILE C 7 " pdb=" N ILE C 7 " pdb=" C ILE C 7 " pdb=" CB ILE C 7 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ASP J2135 " pdb=" N ASP J2135 " pdb=" C ASP J2135 " pdb=" CB ASP J2135 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CG LEU B 748 " pdb=" CB LEU B 748 " pdb=" CD1 LEU B 748 " pdb=" CD2 LEU B 748 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2559 not shown) Planarity restraints: 2933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 447 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 448 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 448 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 448 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 404 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 405 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 405 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 405 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 625 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO B 626 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.025 5.00e-02 4.00e+02 ... (remaining 2930 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2221 2.75 - 3.29: 16366 3.29 - 3.82: 27486 3.82 - 4.36: 33342 4.36 - 4.90: 57288 Nonbonded interactions: 136703 Sorted by model distance: nonbonded pdb=" O THR B1338 " pdb=" OG SER B1342 " model vdw 2.209 3.040 nonbonded pdb=" O GLY B 474 " pdb=" NH1 ARG B 558 " model vdw 2.217 3.120 nonbonded pdb=" O ASP B1753 " pdb=" OG1 THR B1756 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN J2280 " pdb=" ND2 ASN J2282 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN B1866 " pdb=" NH2 ARG B1869 " model vdw 2.250 3.120 ... (remaining 136698 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.005 0.045 16847 Z= 0.350 Angle : 0.564 9.210 22830 Z= 0.292 Chirality : 0.044 0.153 2562 Planarity : 0.004 0.060 2933 Dihedral : 12.082 85.881 6362 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.93 % Allowed : 5.24 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2040 helix: 1.10 (0.18), residues: 866 sheet: 0.19 (0.28), residues: 368 loop : -0.04 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2065 HIS 0.005 0.001 HIS B1179 PHE 0.014 0.001 PHE B1713 TYR 0.021 0.001 TYR B1238 ARG 0.004 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 423 MET cc_start: 0.9244 (ptm) cc_final: 0.8858 (ptm) REVERT: B 741 MET cc_start: 0.9203 (tpp) cc_final: 0.8981 (tpp) REVERT: B 791 ARG cc_start: 0.8498 (tpm170) cc_final: 0.7820 (tpm170) REVERT: B 1152 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8148 (mtm110) REVERT: B 1719 TYR cc_start: 0.8613 (m-80) cc_final: 0.8330 (m-80) REVERT: B 1856 GLU cc_start: 0.7991 (tp30) cc_final: 0.7585 (tp30) REVERT: B 1986 MET cc_start: 0.8433 (ttp) cc_final: 0.8138 (ttp) REVERT: B 2017 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 23 ASP cc_start: 0.8919 (t0) cc_final: 0.8369 (t0) REVERT: C 42 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8533 (tttm) REVERT: J 2143 ARG cc_start: 0.8599 (mmt90) cc_final: 0.8399 (mmt-90) outliers start: 17 outliers final: 2 residues processed: 238 average time/residue: 1.9433 time to fit residues: 507.4953 Evaluate side-chains 145 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain C residue 19 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1191 GLN C 39 ASN J2089 HIS J2316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16847 Z= 0.231 Angle : 0.601 10.283 22830 Z= 0.307 Chirality : 0.044 0.163 2562 Planarity : 0.005 0.059 2933 Dihedral : 4.878 59.570 2235 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 9.83 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 2040 helix: 1.23 (0.18), residues: 869 sheet: 0.35 (0.27), residues: 367 loop : 0.07 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J2177 HIS 0.005 0.001 HIS B 421 PHE 0.010 0.001 PHE B2094 TYR 0.017 0.001 TYR B2021 ARG 0.006 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 2.056 Fit side-chains revert: symmetry clash REVERT: B 741 MET cc_start: 0.9234 (tpp) cc_final: 0.8979 (tpp) REVERT: B 1053 GLU cc_start: 0.8145 (mp0) cc_final: 0.7903 (mp0) REVERT: B 1170 MET cc_start: 0.8243 (mmt) cc_final: 0.7872 (mmt) REVERT: B 1856 GLU cc_start: 0.8081 (tp30) cc_final: 0.7572 (tp30) REVERT: B 1966 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 1986 MET cc_start: 0.8404 (ttp) cc_final: 0.8180 (ttp) REVERT: B 2018 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: B 2040 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 10 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7622 (mmp80) REVERT: C 42 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8485 (tttp) outliers start: 44 outliers final: 14 residues processed: 188 average time/residue: 1.3820 time to fit residues: 290.3902 Evaluate side-chains 148 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1279 GLU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2018 GLU Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain B residue 2114 MET Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 148 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN B1191 GLN B1735 HIS B2085 GLN C 39 ASN J2089 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16847 Z= 0.282 Angle : 0.577 11.231 22830 Z= 0.292 Chirality : 0.044 0.168 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.706 59.561 2233 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.67 % Allowed : 11.52 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2040 helix: 1.22 (0.18), residues: 872 sheet: 0.38 (0.27), residues: 366 loop : 0.02 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J2177 HIS 0.004 0.001 HIS B 618 PHE 0.024 0.001 PHE B 751 TYR 0.016 0.001 TYR B1238 ARG 0.010 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.974 Fit side-chains revert: symmetry clash REVERT: B 741 MET cc_start: 0.9246 (tpp) cc_final: 0.8980 (tpp) REVERT: B 1032 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: B 1053 GLU cc_start: 0.8176 (mp0) cc_final: 0.7891 (mp0) REVERT: B 1170 MET cc_start: 0.8396 (mmt) cc_final: 0.8123 (mmt) REVERT: B 1598 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8826 (mm) REVERT: B 1856 GLU cc_start: 0.8106 (tp30) cc_final: 0.7567 (tp30) REVERT: B 1966 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 1986 MET cc_start: 0.8432 (ttp) cc_final: 0.8150 (ttp) REVERT: B 2040 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 42 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8499 (tttm) outliers start: 49 outliers final: 18 residues processed: 173 average time/residue: 1.3168 time to fit residues: 256.3268 Evaluate side-chains 154 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1279 GLU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain B residue 2114 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS J2276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16847 Z= 0.167 Angle : 0.545 10.156 22830 Z= 0.272 Chirality : 0.042 0.165 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.508 56.577 2233 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 12.55 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2040 helix: 1.36 (0.18), residues: 874 sheet: 0.40 (0.27), residues: 359 loop : -0.00 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J2177 HIS 0.004 0.001 HIS B 618 PHE 0.022 0.001 PHE B 701 TYR 0.021 0.001 TYR B2021 ARG 0.008 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: B 437 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7398 (ptm-80) REVERT: B 741 MET cc_start: 0.9240 (tpp) cc_final: 0.8556 (tpp) REVERT: B 1856 GLU cc_start: 0.8099 (tp30) cc_final: 0.7547 (tp30) REVERT: B 1986 MET cc_start: 0.8414 (ttp) cc_final: 0.8143 (ttp) REVERT: B 2040 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7318 (tm-30) outliers start: 36 outliers final: 17 residues processed: 169 average time/residue: 1.4666 time to fit residues: 277.5423 Evaluate side-chains 151 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 0.0000 chunk 49 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B 805 HIS ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16847 Z= 0.169 Angle : 0.538 9.819 22830 Z= 0.269 Chirality : 0.042 0.165 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.388 56.560 2233 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.97 % Allowed : 13.48 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2040 helix: 1.41 (0.18), residues: 875 sheet: 0.38 (0.27), residues: 359 loop : 0.01 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J2177 HIS 0.004 0.001 HIS B1175 PHE 0.023 0.001 PHE B 751 TYR 0.012 0.001 TYR B 991 ARG 0.012 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: B 437 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7243 (ptm-80) REVERT: B 745 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7978 (pttm) REVERT: B 1032 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: B 1152 ARG cc_start: 0.8286 (mtm110) cc_final: 0.7881 (mtm110) REVERT: B 1856 GLU cc_start: 0.8105 (tp30) cc_final: 0.7560 (tp30) REVERT: B 1986 MET cc_start: 0.8460 (ttp) cc_final: 0.8209 (ttp) REVERT: B 2040 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7302 (tm-30) outliers start: 36 outliers final: 18 residues processed: 173 average time/residue: 1.4068 time to fit residues: 271.6070 Evaluate side-chains 152 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 745 LYS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1401 LEU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.5980 chunk 176 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1113 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16847 Z= 0.153 Angle : 0.538 9.964 22830 Z= 0.267 Chirality : 0.042 0.141 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.308 56.750 2233 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.80 % Allowed : 13.97 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2040 helix: 1.47 (0.18), residues: 875 sheet: 0.42 (0.27), residues: 359 loop : 0.02 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J2151 HIS 0.005 0.001 HIS B 805 PHE 0.024 0.001 PHE B 701 TYR 0.018 0.001 TYR B 861 ARG 0.009 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: B 745 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7934 (pttm) REVERT: B 763 ARG cc_start: 0.7910 (mpt90) cc_final: 0.7709 (mtm110) REVERT: B 1847 GLU cc_start: 0.8161 (tp30) cc_final: 0.7902 (tp30) REVERT: B 1856 GLU cc_start: 0.8104 (tp30) cc_final: 0.7552 (tp30) REVERT: B 1966 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7801 (t80) REVERT: B 1986 MET cc_start: 0.8464 (ttp) cc_final: 0.8252 (ttp) REVERT: B 2040 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7287 (tm-30) outliers start: 33 outliers final: 18 residues processed: 167 average time/residue: 1.3337 time to fit residues: 250.8452 Evaluate side-chains 150 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 745 LYS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1401 LEU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 195 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16847 Z= 0.170 Angle : 0.540 10.902 22830 Z= 0.268 Chirality : 0.042 0.146 2562 Planarity : 0.004 0.060 2933 Dihedral : 4.256 56.680 2233 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 14.25 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 2040 helix: 1.48 (0.18), residues: 877 sheet: 0.42 (0.27), residues: 360 loop : 0.04 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 PHE 0.011 0.001 PHE B1148 TYR 0.019 0.001 TYR B2021 ARG 0.010 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: B 1847 GLU cc_start: 0.8171 (tp30) cc_final: 0.7901 (tp30) REVERT: B 1856 GLU cc_start: 0.8103 (tp30) cc_final: 0.7544 (tp30) REVERT: B 1966 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 2040 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7320 (tm-30) outliers start: 34 outliers final: 18 residues processed: 165 average time/residue: 1.3436 time to fit residues: 249.2193 Evaluate side-chains 150 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1352 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain B residue 2047 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS J2247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16847 Z= 0.222 Angle : 0.551 10.773 22830 Z= 0.275 Chirality : 0.043 0.155 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.267 56.778 2233 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.02 % Allowed : 14.52 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2040 helix: 1.46 (0.18), residues: 876 sheet: 0.39 (0.27), residues: 362 loop : 0.07 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 PHE 0.024 0.001 PHE B 701 TYR 0.017 0.001 TYR B 861 ARG 0.012 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: B 437 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7797 (ptm-80) REVERT: B 1011 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 1732 MET cc_start: 0.8514 (mmm) cc_final: 0.8099 (mmm) REVERT: B 1847 GLU cc_start: 0.8180 (tp30) cc_final: 0.7910 (tp30) REVERT: B 1856 GLU cc_start: 0.8112 (tp30) cc_final: 0.7536 (tp30) REVERT: B 1966 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7788 (t80) REVERT: B 1986 MET cc_start: 0.8402 (ttp) cc_final: 0.8097 (mtp) REVERT: B 1988 MET cc_start: 0.8604 (tmm) cc_final: 0.8370 (ppp) REVERT: B 2040 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7246 (tm-30) outliers start: 37 outliers final: 19 residues processed: 165 average time/residue: 1.3342 time to fit residues: 247.2471 Evaluate side-chains 155 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1352 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2103 THR Chi-restraints excluded: chain J residue 2225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 967 ASN B 995 ASN B1332 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16847 Z= 0.367 Angle : 0.619 11.712 22830 Z= 0.309 Chirality : 0.045 0.156 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.492 57.287 2233 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.97 % Allowed : 14.63 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2040 helix: 1.34 (0.18), residues: 871 sheet: 0.30 (0.27), residues: 362 loop : 0.04 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J2177 HIS 0.005 0.001 HIS B1179 PHE 0.032 0.002 PHE B1736 TYR 0.019 0.002 TYR B2021 ARG 0.014 0.000 ARG B1152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: B 437 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7742 (ptm-80) REVERT: B 1011 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: B 1847 GLU cc_start: 0.8181 (tp30) cc_final: 0.7882 (tp30) REVERT: B 1856 GLU cc_start: 0.8127 (tp30) cc_final: 0.7540 (tp30) REVERT: B 1986 MET cc_start: 0.8452 (ttp) cc_final: 0.8141 (mtp) REVERT: B 1988 MET cc_start: 0.8681 (tmm) cc_final: 0.8379 (ppp) REVERT: B 2009 ARG cc_start: 0.9147 (ttp-110) cc_final: 0.8921 (ttp80) REVERT: B 2040 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7272 (tm-30) REVERT: J 2119 ASP cc_start: 0.8834 (t0) cc_final: 0.8508 (t0) outliers start: 36 outliers final: 21 residues processed: 163 average time/residue: 1.3527 time to fit residues: 247.0336 Evaluate side-chains 155 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1279 GLU Chi-restraints excluded: chain B residue 1352 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2103 THR Chi-restraints excluded: chain J residue 2225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 967 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16847 Z= 0.217 Angle : 0.587 12.919 22830 Z= 0.289 Chirality : 0.043 0.158 2562 Planarity : 0.004 0.061 2933 Dihedral : 4.416 57.313 2233 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.31 % Allowed : 15.50 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2040 helix: 1.40 (0.18), residues: 872 sheet: 0.27 (0.27), residues: 362 loop : 0.05 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 PHE 0.028 0.001 PHE B1736 TYR 0.016 0.001 TYR B 861 ARG 0.014 0.000 ARG B1152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 2.065 Fit side-chains revert: symmetry clash REVERT: B 437 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7769 (ptm-80) REVERT: B 1011 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 1847 GLU cc_start: 0.8158 (tp30) cc_final: 0.7890 (tp30) REVERT: B 1856 GLU cc_start: 0.8106 (tp30) cc_final: 0.7507 (tp30) REVERT: B 1986 MET cc_start: 0.8477 (ttp) cc_final: 0.8183 (mtp) REVERT: B 1988 MET cc_start: 0.8673 (tmm) cc_final: 0.8384 (ppp) REVERT: B 2009 ARG cc_start: 0.9131 (ttp-110) cc_final: 0.8907 (ttp80) REVERT: B 2040 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7312 (tm-30) REVERT: J 2119 ASP cc_start: 0.8824 (t0) cc_final: 0.8504 (t0) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 1.4251 time to fit residues: 246.5712 Evaluate side-chains 150 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1352 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 2011 CYS Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2103 THR Chi-restraints excluded: chain J residue 2225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.050912 restraints weight = 40042.760| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.69 r_work: 0.2648 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16847 Z= 0.181 Angle : 0.578 12.857 22830 Z= 0.285 Chirality : 0.042 0.161 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.303 57.007 2233 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.47 % Allowed : 15.28 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2040 helix: 1.45 (0.18), residues: 874 sheet: 0.27 (0.27), residues: 361 loop : 0.07 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 PHE 0.025 0.001 PHE B1736 TYR 0.019 0.001 TYR B2021 ARG 0.013 0.000 ARG B1152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5527.95 seconds wall clock time: 100 minutes 16.14 seconds (6016.14 seconds total)