Starting phenix.real_space_refine on Wed Mar 4 21:59:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_13046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_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 { model { file = "/net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_13046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_13046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_13046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7os2_13046/03_2026/7os2_13046.map" } resolution = 2.76 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= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.26, per 1000 atoms: 0.20 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: 1.38 Conformation dependent library (CDL) restraints added in 731.2 milliseconds 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: 0.93 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: 4.06 Time building geometry restraints manager: 1.87 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- 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= 0.232 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 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: 0.65 (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 ARG 0.004 0.000 ARG C 5 TYR 0.021 0.001 TYR B1238 PHE 0.014 0.001 PHE B1713 TRP 0.010 0.001 TRP B2065 HIS 0.005 0.001 HIS B1179 Details of bonding type rmsd covalent geometry : bond 0.00541 (16847) covalent geometry : angle 0.56365 (22830) hydrogen bonds : bond 0.17176 ( 758) hydrogen bonds : angle 6.43932 ( 2184) *********************** 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 : 0.677 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: 0.8065 time to fit residues: 208.2861 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 : 0.540 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 B1191 GLN B1735 HIS C 39 ASN J2089 HIS J2316 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.049847 restraints weight = 40451.501| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.69 r_work: 0.2615 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16847 Z= 0.210 Angle : 0.625 11.343 22830 Z= 0.319 Chirality : 0.045 0.161 2562 Planarity : 0.005 0.059 2933 Dihedral : 4.952 59.629 2235 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.51 % Allowed : 9.72 % 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 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: 0.78 (0.19), residues: 2040 helix: 1.17 (0.18), residues: 869 sheet: 0.32 (0.27), residues: 367 loop : 0.06 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 28 TYR 0.017 0.002 TYR B2021 PHE 0.011 0.001 PHE B 664 TRP 0.013 0.001 TRP J2177 HIS 0.005 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00493 (16847) covalent geometry : angle 0.62489 (22830) hydrogen bonds : bond 0.04622 ( 758) hydrogen bonds : angle 4.97158 ( 2184) *********************** 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 200 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9259 (ptm) cc_final: 0.9013 (ptm) REVERT: B 432 ASP cc_start: 0.8539 (p0) cc_final: 0.8305 (p0) REVERT: B 741 MET cc_start: 0.9451 (tpp) cc_final: 0.9146 (tpp) REVERT: B 1022 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 1053 GLU cc_start: 0.8519 (mp0) cc_final: 0.8259 (mp0) REVERT: B 1151 GLU cc_start: 0.8772 (mp0) cc_final: 0.8534 (tm-30) REVERT: B 1152 ARG cc_start: 0.8624 (ttm170) cc_final: 0.8422 (mtm110) REVERT: B 1170 MET cc_start: 0.8531 (mmt) cc_final: 0.8273 (mmt) REVERT: B 1664 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8249 (tpp) REVERT: B 1856 GLU cc_start: 0.8592 (tp30) cc_final: 0.8006 (tp30) REVERT: B 1966 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7859 (t80) REVERT: B 1986 MET cc_start: 0.8585 (ttp) cc_final: 0.8328 (ttp) REVERT: B 2018 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: B 2040 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 2087 LYS cc_start: 0.9020 (tttt) cc_final: 0.8779 (ttmm) REVERT: C 10 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7822 (mmp80) REVERT: C 42 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8538 (tttp) outliers start: 46 outliers final: 17 residues processed: 182 average time/residue: 0.6585 time to fit residues: 133.3341 Evaluate side-chains 156 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 565 THR 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 1022 SER Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1167 MET 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 1664 MET 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 99 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN B1191 GLN B2085 GLN J2089 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.049058 restraints weight = 40935.507| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.71 r_work: 0.2592 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16847 Z= 0.226 Angle : 0.596 12.171 22830 Z= 0.302 Chirality : 0.045 0.173 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.794 59.673 2233 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.78 % Allowed : 11.79 % Favored : 85.43 % 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: 0.73 (0.19), residues: 2040 helix: 1.13 (0.18), residues: 872 sheet: 0.36 (0.27), residues: 364 loop : -0.03 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 700 TYR 0.017 0.001 TYR B1238 PHE 0.022 0.001 PHE B 751 TRP 0.011 0.001 TRP J2177 HIS 0.004 0.001 HIS B 990 Details of bonding type rmsd covalent geometry : bond 0.00536 (16847) covalent geometry : angle 0.59635 (22830) hydrogen bonds : bond 0.04405 ( 758) hydrogen bonds : angle 4.77408 ( 2184) *********************** 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 197 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 432 ASP cc_start: 0.8547 (p0) cc_final: 0.8298 (p0) REVERT: B 741 MET cc_start: 0.9462 (tpp) cc_final: 0.9131 (tpp) REVERT: B 1022 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8906 (p) REVERT: B 1032 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: B 1053 GLU cc_start: 0.8558 (mp0) cc_final: 0.8242 (mp0) REVERT: B 1151 GLU cc_start: 0.8785 (mp0) cc_final: 0.8498 (tm-30) REVERT: B 1170 MET cc_start: 0.8665 (mmt) cc_final: 0.8338 (mmt) REVERT: B 1598 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 1664 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: B 1856 GLU cc_start: 0.8633 (tp30) cc_final: 0.8004 (tp30) REVERT: B 1966 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 1986 MET cc_start: 0.8588 (ttp) cc_final: 0.8316 (ttp) REVERT: B 2018 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: B 2040 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7468 (tm-30) REVERT: C 42 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8553 (tttp) outliers start: 51 outliers final: 20 residues processed: 182 average time/residue: 0.6403 time to fit residues: 130.3505 Evaluate side-chains 158 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 748 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1167 MET 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 1664 MET Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2018 GLU 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 Chi-restraints excluded: chain J residue 2157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 123 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN B1191 GLN J2089 HIS J2276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.050441 restraints weight = 40135.757| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.70 r_work: 0.2632 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16847 Z= 0.123 Angle : 0.555 11.180 22830 Z= 0.278 Chirality : 0.042 0.163 2562 Planarity : 0.004 0.064 2933 Dihedral : 4.610 57.057 2233 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.02 % Allowed : 12.77 % Favored : 85.21 % 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: 0.85 (0.19), residues: 2040 helix: 1.30 (0.18), residues: 873 sheet: 0.34 (0.27), residues: 359 loop : -0.02 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1152 TYR 0.017 0.001 TYR B 861 PHE 0.021 0.001 PHE B 701 TRP 0.008 0.001 TRP J2177 HIS 0.004 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00282 (16847) covalent geometry : angle 0.55515 (22830) hydrogen bonds : bond 0.03692 ( 758) hydrogen bonds : angle 4.54982 ( 2184) *********************** 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 176 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: B 432 ASP cc_start: 0.8573 (p0) cc_final: 0.8318 (p0) REVERT: B 437 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7398 (ptm-80) REVERT: B 741 MET cc_start: 0.9449 (tpp) cc_final: 0.9150 (tpp) REVERT: B 1022 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 1151 GLU cc_start: 0.8782 (mp0) cc_final: 0.8428 (tm-30) REVERT: B 1170 MET cc_start: 0.8635 (mmt) cc_final: 0.8308 (mmt) REVERT: B 1856 GLU cc_start: 0.8619 (tp30) cc_final: 0.7977 (tp30) REVERT: B 1986 MET cc_start: 0.8598 (ttp) cc_final: 0.8309 (ttp) REVERT: B 2040 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 37 outliers final: 18 residues processed: 168 average time/residue: 0.6815 time to fit residues: 127.1285 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 : 0.469 ------------------------------------------------------------------------------- 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 1022 SER Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1279 GLU 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 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 72 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1191 GLN B1332 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.048246 restraints weight = 40611.121| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.70 r_work: 0.2575 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16847 Z= 0.271 Angle : 0.612 13.154 22830 Z= 0.307 Chirality : 0.046 0.162 2562 Planarity : 0.004 0.064 2933 Dihedral : 4.702 57.102 2233 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 13.43 % Favored : 84.17 % 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: 0.75 (0.19), residues: 2040 helix: 1.20 (0.18), residues: 872 sheet: 0.25 (0.27), residues: 367 loop : -0.03 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1152 TYR 0.019 0.002 TYR B2021 PHE 0.021 0.001 PHE B 751 TRP 0.011 0.001 TRP J2177 HIS 0.005 0.001 HIS B1179 Details of bonding type rmsd covalent geometry : bond 0.00643 (16847) covalent geometry : angle 0.61210 (22830) hydrogen bonds : bond 0.04302 ( 758) hydrogen bonds : angle 4.62267 ( 2184) *********************** 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 183 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: B 432 ASP cc_start: 0.8686 (p0) cc_final: 0.8413 (p0) REVERT: B 437 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7402 (ptm-80) REVERT: B 741 MET cc_start: 0.9466 (tpp) cc_final: 0.9158 (tpp) REVERT: B 1022 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 1032 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8911 (mp0) REVERT: B 1151 GLU cc_start: 0.8953 (mp0) cc_final: 0.8556 (tm-30) REVERT: B 1170 MET cc_start: 0.8824 (mmt) cc_final: 0.8471 (mmt) REVERT: B 1664 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (tpp) REVERT: B 1856 GLU cc_start: 0.8843 (tp30) cc_final: 0.8189 (tp30) REVERT: B 1986 MET cc_start: 0.8751 (ttp) cc_final: 0.8491 (ttp) REVERT: B 2040 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7563 (tm-30) REVERT: J 2119 ASP cc_start: 0.9222 (t0) cc_final: 0.8869 (t0) outliers start: 44 outliers final: 21 residues processed: 173 average time/residue: 0.6121 time to fit residues: 119.0896 Evaluate side-chains 157 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 565 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1279 GLU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1456 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 1664 MET 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 B residue 2047 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 112 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B1191 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.050039 restraints weight = 40360.208| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.71 r_work: 0.2621 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16847 Z= 0.126 Angle : 0.565 12.020 22830 Z= 0.281 Chirality : 0.043 0.139 2562 Planarity : 0.004 0.064 2933 Dihedral : 4.555 56.982 2233 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.29 % Allowed : 13.97 % Favored : 83.73 % 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: 0.88 (0.19), residues: 2040 helix: 1.34 (0.18), residues: 872 sheet: 0.32 (0.27), residues: 359 loop : 0.00 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1152 TYR 0.018 0.001 TYR B 861 PHE 0.022 0.001 PHE B 701 TRP 0.007 0.001 TRP J2177 HIS 0.004 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00292 (16847) covalent geometry : angle 0.56527 (22830) hydrogen bonds : bond 0.03611 ( 758) hydrogen bonds : angle 4.44550 ( 2184) *********************** 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 181 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9065 (ptm) cc_final: 0.8752 (ttp) REVERT: B 432 ASP cc_start: 0.8596 (p0) cc_final: 0.8343 (p0) REVERT: B 437 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7367 (ptm-80) REVERT: B 741 MET cc_start: 0.9444 (tpp) cc_final: 0.8615 (tpp) REVERT: B 763 ARG cc_start: 0.8173 (mpt90) cc_final: 0.7888 (mtm110) REVERT: B 1022 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8917 (p) REVERT: B 1151 GLU cc_start: 0.8792 (mp0) cc_final: 0.8490 (tm-30) REVERT: B 1170 MET cc_start: 0.8696 (mmt) cc_final: 0.8355 (mmt) REVERT: B 1856 GLU cc_start: 0.8618 (tp30) cc_final: 0.7945 (tp30) REVERT: B 1966 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7741 (t80) REVERT: B 1986 MET cc_start: 0.8652 (ttp) cc_final: 0.7950 (ttp) REVERT: B 2011 CYS cc_start: 0.8856 (m) cc_final: 0.8109 (t) REVERT: B 2040 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7446 (tm-30) REVERT: J 2119 ASP cc_start: 0.9071 (t0) cc_final: 0.8711 (t0) outliers start: 42 outliers final: 20 residues processed: 176 average time/residue: 0.6579 time to fit residues: 128.7859 Evaluate side-chains 154 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 748 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1022 SER 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 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 2037 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 Chi-restraints excluded: chain J residue 2157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1191 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.049850 restraints weight = 40279.695| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.70 r_work: 0.2619 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16847 Z= 0.151 Angle : 0.572 11.616 22830 Z= 0.284 Chirality : 0.043 0.139 2562 Planarity : 0.004 0.063 2933 Dihedral : 4.506 57.089 2233 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 14.74 % Favored : 83.30 % 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: 0.87 (0.19), residues: 2040 helix: 1.34 (0.18), residues: 872 sheet: 0.28 (0.27), residues: 361 loop : 0.01 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1152 TYR 0.020 0.001 TYR B2021 PHE 0.023 0.001 PHE B 751 TRP 0.008 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00356 (16847) covalent geometry : angle 0.57174 (22830) hydrogen bonds : bond 0.03622 ( 758) hydrogen bonds : angle 4.40293 ( 2184) *********************** 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: 36 poor density : 135 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9089 (ptm) cc_final: 0.8785 (ttp) REVERT: B 432 ASP cc_start: 0.8572 (p0) cc_final: 0.8327 (p0) REVERT: B 437 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7454 (ptm-80) REVERT: B 741 MET cc_start: 0.9331 (tpp) cc_final: 0.8844 (tpp) REVERT: B 745 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7733 (pttm) REVERT: B 1022 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (p) REVERT: B 1023 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8798 (mp0) REVERT: B 1151 GLU cc_start: 0.8795 (mp0) cc_final: 0.8504 (tm-30) REVERT: B 1170 MET cc_start: 0.8718 (mmt) cc_final: 0.8376 (mmt) REVERT: B 1732 MET cc_start: 0.9083 (mmm) cc_final: 0.8465 (mmm) REVERT: B 1736 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9111 (m-10) REVERT: B 1856 GLU cc_start: 0.8624 (tp30) cc_final: 0.7951 (tp30) REVERT: B 1966 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 1986 MET cc_start: 0.8677 (ttp) cc_final: 0.7935 (ttp) REVERT: B 2011 CYS cc_start: 0.8865 (m) cc_final: 0.8086 (t) REVERT: B 2040 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7461 (tm-30) REVERT: J 2119 ASP cc_start: 0.9079 (t0) cc_final: 0.8724 (t0) outliers start: 36 outliers final: 20 residues processed: 165 average time/residue: 0.6916 time to fit residues: 126.9148 Evaluate side-chains 154 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 745 LYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1167 MET 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 1736 PHE Chi-restraints excluded: chain B residue 1966 PHE Chi-restraints excluded: chain B residue 2037 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 Chi-restraints excluded: chain J residue 2157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 151 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 190 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 657 ASN B1191 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.050118 restraints weight = 40361.940| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.70 r_work: 0.2624 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2199 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= 0.137 Angle : 0.562 11.341 22830 Z= 0.280 Chirality : 0.043 0.140 2562 Planarity : 0.004 0.063 2933 Dihedral : 4.442 56.959 2233 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.02 % Allowed : 15.12 % Favored : 82.86 % 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: 2040 helix: 1.38 (0.18), residues: 873 sheet: 0.29 (0.27), residues: 363 loop : 0.03 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1152 TYR 0.018 0.001 TYR B 861 PHE 0.024 0.001 PHE B 701 TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00321 (16847) covalent geometry : angle 0.56217 (22830) hydrogen bonds : bond 0.03514 ( 758) hydrogen bonds : angle 4.35122 ( 2184) *********************** 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 : 0.753 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9080 (ptm) cc_final: 0.8761 (ttp) REVERT: B 432 ASP cc_start: 0.8553 (p0) cc_final: 0.8288 (p0) REVERT: B 437 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7479 (ptm-80) REVERT: B 763 ARG cc_start: 0.8148 (mpt90) cc_final: 0.7822 (mtm110) REVERT: B 1022 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 1023 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: B 1109 ASP cc_start: 0.8502 (t0) cc_final: 0.8296 (t0) REVERT: B 1151 GLU cc_start: 0.8802 (mp0) cc_final: 0.8508 (tm-30) REVERT: B 1170 MET cc_start: 0.8714 (mmt) cc_final: 0.8365 (mmt) REVERT: B 1611 GLU cc_start: 0.8928 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 1732 MET cc_start: 0.9049 (mmm) cc_final: 0.8383 (mmm) REVERT: B 1736 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9097 (m-10) REVERT: B 1856 GLU cc_start: 0.8627 (tp30) cc_final: 0.7944 (tp30) REVERT: B 1966 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7708 (t80) REVERT: B 1986 MET cc_start: 0.8703 (ttp) cc_final: 0.7991 (ttp) REVERT: B 2011 CYS cc_start: 0.8872 (m) cc_final: 0.8118 (t) REVERT: B 2040 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7419 (tm-30) REVERT: J 2119 ASP cc_start: 0.9076 (t0) cc_final: 0.8724 (t0) outliers start: 37 outliers final: 20 residues processed: 168 average time/residue: 0.6747 time to fit residues: 126.4270 Evaluate side-chains 157 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 748 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1167 MET 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 1614 LEU Chi-restraints excluded: chain B residue 1712 ASP Chi-restraints excluded: chain B residue 1736 PHE 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 2114 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 121 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 chunk 186 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1191 GLN B1332 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.067499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.050553 restraints weight = 40029.397| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.70 r_work: 0.2638 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16847 Z= 0.117 Angle : 0.564 11.489 22830 Z= 0.278 Chirality : 0.042 0.142 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.365 56.833 2233 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.80 % Allowed : 15.34 % Favored : 82.86 % 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: 0.95 (0.19), residues: 2040 helix: 1.41 (0.18), residues: 873 sheet: 0.32 (0.27), residues: 363 loop : 0.04 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1152 TYR 0.019 0.001 TYR B2021 PHE 0.023 0.001 PHE B 751 TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00270 (16847) covalent geometry : angle 0.56393 (22830) hydrogen bonds : bond 0.03344 ( 758) hydrogen bonds : angle 4.28394 ( 2184) *********************** 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 169 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9042 (ptm) cc_final: 0.8673 (ttp) REVERT: B 432 ASP cc_start: 0.8519 (p0) cc_final: 0.8256 (p0) REVERT: B 437 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7474 (ptm-80) REVERT: B 763 ARG cc_start: 0.8163 (mpt90) cc_final: 0.7859 (mtm110) REVERT: B 1022 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 1023 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: B 1151 GLU cc_start: 0.8802 (mp0) cc_final: 0.8509 (tm-30) REVERT: B 1170 MET cc_start: 0.8689 (mmt) cc_final: 0.8341 (mmt) REVERT: B 1611 GLU cc_start: 0.8940 (tt0) cc_final: 0.8617 (tm-30) REVERT: B 1847 GLU cc_start: 0.8518 (tp30) cc_final: 0.8160 (tp30) REVERT: B 1856 GLU cc_start: 0.8624 (tp30) cc_final: 0.7936 (tp30) REVERT: B 1966 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7704 (t80) REVERT: B 1986 MET cc_start: 0.8710 (ttp) cc_final: 0.8047 (ttp) REVERT: B 1988 MET cc_start: 0.8693 (tmm) cc_final: 0.8426 (ppp) REVERT: B 2011 CYS cc_start: 0.8859 (m) cc_final: 0.8142 (t) REVERT: B 2040 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7403 (tm-30) REVERT: J 2119 ASP cc_start: 0.9072 (t0) cc_final: 0.8704 (t0) outliers start: 33 outliers final: 20 residues processed: 166 average time/residue: 0.6778 time to fit residues: 125.5032 Evaluate side-chains 154 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 948 LEU Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1167 MET Chi-restraints excluded: chain B residue 1228 VAL 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 1966 PHE Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain B residue 2037 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 Chi-restraints excluded: chain J residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 94 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1191 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS J2247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.050076 restraints weight = 39984.406| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.69 r_work: 0.2627 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2281 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= 0.147 Angle : 0.572 11.807 22830 Z= 0.283 Chirality : 0.043 0.152 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.361 56.799 2233 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.58 % Allowed : 15.83 % Favored : 82.59 % 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: 0.95 (0.19), residues: 2040 helix: 1.41 (0.18), residues: 873 sheet: 0.31 (0.27), residues: 362 loop : 0.06 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1152 TYR 0.016 0.001 TYR B 861 PHE 0.024 0.001 PHE B 701 TRP 0.009 0.001 TRP J2151 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00347 (16847) covalent geometry : angle 0.57214 (22830) hydrogen bonds : bond 0.03462 ( 758) hydrogen bonds : angle 4.28148 ( 2184) ********************** 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 162 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: B 423 MET cc_start: 0.9087 (ptm) cc_final: 0.8778 (ttp) REVERT: B 432 ASP cc_start: 0.8505 (p0) cc_final: 0.8246 (p0) REVERT: B 437 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7483 (ptm-80) REVERT: B 763 ARG cc_start: 0.8199 (mpt90) cc_final: 0.7899 (mtm110) REVERT: B 1022 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 1023 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: B 1151 GLU cc_start: 0.8811 (mp0) cc_final: 0.8517 (tm-30) REVERT: B 1170 MET cc_start: 0.8707 (mmt) cc_final: 0.8361 (mmt) REVERT: B 1611 GLU cc_start: 0.8939 (tt0) cc_final: 0.8613 (tm-30) REVERT: B 1847 GLU cc_start: 0.8530 (tp30) cc_final: 0.8177 (tp30) REVERT: B 1856 GLU cc_start: 0.8636 (tp30) cc_final: 0.7944 (tp30) REVERT: B 1986 MET cc_start: 0.8712 (ttp) cc_final: 0.8020 (ttp) REVERT: B 1988 MET cc_start: 0.8691 (tmm) cc_final: 0.8367 (ppp) REVERT: B 2011 CYS cc_start: 0.8878 (m) cc_final: 0.8145 (t) REVERT: B 2040 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7401 (tm-30) REVERT: J 2119 ASP cc_start: 0.9068 (t0) cc_final: 0.8713 (t0) outliers start: 29 outliers final: 22 residues processed: 158 average time/residue: 0.6684 time to fit residues: 117.9277 Evaluate side-chains 155 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 748 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1167 MET Chi-restraints excluded: chain B residue 1228 VAL 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 2017 ILE Chi-restraints excluded: chain B residue 2037 VAL Chi-restraints excluded: chain B residue 2114 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain J residue 2087 THR Chi-restraints excluded: chain J residue 2157 VAL 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 172 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1113 ASN B1191 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2089 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.049255 restraints weight = 40094.680| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.69 r_work: 0.2606 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16847 Z= 0.199 Angle : 0.591 12.744 22830 Z= 0.291 Chirality : 0.044 0.156 2562 Planarity : 0.004 0.062 2933 Dihedral : 4.422 56.889 2233 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.58 % Allowed : 15.94 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.19), residues: 2040 helix: 1.38 (0.18), residues: 871 sheet: 0.28 (0.27), residues: 363 loop : 0.05 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1152 TYR 0.017 0.001 TYR B2021 PHE 0.021 0.001 PHE B1713 TRP 0.008 0.001 TRP J2151 HIS 0.004 0.001 HIS B1179 Details of bonding type rmsd covalent geometry : bond 0.00475 (16847) covalent geometry : angle 0.59137 (22830) hydrogen bonds : bond 0.03734 ( 758) hydrogen bonds : angle 4.33860 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5317.77 seconds wall clock time: 91 minutes 32.98 seconds (5492.98 seconds total)