Starting phenix.real_space_refine on Wed Mar 4 14:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.cif Found real_map, /net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7os1_13045/03_2026/7os1_13045.map" } resolution = 3.3 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= 0.008 sd= 0.050 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 72 5.16 5 C 8970 2.51 5 N 2416 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14054 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 13834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1720, 13834 Classifications: {'peptide': 1720} Link IDs: {'PTRANS': 78, 'TRANS': 1641} Chain: "F" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 220 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain breaks: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.20 Number of scatterers: 14054 At special positions: 0 Unit cell: (104, 102.336, 157.248, 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 72 16.00 O 2596 8.00 N 2416 7.00 C 8970 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: 1.28 Conformation dependent library (CDL) restraints added in 425.9 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 52.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.552A 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: 3.558A pdb=" N LEU B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 4.105A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 5.021A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.807A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 4.285A pdb=" N PHE B 536 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.590A 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 Processing helix chain 'B' and resid 589 through 599 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.923A pdb=" N LEU B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS B 621 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 623 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 643 Processing helix chain 'B' and resid 657 through 665 removed outlier: 3.691A pdb=" N VAL B 661 " --> pdb=" O ASN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 696 through 715 removed outlier: 3.634A pdb=" N ASN B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 745 removed outlier: 3.573A pdb=" N LYS B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 3.711A 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: 4.437A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.579A 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: 4.007A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.638A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 856 " --> pdb=" O MET B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 884 removed outlier: 3.595A pdb=" N TYR B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 908 removed outlier: 4.150A pdb=" N LYS B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Proline residue: B 898 - end of helix Processing helix chain 'B' and resid 912 through 920 Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.552A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (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 991 Processing helix chain 'B' and resid 994 through 1005 removed outlier: 3.664A pdb=" N GLN B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1020 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1033 through 1042 removed outlier: 3.896A pdb=" N LYS B1039 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1040 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1074 through 1102 removed outlier: 3.582A pdb=" N MET B1078 " --> pdb=" O GLY B1074 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B1079 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B1093 " --> pdb=" O GLY B1089 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B1102 " --> pdb=" O ILE B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 removed outlier: 3.508A pdb=" N ASP B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 3.517A pdb=" N ARG B1130 " --> pdb=" O CYS B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1146 removed outlier: 3.508A pdb=" N LYS B1146 " --> pdb=" O LYS B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1156 removed outlier: 4.289A pdb=" N ASP B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B1156 " --> pdb=" O ARG B1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1151 through 1156' Processing helix chain 'B' and resid 1157 through 1166 Processing helix chain 'B' and resid 1167 through 1169 No H-bonds generated for 'chain 'B' and resid 1167 through 1169' Processing helix chain 'B' and resid 1170 through 1179 Processing helix chain 'B' and resid 1308 through 1312 Processing helix chain 'B' and resid 1314 through 1322 removed outlier: 3.654A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1342 removed outlier: 4.442A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1371 removed outlier: 3.857A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 Processing helix chain 'B' and resid 1397 through 1402 Processing helix chain 'B' and resid 1411 through 1422 Processing helix chain 'B' and resid 1428 through 1438 removed outlier: 3.566A pdb=" N LEU B1435 " --> pdb=" O LYS B1431 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG B1438 " --> pdb=" O ILE B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1442 through 1447 removed outlier: 3.943A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B1447 " --> pdb=" O LYS B1443 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1442 through 1447' Processing helix chain 'B' and resid 1456 through 1461 removed outlier: 3.514A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1464 through 1482 removed outlier: 3.932A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1505 removed outlier: 3.605A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1519 removed outlier: 3.711A pdb=" N ARG B1519 " --> pdb=" O PRO B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1554 removed outlier: 4.859A pdb=" N LYS B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Proline residue: B1545 - end of helix Processing helix chain 'B' and resid 1565 through 1583 removed outlier: 4.020A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B1571 " --> pdb=" O LYS B1567 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1604 Proline residue: B1599 - end of helix removed outlier: 4.029A pdb=" N LYS B1603 " --> pdb=" O PRO B1599 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B1604 " --> pdb=" O TYR B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1614 removed outlier: 3.552A pdb=" N LYS B1610 " --> pdb=" O ASP B1606 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1638 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1680 through 1689 Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 4.034A pdb=" N TYR B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1732 through 1742 Processing helix chain 'B' and resid 1747 through 1756 removed outlier: 3.606A pdb=" N THR B1756 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing helix chain 'B' and resid 1758 through 1764 removed outlier: 3.685A pdb=" N ARG B1762 " --> pdb=" O THR B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1767 through 1772 Processing helix chain 'B' and resid 1777 through 1799 Processing helix chain 'B' and resid 1813 through 1822 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1850 Processing helix chain 'B' and resid 1851 through 1856 removed outlier: 6.144A pdb=" N GLU B1854 " --> pdb=" O ASN B1851 " (cutoff:3.500A) Processing helix chain 'B' and resid 1863 through 1875 removed outlier: 4.160A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B1873 " --> pdb=" O ARG B1869 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.855A pdb=" N SER B1910 " --> pdb=" O ALA B1906 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP B1911 " --> pdb=" O GLU B1907 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B1912 " --> pdb=" O LEU B1908 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B1922 " --> pdb=" O LYS B1918 " (cutoff:3.500A) Processing helix chain 'B' and resid 1936 through 1952 Processing helix chain 'B' and resid 1958 through 1963 Processing helix chain 'B' and resid 1967 through 1978 removed outlier: 3.582A pdb=" N ASP B1976 " --> pdb=" O LYS B1972 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B1977 " --> pdb=" O ARG B1973 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B1978 " --> pdb=" O CYS B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1987 removed outlier: 3.737A pdb=" N ILE B1985 " --> pdb=" O SER B1981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1997 removed outlier: 3.648A pdb=" N ARG B1993 " --> pdb=" O GLU B1989 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2014 removed outlier: 3.758A pdb=" N ILE B2004 " --> pdb=" O THR B2000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 435 through 439 removed outlier: 6.373A pdb=" N LEU B 722 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 721 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER B 811 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 723 " --> pdb=" O SER B 811 " (cutoff:3.500A) removed outlier: 6.181A 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: 6.261A pdb=" N LYS B 537 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 611 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 610 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 649 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 612 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 651 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 614 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 499 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER B 652 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.024A 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 1184 through 1191 Processing sheet with id=AA6, first strand: chain 'B' and resid 1233 through 1242 removed outlier: 3.528A pdb=" N HIS B1235 " --> pdb=" O VAL B1225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1405 through 1407 removed outlier: 6.815A pdb=" N CYS B1376 " --> pdb=" O ILE B1425 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N SER B1427 " --> pdb=" O CYS B1376 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B1378 " --> pdb=" O SER B1427 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B1377 " --> pdb=" O VAL B1452 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B1454 " --> pdb=" O VAL B1377 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B1379 " --> pdb=" O ASP B1454 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B1346 " --> pdb=" O ALA B1489 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N SER B1491 " --> pdb=" O VAL B1346 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B1348 " --> pdb=" O SER B1491 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1523 through 1530 removed outlier: 6.264A pdb=" N GLU B1524 " --> pdb=" O CYS B1702 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE B1704 " --> pdb=" O GLU B1524 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS B1526 " --> pdb=" O ILE B1704 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N CYS B1706 " --> pdb=" O HIS B1526 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN B1528 " --> pdb=" O CYS B1706 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1667 through 1670 Processing sheet with id=AB1, first strand: chain 'B' and resid 1802 through 1805 Processing sheet with id=AB2, first strand: chain 'B' and resid 2018 through 2023 Processing sheet with id=AB3, first strand: chain 'B' and resid 2075 through 2082 removed outlier: 5.815A pdb=" N LEU B2076 " --> pdb=" O ASP B2070 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B2070 " --> pdb=" O LEU B2076 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B2102 " --> pdb=" O VAL B2124 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1839 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: 2.95 Time building geometry restraints manager: 1.70 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: 4617 1.34 - 1.46: 2699 1.46 - 1.58: 6911 1.58 - 1.70: 0 1.70 - 1.81: 119 Bond restraints: 14346 Sorted by residual: bond pdb=" C GLY B 625 " pdb=" O GLY B 625 " ideal model delta sigma weight residual 1.238 1.222 0.016 9.70e-03 1.06e+04 2.76e+00 bond pdb=" C TYR B2107 " pdb=" N PHE B2108 " ideal model delta sigma weight residual 1.331 1.312 0.020 1.44e-02 4.82e+03 1.87e+00 bond pdb=" CB PHE B2108 " pdb=" CG PHE B2108 " ideal model delta sigma weight residual 1.502 1.474 0.028 2.30e-02 1.89e+03 1.54e+00 bond pdb=" C TYR B2014 " pdb=" N PRO B2015 " ideal model delta sigma weight residual 1.334 1.306 0.028 2.34e-02 1.83e+03 1.46e+00 bond pdb=" CA GLY B1074 " pdb=" C GLY B1074 " ideal model delta sigma weight residual 1.517 1.526 -0.008 7.00e-03 2.04e+04 1.35e+00 ... (remaining 14341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 18795 1.42 - 2.85: 516 2.85 - 4.27: 87 4.27 - 5.69: 20 5.69 - 7.12: 6 Bond angle restraints: 19424 Sorted by residual: angle pdb=" N VAL B1518 " pdb=" CA VAL B1518 " pdb=" C VAL B1518 " ideal model delta sigma weight residual 111.91 108.70 3.21 8.90e-01 1.26e+00 1.30e+01 angle pdb=" C ARG B 624 " pdb=" N GLY B 625 " pdb=" CA GLY B 625 " ideal model delta sigma weight residual 121.13 123.63 -2.50 7.30e-01 1.88e+00 1.17e+01 angle pdb=" N THR B2000 " pdb=" CA THR B2000 " pdb=" C THR B2000 " ideal model delta sigma weight residual 110.80 103.68 7.12 2.13e+00 2.20e-01 1.12e+01 angle pdb=" C TYR B1719 " pdb=" N GLU B1720 " pdb=" CA GLU B1720 " ideal model delta sigma weight residual 123.96 119.56 4.40 1.44e+00 4.82e-01 9.32e+00 angle pdb=" C LYS B1716 " pdb=" N PHE B1717 " pdb=" CA PHE B1717 " ideal model delta sigma weight residual 122.53 117.01 5.52 1.92e+00 2.71e-01 8.26e+00 ... (remaining 19419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 7938 15.46 - 30.92: 637 30.92 - 46.37: 142 46.37 - 61.83: 28 61.83 - 77.29: 9 Dihedral angle restraints: 8754 sinusoidal: 3622 harmonic: 5132 Sorted by residual: dihedral pdb=" CA TRP B 817 " pdb=" C TRP B 817 " pdb=" N GLY B 818 " pdb=" CA GLY B 818 " ideal model delta harmonic sigma weight residual -180.00 -159.55 -20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA THR B2000 " pdb=" C THR B2000 " pdb=" N ASP B2001 " pdb=" CA ASP B2001 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP B 623 " pdb=" C ASP B 623 " pdb=" N ARG B 624 " pdb=" CA ARG B 624 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1277 0.031 - 0.063: 621 0.063 - 0.094: 178 0.094 - 0.126: 108 0.126 - 0.157: 17 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CA PRO B 859 " pdb=" N PRO B 859 " pdb=" C PRO B 859 " pdb=" CB PRO B 859 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CG LEU B 514 " pdb=" CB LEU B 514 " pdb=" CD1 LEU B 514 " pdb=" CD2 LEU B 514 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA GLN B 418 " pdb=" N GLN B 418 " pdb=" C GLN B 418 " pdb=" CB GLN B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2198 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 880 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C LEU B 880 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B 880 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 881 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 625 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 626 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B1515 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO B1516 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B1516 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B1516 " -0.027 5.00e-02 4.00e+02 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2463 2.76 - 3.30: 14237 3.30 - 3.83: 23040 3.83 - 4.37: 27244 4.37 - 4.90: 46355 Nonbonded interactions: 113339 Sorted by model distance: nonbonded pdb=" O TYR B 470 " pdb=" OH TYR B 562 " model vdw 2.229 3.040 nonbonded pdb=" O ALA B2008 " pdb=" ND2 ASN B2012 " model vdw 2.236 3.120 nonbonded pdb=" O PHE B1208 " pdb=" NE2 GLN B1247 " model vdw 2.273 3.120 nonbonded pdb=" ND1 HIS B 715 " pdb=" OD1 ASN B 719 " model vdw 2.274 3.120 nonbonded pdb=" O LEU B 969 " pdb=" OG1 THR B 982 " model vdw 2.280 3.040 ... (remaining 113334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.037 14346 Z= 0.213 Angle : 0.602 7.115 19424 Z= 0.330 Chirality : 0.044 0.157 2201 Planarity : 0.005 0.049 2486 Dihedral : 12.085 77.291 5426 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.96 % Allowed : 5.31 % Favored : 93.73 % 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: 0.53 (0.20), residues: 1740 helix: 0.88 (0.19), residues: 779 sheet: 0.94 (0.30), residues: 301 loop : -0.46 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 367 TYR 0.025 0.002 TYR B1619 PHE 0.024 0.001 PHE B1713 TRP 0.010 0.001 TRP B 817 HIS 0.006 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00478 (14346) covalent geometry : angle 0.60160 (19424) hydrogen bonds : bond 0.15862 ( 650) hydrogen bonds : angle 6.49555 ( 1839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 446 HIS cc_start: 0.8503 (m-70) cc_final: 0.8247 (m170) REVERT: B 505 THR cc_start: 0.6206 (OUTLIER) cc_final: 0.5129 (m) REVERT: B 661 VAL cc_start: 0.9518 (t) cc_final: 0.9226 (t) REVERT: B 664 PHE cc_start: 0.8957 (t80) cc_final: 0.8483 (t80) REVERT: B 680 PHE cc_start: 0.8312 (m-80) cc_final: 0.7903 (m-80) REVERT: B 722 LEU cc_start: 0.9238 (mt) cc_final: 0.9001 (mm) REVERT: B 828 ILE cc_start: 0.8851 (mm) cc_final: 0.8604 (mm) REVERT: B 879 TYR cc_start: 0.9119 (m-80) cc_final: 0.8842 (m-80) REVERT: B 990 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8324 (m90) REVERT: B 1126 MET cc_start: 0.7789 (ptp) cc_final: 0.7355 (ptp) REVERT: B 1731 CYS cc_start: 0.8304 (t) cc_final: 0.8100 (t) REVERT: B 1986 MET cc_start: 0.8321 (mmm) cc_final: 0.8045 (mmm) REVERT: B 2012 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: B 2114 MET cc_start: 0.9104 (mtp) cc_final: 0.8713 (mtp) REVERT: F 340 THR cc_start: 0.8678 (m) cc_final: 0.8375 (p) outliers start: 15 outliers final: 4 residues processed: 185 average time/residue: 0.1471 time to fit residues: 37.3969 Evaluate side-chains 118 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1569 THR Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B 573 HIS ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1086 GLN B1568 GLN ** B2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.090988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058586 restraints weight = 42962.248| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.32 r_work: 0.2779 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14346 Z= 0.140 Angle : 0.598 9.607 19424 Z= 0.308 Chirality : 0.044 0.219 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.828 59.224 1910 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.21 % Allowed : 9.46 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1740 helix: 1.12 (0.18), residues: 794 sheet: 0.92 (0.29), residues: 307 loop : -0.26 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 624 TYR 0.015 0.001 TYR B1619 PHE 0.013 0.001 PHE B1713 TRP 0.007 0.001 TRP B1432 HIS 0.010 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00289 (14346) covalent geometry : angle 0.59814 (19424) hydrogen bonds : bond 0.04904 ( 650) hydrogen bonds : angle 5.32207 ( 1839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 515 MET cc_start: 0.7982 (ttm) cc_final: 0.7338 (ptm) REVERT: B 551 MET cc_start: 0.9154 (mmm) cc_final: 0.8812 (mmm) REVERT: B 664 PHE cc_start: 0.8858 (t80) cc_final: 0.8313 (t80) REVERT: B 722 LEU cc_start: 0.9244 (mt) cc_final: 0.8939 (mt) REVERT: B 789 MET cc_start: 0.7731 (mtt) cc_final: 0.7517 (mtt) REVERT: B 837 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 879 TYR cc_start: 0.9065 (m-80) cc_final: 0.8860 (m-80) REVERT: B 980 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8728 (tp40) REVERT: B 1078 MET cc_start: 0.9285 (mmp) cc_final: 0.9005 (mmp) REVERT: B 1122 MET cc_start: 0.8519 (ttm) cc_final: 0.8284 (ttm) REVERT: B 1126 MET cc_start: 0.8054 (ptp) cc_final: 0.7515 (ptp) REVERT: B 1170 MET cc_start: 0.9117 (ptp) cc_final: 0.8824 (ptp) REVERT: B 1731 CYS cc_start: 0.9015 (t) cc_final: 0.8803 (t) REVERT: B 1818 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.9015 (mp) REVERT: B 1988 MET cc_start: 0.8885 (tpp) cc_final: 0.8653 (tpp) REVERT: B 2114 MET cc_start: 0.9072 (mtp) cc_final: 0.8632 (mtp) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 0.1229 time to fit residues: 24.6670 Evaluate side-chains 114 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain B residue 1818 ILE Chi-restraints excluded: chain B residue 1834 MET Chi-restraints excluded: chain B residue 2017 ILE Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2012 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054327 restraints weight = 43355.381| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.81 r_work: 0.2705 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14346 Z= 0.167 Angle : 0.564 12.534 19424 Z= 0.288 Chirality : 0.043 0.144 2201 Planarity : 0.004 0.049 2486 Dihedral : 4.601 57.903 1904 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.41 % Allowed : 10.49 % Favored : 88.11 % 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: 0.84 (0.20), residues: 1740 helix: 1.10 (0.18), residues: 814 sheet: 0.88 (0.29), residues: 309 loop : -0.20 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 794 TYR 0.015 0.001 TYR B1619 PHE 0.017 0.001 PHE B 435 TRP 0.006 0.001 TRP B1432 HIS 0.008 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00376 (14346) covalent geometry : angle 0.56397 (19424) hydrogen bonds : bond 0.04166 ( 650) hydrogen bonds : angle 4.99068 ( 1839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 517 MET cc_start: 0.9033 (ptp) cc_final: 0.8792 (ptp) REVERT: B 551 MET cc_start: 0.9214 (mmm) cc_final: 0.8829 (mmm) REVERT: B 664 PHE cc_start: 0.8719 (t80) cc_final: 0.8034 (t80) REVERT: B 711 LYS cc_start: 0.9503 (mmtt) cc_final: 0.9197 (mmmt) REVERT: B 722 LEU cc_start: 0.9255 (mt) cc_final: 0.8876 (mt) REVERT: B 786 HIS cc_start: 0.8598 (p90) cc_final: 0.8160 (p90) REVERT: B 789 MET cc_start: 0.7845 (mtt) cc_final: 0.6436 (mpp) REVERT: B 852 MET cc_start: 0.9434 (mtm) cc_final: 0.9232 (mmm) REVERT: B 875 GLU cc_start: 0.8525 (tp30) cc_final: 0.7679 (tp30) REVERT: B 879 TYR cc_start: 0.9098 (m-80) cc_final: 0.8328 (m-80) REVERT: B 980 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8642 (tp40) REVERT: B 1078 MET cc_start: 0.9251 (mmp) cc_final: 0.8983 (mmp) REVERT: B 1126 MET cc_start: 0.8071 (ptp) cc_final: 0.7476 (ptp) REVERT: B 1170 MET cc_start: 0.9172 (ptp) cc_final: 0.8913 (ptp) REVERT: B 1986 MET cc_start: 0.8214 (mmm) cc_final: 0.7775 (mmm) REVERT: B 2114 MET cc_start: 0.9156 (mtp) cc_final: 0.8944 (mtp) outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 0.1197 time to fit residues: 22.9391 Evaluate side-chains 116 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 701 PHE Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055244 restraints weight = 41188.879| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.43 r_work: 0.2740 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14346 Z= 0.116 Angle : 0.524 9.978 19424 Z= 0.268 Chirality : 0.042 0.152 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.470 58.292 1904 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.41 % Allowed : 11.64 % Favored : 86.96 % 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: 0.96 (0.20), residues: 1740 helix: 1.23 (0.18), residues: 816 sheet: 0.91 (0.30), residues: 305 loop : -0.19 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.012 0.001 TYR B1619 PHE 0.011 0.001 PHE B 664 TRP 0.006 0.001 TRP B1432 HIS 0.005 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00253 (14346) covalent geometry : angle 0.52356 (19424) hydrogen bonds : bond 0.03654 ( 650) hydrogen bonds : angle 4.71097 ( 1839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 551 MET cc_start: 0.9234 (mmm) cc_final: 0.8830 (mmm) REVERT: B 664 PHE cc_start: 0.8585 (t80) cc_final: 0.8032 (t80) REVERT: B 722 LEU cc_start: 0.9171 (mt) cc_final: 0.8859 (mt) REVERT: B 786 HIS cc_start: 0.8465 (p90) cc_final: 0.7768 (p90) REVERT: B 789 MET cc_start: 0.7927 (mtt) cc_final: 0.5948 (mpp) REVERT: B 879 TYR cc_start: 0.9100 (m-80) cc_final: 0.8891 (m-80) REVERT: B 900 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8108 (mtm) REVERT: B 980 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8564 (tp40) REVERT: B 1078 MET cc_start: 0.9195 (mmp) cc_final: 0.8909 (mmp) REVERT: B 1122 MET cc_start: 0.8548 (ttm) cc_final: 0.8229 (ttm) REVERT: B 1126 MET cc_start: 0.8013 (ptp) cc_final: 0.7321 (ptp) REVERT: B 1170 MET cc_start: 0.9182 (ptp) cc_final: 0.8438 (pmm) REVERT: B 1808 MET cc_start: 0.8585 (tpp) cc_final: 0.8163 (tpt) REVERT: B 2114 MET cc_start: 0.9007 (mtp) cc_final: 0.8481 (mtp) outliers start: 22 outliers final: 11 residues processed: 127 average time/residue: 0.1141 time to fit residues: 21.3019 Evaluate side-chains 111 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 165 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055576 restraints weight = 42415.213| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.56 r_work: 0.2739 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14346 Z= 0.109 Angle : 0.525 8.194 19424 Z= 0.267 Chirality : 0.042 0.142 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.423 58.601 1904 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.60 % Allowed : 12.02 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1740 helix: 1.27 (0.19), residues: 815 sheet: 0.95 (0.30), residues: 307 loop : -0.22 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 794 TYR 0.015 0.001 TYR B 442 PHE 0.019 0.001 PHE B 435 TRP 0.006 0.001 TRP B1432 HIS 0.011 0.001 HIS B 785 Details of bonding type rmsd covalent geometry : bond 0.00239 (14346) covalent geometry : angle 0.52459 (19424) hydrogen bonds : bond 0.03487 ( 650) hydrogen bonds : angle 4.57951 ( 1839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7937 (p90) REVERT: B 551 MET cc_start: 0.9254 (mmm) cc_final: 0.8844 (mmm) REVERT: B 664 PHE cc_start: 0.8511 (t80) cc_final: 0.7982 (t80) REVERT: B 722 LEU cc_start: 0.9208 (mt) cc_final: 0.8905 (mt) REVERT: B 786 HIS cc_start: 0.8538 (p90) cc_final: 0.8241 (p90) REVERT: B 789 MET cc_start: 0.8160 (mtt) cc_final: 0.6991 (mpp) REVERT: B 875 GLU cc_start: 0.8425 (tp30) cc_final: 0.7798 (tp30) REVERT: B 900 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: B 1078 MET cc_start: 0.9166 (mmp) cc_final: 0.8918 (mmp) REVERT: B 1126 MET cc_start: 0.8018 (ptp) cc_final: 0.7364 (ptp) REVERT: B 1170 MET cc_start: 0.9192 (ptp) cc_final: 0.8437 (pmm) REVERT: B 1808 MET cc_start: 0.8597 (tpp) cc_final: 0.8203 (tpt) REVERT: B 1880 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8804 (p0) REVERT: B 1986 MET cc_start: 0.8090 (mmm) cc_final: 0.7726 (mmm) REVERT: B 1988 MET cc_start: 0.8770 (tpp) cc_final: 0.8465 (tpt) REVERT: B 2114 MET cc_start: 0.9008 (mtp) cc_final: 0.8481 (mtp) outliers start: 25 outliers final: 14 residues processed: 127 average time/residue: 0.1140 time to fit residues: 21.9641 Evaluate side-chains 117 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain B residue 1880 ASN Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 0.0570 chunk 172 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.089971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055626 restraints weight = 41825.141| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.48 r_work: 0.2736 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14346 Z= 0.122 Angle : 0.528 7.683 19424 Z= 0.269 Chirality : 0.042 0.145 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.404 58.661 1904 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.53 % Allowed : 12.28 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1740 helix: 1.28 (0.19), residues: 817 sheet: 0.92 (0.29), residues: 309 loop : -0.15 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 359 TYR 0.014 0.001 TYR B 709 PHE 0.011 0.001 PHE B1713 TRP 0.006 0.001 TRP B 817 HIS 0.004 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00271 (14346) covalent geometry : angle 0.52799 (19424) hydrogen bonds : bond 0.03426 ( 650) hydrogen bonds : angle 4.50716 ( 1839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.7745 (p90) REVERT: B 551 MET cc_start: 0.9283 (mmm) cc_final: 0.8875 (mmm) REVERT: B 664 PHE cc_start: 0.8454 (t80) cc_final: 0.7919 (t80) REVERT: B 709 TYR cc_start: 0.9435 (t80) cc_final: 0.9227 (t80) REVERT: B 722 LEU cc_start: 0.9305 (mt) cc_final: 0.8933 (mt) REVERT: B 786 HIS cc_start: 0.8459 (p90) cc_final: 0.8080 (p90) REVERT: B 789 MET cc_start: 0.8090 (mtt) cc_final: 0.6310 (mpp) REVERT: B 875 GLU cc_start: 0.8324 (tp30) cc_final: 0.7834 (tp30) REVERT: B 900 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: B 1078 MET cc_start: 0.9148 (mmp) cc_final: 0.8935 (mmp) REVERT: B 1126 MET cc_start: 0.8074 (ptp) cc_final: 0.7368 (ptp) REVERT: B 1170 MET cc_start: 0.9185 (ptp) cc_final: 0.8443 (pmm) REVERT: B 1808 MET cc_start: 0.8569 (tpp) cc_final: 0.8202 (tpt) REVERT: B 1880 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8839 (p0) REVERT: B 1986 MET cc_start: 0.8075 (mmm) cc_final: 0.7650 (mmm) REVERT: B 2114 MET cc_start: 0.9006 (mtp) cc_final: 0.8464 (mtp) outliers start: 24 outliers final: 14 residues processed: 126 average time/residue: 0.1133 time to fit residues: 21.5563 Evaluate side-chains 119 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain B residue 1764 MET Chi-restraints excluded: chain B residue 1880 ASN Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 0.0570 chunk 99 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.055776 restraints weight = 41545.576| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.45 r_work: 0.2744 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14346 Z= 0.115 Angle : 0.534 8.697 19424 Z= 0.269 Chirality : 0.042 0.141 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.393 58.537 1904 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.79 % Allowed : 12.85 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1740 helix: 1.28 (0.19), residues: 817 sheet: 0.91 (0.30), residues: 309 loop : -0.18 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 558 TYR 0.011 0.001 TYR B1619 PHE 0.019 0.001 PHE B 435 TRP 0.007 0.001 TRP B 817 HIS 0.004 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00257 (14346) covalent geometry : angle 0.53374 (19424) hydrogen bonds : bond 0.03363 ( 650) hydrogen bonds : angle 4.46307 ( 1839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 551 MET cc_start: 0.9263 (mmm) cc_final: 0.8851 (mmm) REVERT: B 664 PHE cc_start: 0.8436 (t80) cc_final: 0.7916 (t80) REVERT: B 711 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9073 (mmmt) REVERT: B 722 LEU cc_start: 0.9310 (mt) cc_final: 0.8969 (mt) REVERT: B 786 HIS cc_start: 0.8439 (p90) cc_final: 0.8074 (p90) REVERT: B 789 MET cc_start: 0.8069 (mtt) cc_final: 0.6234 (mpp) REVERT: B 875 GLU cc_start: 0.8330 (tp30) cc_final: 0.7870 (tp30) REVERT: B 900 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: B 996 ASP cc_start: 0.8776 (t0) cc_final: 0.8561 (t0) REVERT: B 1126 MET cc_start: 0.8116 (ptp) cc_final: 0.7400 (ptp) REVERT: B 1170 MET cc_start: 0.9189 (ptp) cc_final: 0.8455 (pmm) REVERT: B 1808 MET cc_start: 0.8553 (tpp) cc_final: 0.8192 (tpt) REVERT: B 1880 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (p0) REVERT: B 1988 MET cc_start: 0.8286 (tpp) cc_final: 0.7924 (tpp) REVERT: B 2114 MET cc_start: 0.9004 (mtp) cc_final: 0.8506 (mtp) outliers start: 28 outliers final: 16 residues processed: 129 average time/residue: 0.1108 time to fit residues: 21.8247 Evaluate side-chains 117 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1734 ASP Chi-restraints excluded: chain B residue 1880 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 2006 ASP Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.087867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054208 restraints weight = 41174.655| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.43 r_work: 0.2724 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14346 Z= 0.149 Angle : 0.551 8.927 19424 Z= 0.280 Chirality : 0.042 0.144 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.460 56.895 1904 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.66 % Allowed : 12.98 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1740 helix: 1.29 (0.19), residues: 812 sheet: 0.89 (0.29), residues: 309 loop : -0.22 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 519 TYR 0.016 0.001 TYR B 709 PHE 0.012 0.001 PHE B1713 TRP 0.006 0.001 TRP B 817 HIS 0.004 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00337 (14346) covalent geometry : angle 0.55092 (19424) hydrogen bonds : bond 0.03523 ( 650) hydrogen bonds : angle 4.53819 ( 1839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 TYR cc_start: 0.8522 (t80) cc_final: 0.8301 (t80) REVERT: B 551 MET cc_start: 0.9303 (mmm) cc_final: 0.8883 (mmm) REVERT: B 664 PHE cc_start: 0.8461 (t80) cc_final: 0.7979 (t80) REVERT: B 722 LEU cc_start: 0.9309 (mt) cc_final: 0.9047 (mt) REVERT: B 786 HIS cc_start: 0.8454 (p90) cc_final: 0.8061 (p90) REVERT: B 789 MET cc_start: 0.8088 (mtt) cc_final: 0.6221 (mpp) REVERT: B 798 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: B 827 ILE cc_start: 0.9028 (mt) cc_final: 0.8636 (tp) REVERT: B 875 GLU cc_start: 0.8317 (tp30) cc_final: 0.7956 (mm-30) REVERT: B 900 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: B 996 ASP cc_start: 0.8840 (t0) cc_final: 0.8615 (t0) REVERT: B 1126 MET cc_start: 0.8200 (ptp) cc_final: 0.7475 (ptp) REVERT: B 1170 MET cc_start: 0.9177 (ptp) cc_final: 0.8445 (pmm) REVERT: B 1808 MET cc_start: 0.8534 (tpp) cc_final: 0.8176 (tpt) REVERT: B 1880 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 1986 MET cc_start: 0.8033 (mmm) cc_final: 0.7735 (mmm) REVERT: B 1988 MET cc_start: 0.8408 (tpp) cc_final: 0.8089 (tpp) REVERT: B 2114 MET cc_start: 0.9019 (mtp) cc_final: 0.8563 (mtp) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.1155 time to fit residues: 21.3881 Evaluate side-chains 121 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1817 MET Chi-restraints excluded: chain B residue 1858 ILE Chi-restraints excluded: chain B residue 1880 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 143 optimal weight: 4.9990 chunk 133 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.088826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055395 restraints weight = 41342.838| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.45 r_work: 0.2756 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14346 Z= 0.106 Angle : 0.560 13.885 19424 Z= 0.279 Chirality : 0.041 0.142 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.397 57.131 1904 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.21 % Allowed : 13.62 % Favored : 85.17 % 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: 1.02 (0.21), residues: 1740 helix: 1.32 (0.19), residues: 811 sheet: 0.91 (0.30), residues: 309 loop : -0.21 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 603 TYR 0.011 0.001 TYR B1619 PHE 0.018 0.001 PHE B 435 TRP 0.008 0.001 TRP B 817 HIS 0.003 0.000 HIS B 824 Details of bonding type rmsd covalent geometry : bond 0.00232 (14346) covalent geometry : angle 0.56043 (19424) hydrogen bonds : bond 0.03278 ( 650) hydrogen bonds : angle 4.44866 ( 1839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 551 MET cc_start: 0.9312 (mmm) cc_final: 0.8893 (mmm) REVERT: B 664 PHE cc_start: 0.8424 (t80) cc_final: 0.7918 (t80) REVERT: B 711 LYS cc_start: 0.9314 (mmtt) cc_final: 0.9065 (mmmt) REVERT: B 722 LEU cc_start: 0.9294 (mt) cc_final: 0.9043 (mt) REVERT: B 786 HIS cc_start: 0.8410 (p90) cc_final: 0.8058 (p90) REVERT: B 789 MET cc_start: 0.8039 (mtt) cc_final: 0.6074 (mpp) REVERT: B 798 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8454 (pp20) REVERT: B 827 ILE cc_start: 0.8936 (mt) cc_final: 0.8557 (tp) REVERT: B 875 GLU cc_start: 0.8174 (tp30) cc_final: 0.7683 (tp30) REVERT: B 900 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: B 996 ASP cc_start: 0.8811 (t0) cc_final: 0.8582 (t0) REVERT: B 1126 MET cc_start: 0.8194 (ptp) cc_final: 0.7444 (ptp) REVERT: B 1170 MET cc_start: 0.9157 (ptp) cc_final: 0.8415 (pmm) REVERT: B 1808 MET cc_start: 0.8536 (tpp) cc_final: 0.8175 (tpt) REVERT: B 1986 MET cc_start: 0.8021 (mmm) cc_final: 0.7688 (mmm) REVERT: B 1988 MET cc_start: 0.8367 (tpp) cc_final: 0.8044 (tpp) REVERT: B 2114 MET cc_start: 0.8974 (mtp) cc_final: 0.8510 (mtp) REVERT: F 365 LYS cc_start: 0.5423 (pttm) cc_final: 0.4737 (mmmt) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.1086 time to fit residues: 19.5634 Evaluate side-chains 116 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1858 ILE Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 0.0010 chunk 44 optimal weight: 0.0670 chunk 27 optimal weight: 0.0070 chunk 55 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056268 restraints weight = 41184.795| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.46 r_work: 0.2786 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14346 Z= 0.099 Angle : 0.558 11.522 19424 Z= 0.278 Chirality : 0.041 0.145 2201 Planarity : 0.004 0.051 2486 Dihedral : 4.315 57.306 1904 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.41 % Allowed : 13.43 % Favored : 85.17 % 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: 1.02 (0.21), residues: 1740 helix: 1.36 (0.19), residues: 812 sheet: 0.93 (0.30), residues: 303 loop : -0.27 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 603 TYR 0.023 0.001 TYR B 924 PHE 0.014 0.001 PHE B 664 TRP 0.009 0.001 TRP B 817 HIS 0.004 0.000 HIS B 824 Details of bonding type rmsd covalent geometry : bond 0.00213 (14346) covalent geometry : angle 0.55839 (19424) hydrogen bonds : bond 0.03087 ( 650) hydrogen bonds : angle 4.36067 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 423 MET cc_start: 0.6806 (ppp) cc_final: 0.6577 (tmm) REVERT: B 551 MET cc_start: 0.9291 (mmm) cc_final: 0.8863 (mmm) REVERT: B 711 LYS cc_start: 0.9325 (mmtt) cc_final: 0.9051 (mmmt) REVERT: B 728 ARG cc_start: 0.9494 (tpp80) cc_final: 0.9251 (tpp80) REVERT: B 786 HIS cc_start: 0.8441 (p90) cc_final: 0.8115 (p90) REVERT: B 789 MET cc_start: 0.8023 (mtt) cc_final: 0.6229 (mpp) REVERT: B 827 ILE cc_start: 0.8909 (mt) cc_final: 0.8595 (tp) REVERT: B 875 GLU cc_start: 0.8267 (tp30) cc_final: 0.7734 (tp30) REVERT: B 879 TYR cc_start: 0.9201 (m-80) cc_final: 0.8660 (m-80) REVERT: B 996 ASP cc_start: 0.8757 (t0) cc_final: 0.8524 (t0) REVERT: B 1126 MET cc_start: 0.8207 (ptp) cc_final: 0.7323 (ptp) REVERT: B 1170 MET cc_start: 0.9149 (ptp) cc_final: 0.8413 (pmm) REVERT: B 1808 MET cc_start: 0.8576 (tpp) cc_final: 0.8242 (tpt) REVERT: B 1825 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7921 (t0) REVERT: B 1986 MET cc_start: 0.8071 (mmm) cc_final: 0.7748 (mmm) REVERT: B 1988 MET cc_start: 0.8358 (tpp) cc_final: 0.8045 (tpp) REVERT: B 2114 MET cc_start: 0.8946 (mtp) cc_final: 0.8497 (mtp) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.1218 time to fit residues: 22.8739 Evaluate side-chains 119 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1713 PHE Chi-restraints excluded: chain B residue 1825 ASN Chi-restraints excluded: chain B residue 1858 ILE Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain F residue 360 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 80 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 85 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 719 ASN ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058831 restraints weight = 41925.837| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.37 r_work: 0.2758 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14346 Z= 0.123 Angle : 0.566 12.304 19424 Z= 0.284 Chirality : 0.042 0.143 2201 Planarity : 0.004 0.050 2486 Dihedral : 4.381 57.675 1904 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.02 % Allowed : 13.94 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1740 helix: 1.36 (0.19), residues: 812 sheet: 0.95 (0.30), residues: 301 loop : -0.25 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 700 TYR 0.025 0.001 TYR B 709 PHE 0.037 0.001 PHE B 664 TRP 0.006 0.001 TRP B1432 HIS 0.006 0.001 HIS B 824 Details of bonding type rmsd covalent geometry : bond 0.00275 (14346) covalent geometry : angle 0.56576 (19424) hydrogen bonds : bond 0.03315 ( 650) hydrogen bonds : angle 4.42710 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3477.49 seconds wall clock time: 60 minutes 15.34 seconds (3615.34 seconds total)