Starting phenix.real_space_refine on Wed Mar 4 22:01:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.map" model { file = "/net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7px3_13690/03_2026/7px3_13690.cif" } resolution = 3.05 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= 0.069 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 84 5.16 5 C 10498 2.51 5 N 2826 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 16430 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 13870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1725, 13870 Classifications: {'peptide': 1725} Link IDs: {'PTRANS': 79, 'TRANS': 1645} Chain: "J" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2030 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "T" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 530 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 3 Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16430 At special positions: 0 Unit cell: (105.12, 142.788, 149.796, 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 84 16.00 O 3022 8.00 N 2826 7.00 C 10498 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: 1.29 Conformation dependent library (CDL) restraints added in 743.0 milliseconds 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 48.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.620A 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 468 through 473 removed outlier: 4.108A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.998A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 589 through 600 removed outlier: 3.947A pdb=" N GLY B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.939A pdb=" N TYR B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 removed outlier: 3.603A pdb=" N LEU B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 621 " --> pdb=" O HIS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.656A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 696 through 716 removed outlier: 3.721A pdb=" N PHE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 702 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 716 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 745 Processing helix chain 'B' and resid 749 through 753 removed outlier: 3.534A pdb=" N LEU B 752 " --> pdb=" O GLY B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 767 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.818A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 803 removed outlier: 3.778A pdb=" N ASP B 799 " --> pdb=" O THR B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.891A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 854 Processing helix chain 'B' and resid 878 through 884 Processing helix chain 'B' and resid 896 through 908 Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.504A pdb=" N GLY B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.677A 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 992 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1020 Processing helix chain 'B' and resid 1021 through 1025 removed outlier: 3.587A pdb=" N PHE B1024 " --> pdb=" O SER B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1043 removed outlier: 3.841A pdb=" N ARG B1043 " --> pdb=" O LYS B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1068 Processing helix chain 'B' and resid 1074 through 1103 removed outlier: 4.200A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1121 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1136 through 1146 Processing helix chain 'B' and resid 1150 through 1155 Processing helix chain 'B' and resid 1157 through 1166 Processing helix chain 'B' and resid 1170 through 1181 removed outlier: 3.711A pdb=" N HIS B1179 " --> pdb=" O HIS B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1312 Processing helix chain 'B' and resid 1314 through 1322 removed outlier: 3.737A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1341 removed outlier: 4.567A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1371 removed outlier: 3.932A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1398 removed outlier: 4.094A pdb=" N GLU B1395 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B1396 " --> pdb=" O ASP B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1422 Processing helix chain 'B' and resid 1428 through 1437 Processing helix chain 'B' and resid 1442 through 1447 removed outlier: 3.700A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1460 removed outlier: 3.501A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.850A pdb=" N LEU B1467 " --> pdb=" O ASN B1463 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1504 removed outlier: 3.636A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1519 removed outlier: 3.858A pdb=" N ARG B1519 " --> pdb=" O PRO B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1554 removed outlier: 4.620A 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: 3.650A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1604 Proline residue: B1599 - end of helix removed outlier: 3.907A pdb=" N LYS B1603 " --> pdb=" O PRO B1599 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B1604 " --> pdb=" O TYR B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1615 removed outlier: 3.512A pdb=" N ASN B1615 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1639 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1680 through 1690 removed outlier: 3.549A pdb=" N HIS B1690 " --> pdb=" O GLN B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 4.195A pdb=" N TYR B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1731 through 1742 removed outlier: 4.554A pdb=" N HIS B1735 " --> pdb=" O CYS B1731 " (cutoff:3.500A) Processing helix chain 'B' and resid 1747 through 1755 removed outlier: 3.544A pdb=" N VAL B1752 " --> pdb=" O LYS B1748 " (cutoff:3.500A) Processing helix chain 'B' and resid 1758 through 1767 removed outlier: 3.652A pdb=" N ARG B1762 " --> pdb=" O THR B1758 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B1766 " --> pdb=" O ARG B1762 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1772 Processing helix chain 'B' and resid 1777 through 1799 Processing helix chain 'B' and resid 1813 through 1823 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1851 Processing helix chain 'B' and resid 1852 through 1858 removed outlier: 4.291A pdb=" N ASN B1857 " --> pdb=" O GLU B1854 " (cutoff:3.500A) Processing helix chain 'B' and resid 1863 through 1875 removed outlier: 4.124A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B1873 " --> pdb=" O ARG B1869 " (cutoff:3.500A) removed outlier: 3.907A 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: 3.827A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1952 removed outlier: 3.676A pdb=" N ALA B1939 " --> pdb=" O TRP B1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1963 removed outlier: 3.559A pdb=" N GLN B1962 " --> pdb=" O TYR B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1978 Processing helix chain 'B' and resid 1981 through 1988 removed outlier: 3.946A pdb=" N ILE B1985 " --> pdb=" O SER B1981 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B1986 " --> pdb=" O VAL B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1997 removed outlier: 3.685A pdb=" N LEU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2014 Processing helix chain 'J' and resid 2072 through 2082 removed outlier: 4.107A pdb=" N ASN J2082 " --> pdb=" O ILE J2078 " (cutoff:3.500A) Processing helix chain 'J' and resid 2083 through 2088 removed outlier: 3.557A pdb=" N ARG J2086 " --> pdb=" O LEU J2083 " (cutoff:3.500A) Processing helix chain 'J' and resid 2108 through 2117 Processing helix chain 'J' and resid 2166 through 2170 Processing helix chain 'J' and resid 2189 through 2203 Processing helix chain 'J' and resid 2231 through 2241 removed outlier: 3.797A pdb=" N GLN J2240 " --> pdb=" O GLU J2236 " (cutoff:3.500A) Processing helix chain 'J' and resid 2252 through 2254 No H-bonds generated for 'chain 'J' and resid 2252 through 2254' Processing helix chain 'J' and resid 2284 through 2288 Processing helix chain 'J' and resid 2306 through 2309 Processing helix chain 'J' and resid 2310 through 2320 removed outlier: 3.907A pdb=" N PHE J2314 " --> pdb=" O ARG J2310 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 158 Processing sheet with id=AA1, first strand: chain 'B' and resid 436 through 438 removed outlier: 6.969A pdb=" N THR B 688 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR B 871 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 690 " --> pdb=" O THR B 871 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 722 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 783 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 812 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HIS B 785 " --> pdb=" O THR B 812 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 568 removed outlier: 3.584A pdb=" N VAL B 587 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS B 537 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 611 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 610 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE B 649 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 612 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU B 651 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 614 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 499 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER B 652 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.901A 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 removed outlier: 3.750A pdb=" N ARG B 840 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 970 through 973 removed outlier: 3.586A pdb=" N ASP B 973 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 978 " --> pdb=" O ASP B 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1184 through 1192 Processing sheet with id=AA6, first strand: chain 'B' and resid 1233 through 1242 removed outlier: 3.623A 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: 6.229A pdb=" N VAL B1377 " --> pdb=" O VAL B1452 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP B1454 " --> pdb=" O VAL B1377 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B1379 " --> pdb=" O ASP B1454 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B1451 " --> pdb=" O VAL B1488 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B1490 " --> pdb=" O PHE B1451 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B1453 " --> pdb=" O LEU B1490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1523 through 1530 removed outlier: 6.350A pdb=" N VAL B1661 " --> pdb=" O VAL B1703 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET B1705 " --> pdb=" O VAL B1661 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B1663 " --> pdb=" O MET B1705 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN B1707 " --> pdb=" O ILE B1663 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B1559 " --> pdb=" O VAL B1644 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA B1646 " --> pdb=" O VAL B1559 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B1561 " --> pdb=" O ALA B1646 " (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 2017 through 2023 removed outlier: 3.654A pdb=" N GLU B2018 " --> pdb=" O GLU B2042 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B2042 " --> pdb=" O GLU B2018 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B2041 " --> pdb=" O ALA B2088 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2075 through 2082 removed outlier: 5.826A pdb=" N LEU B2076 " --> pdb=" O ASP B2070 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP B2070 " --> pdb=" O LEU B2076 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 2256 through 2258 removed outlier: 9.477A pdb=" N ILE J2212 " --> pdb=" O GLU J2173 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J2175 " --> pdb=" O ILE J2212 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE J2214 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP J2177 " --> pdb=" O ILE J2214 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS J2216 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS J2179 " --> pdb=" O CYS J2216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE J2218 " --> pdb=" O HIS J2179 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN J2181 " --> pdb=" O PHE J2218 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU J2128 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP J2177 " --> pdb=" O GLY J2126 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY J2126 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 2260 through 2264 removed outlier: 6.450A pdb=" N THR J2103 " --> pdb=" O LYS J2140 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE J2142 " --> pdb=" O THR J2103 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE J2105 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS J2144 " --> pdb=" O ILE J2105 " (cutoff:3.500A) removed outlier: 12.051A pdb=" N VAL J2146 " --> pdb=" O PRO J2107 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY J2126 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP J2177 " --> pdb=" O GLY J2126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU J2128 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ILE J2212 " --> pdb=" O GLU J2173 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J2175 " --> pdb=" O ILE J2212 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE J2214 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP J2177 " --> pdb=" O ILE J2214 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS J2216 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS J2179 " --> pdb=" O CYS J2216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE J2218 " --> pdb=" O HIS J2179 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN J2181 " --> pdb=" O PHE J2218 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR J2091 " --> pdb=" O LEU J2225 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ALA J2227 " --> pdb=" O TYR J2091 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N SER J2093 " --> pdb=" O ALA J2227 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N LYS J2229 " --> pdb=" O SER J2093 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 2151 through 2152 743 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5378 1.34 - 1.46: 3427 1.46 - 1.58: 7860 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 16803 Sorted by residual: bond pdb=" C ARG B 624 " pdb=" N GLY B 625 " ideal model delta sigma weight residual 1.340 1.331 0.009 6.60e-03 2.30e+04 2.04e+00 bond pdb=" CA VAL B1563 " pdb=" CB VAL B1563 " ideal model delta sigma weight residual 1.546 1.535 0.011 8.80e-03 1.29e+04 1.70e+00 bond pdb=" CA VAL J2148 " pdb=" CB VAL J2148 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.32e+00 bond pdb=" CA THR B 606 " pdb=" C THR B 606 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.80e-02 3.09e+03 1.23e+00 bond pdb=" CA VAL J2273 " pdb=" CB VAL J2273 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.09e+00 ... (remaining 16798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 22336 1.56 - 3.13: 370 3.13 - 4.69: 59 4.69 - 6.26: 5 6.26 - 7.82: 4 Bond angle restraints: 22774 Sorted by residual: angle pdb=" C ARG T 312 " pdb=" N ASP T 313 " pdb=" CA ASP T 313 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N ILE B1776 " pdb=" CA ILE B1776 " pdb=" C ILE B1776 " ideal model delta sigma weight residual 112.43 109.21 3.22 9.20e-01 1.18e+00 1.23e+01 angle pdb=" N ILE B 617 " pdb=" CA ILE B 617 " pdb=" C ILE B 617 " ideal model delta sigma weight residual 112.98 109.46 3.52 1.25e+00 6.40e-01 7.94e+00 angle pdb=" C LYS B 426 " pdb=" CA LYS B 426 " pdb=" CB LYS B 426 " ideal model delta sigma weight residual 110.42 115.99 -5.57 1.99e+00 2.53e-01 7.83e+00 angle pdb=" C GLY B 874 " pdb=" N GLU B 875 " pdb=" CA GLU B 875 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.73e+00 ... (remaining 22769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9599 17.96 - 35.92: 456 35.92 - 53.88: 120 53.88 - 71.84: 24 71.84 - 89.80: 4 Dihedral angle restraints: 10203 sinusoidal: 4210 harmonic: 5993 Sorted by residual: dihedral pdb=" CA ALA B 757 " pdb=" C ALA B 757 " pdb=" N SER B 758 " pdb=" CA SER B 758 " ideal model delta harmonic sigma weight residual 180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET B1664 " pdb=" C MET B1664 " pdb=" N ASP B1665 " pdb=" CA ASP B1665 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LYS B1716 " pdb=" C LYS B1716 " pdb=" N PHE B1717 " pdb=" CA PHE B1717 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1637 0.030 - 0.061: 609 0.061 - 0.091: 152 0.091 - 0.122: 143 0.122 - 0.152: 10 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CG LEU B1999 " pdb=" CB LEU B1999 " pdb=" CD1 LEU B1999 " pdb=" CD2 LEU B1999 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CB VAL T 219 " pdb=" CA VAL T 219 " pdb=" CG1 VAL T 219 " pdb=" CG2 VAL T 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE J2213 " pdb=" N ILE J2213 " pdb=" C ILE J2213 " pdb=" CB ILE J2213 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2548 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B1515 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B1516 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B1516 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B1516 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 625 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 626 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B1464 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B1465 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B1465 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1465 " 0.025 5.00e-02 4.00e+02 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3194 2.77 - 3.30: 15962 3.30 - 3.84: 27067 3.84 - 4.37: 32432 4.37 - 4.90: 55880 Nonbonded interactions: 134535 Sorted by model distance: nonbonded pdb=" OG SER B1981 " pdb=" OD1 ASP B1984 " model vdw 2.241 3.040 nonbonded pdb=" O HIS J2084 " pdb=" OG1 THR J2087 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG B 436 " pdb=" OE2 GLU B 443 " model vdw 2.255 3.120 nonbonded pdb=" OD2 ASP B 973 " pdb=" OG1 THR B 976 " model vdw 2.258 3.040 nonbonded pdb=" ND1 HIS B1515 " pdb=" OD1 ASN B1517 " model vdw 2.268 3.120 ... (remaining 134530 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: 2.620 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16803 Z= 0.132 Angle : 0.524 7.821 22774 Z= 0.300 Chirality : 0.040 0.152 2551 Planarity : 0.004 0.047 2919 Dihedral : 11.547 89.797 6321 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.20 % Allowed : 6.57 % Favored : 88.23 % 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: 1.05 (0.19), residues: 2029 helix: 1.44 (0.18), residues: 848 sheet: 0.97 (0.28), residues: 359 loop : -0.12 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2060 TYR 0.013 0.001 TYR B1238 PHE 0.010 0.001 PHE B1759 TRP 0.010 0.001 TRP B2065 HIS 0.003 0.001 HIS B1735 Details of bonding type rmsd covalent geometry : bond 0.00266 (16803) covalent geometry : angle 0.52446 (22774) hydrogen bonds : bond 0.16377 ( 730) hydrogen bonds : angle 6.09474 ( 2097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 265 time to evaluate : 0.526 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 499 LEU cc_start: 0.8459 (mt) cc_final: 0.8237 (mt) REVERT: B 541 ILE cc_start: 0.8878 (mt) cc_final: 0.8606 (mm) REVERT: B 592 LYS cc_start: 0.9160 (tptt) cc_final: 0.8781 (tppt) REVERT: B 616 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7620 (mp0) REVERT: B 619 LEU cc_start: 0.8514 (tp) cc_final: 0.8266 (tp) REVERT: B 641 MET cc_start: 0.8162 (mtt) cc_final: 0.7654 (mmp) REVERT: B 668 ASP cc_start: 0.8101 (t0) cc_final: 0.7866 (t0) REVERT: B 709 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8570 (t80) REVERT: B 789 MET cc_start: 0.7870 (mtt) cc_final: 0.7508 (mtt) REVERT: B 817 TRP cc_start: 0.8661 (m100) cc_final: 0.7951 (m100) REVERT: B 920 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8804 (tt) REVERT: B 1148 PHE cc_start: 0.8249 (t80) cc_final: 0.8010 (t80) REVERT: B 1187 SER cc_start: 0.8962 (t) cc_final: 0.8700 (p) REVERT: B 1442 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.5984 (mmt180) REVERT: B 1627 MET cc_start: 0.8368 (tmm) cc_final: 0.7930 (tmm) REVERT: B 1856 GLU cc_start: 0.8317 (tp30) cc_final: 0.8074 (tm-30) REVERT: B 2036 VAL cc_start: 0.9088 (t) cc_final: 0.8555 (t) REVERT: B 2092 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8238 (pp) REVERT: J 2089 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.7942 (p90) REVERT: J 2192 ASP cc_start: 0.8225 (m-30) cc_final: 0.8004 (m-30) outliers start: 95 outliers final: 27 residues processed: 348 average time/residue: 0.1795 time to fit residues: 85.0758 Evaluate side-chains 197 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1677 VAL Chi-restraints excluded: chain B residue 1742 THR Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2144 CYS Chi-restraints excluded: chain J residue 2203 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2226 THR Chi-restraints excluded: chain J residue 2252 LEU Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN B1101 ASN B1209 GLN B1447 ASN B1517 ASN J2183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052795 restraints weight = 44326.006| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.99 r_work: 0.2709 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16803 Z= 0.156 Angle : 0.593 10.088 22774 Z= 0.304 Chirality : 0.044 0.166 2551 Planarity : 0.005 0.149 2919 Dihedral : 6.280 55.247 2269 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.12 % Allowed : 10.24 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2029 helix: 1.31 (0.18), residues: 870 sheet: 0.79 (0.27), residues: 376 loop : -0.11 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 728 TYR 0.012 0.001 TYR B1619 PHE 0.014 0.001 PHE B 555 TRP 0.010 0.001 TRP B1935 HIS 0.004 0.001 HIS B 785 Details of bonding type rmsd covalent geometry : bond 0.00358 (16803) covalent geometry : angle 0.59299 (22774) hydrogen bonds : bond 0.04488 ( 730) hydrogen bonds : angle 4.93982 ( 2097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8186 (ptt180) REVERT: B 475 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: B 541 ILE cc_start: 0.9012 (mt) cc_final: 0.8679 (mm) REVERT: B 619 LEU cc_start: 0.8499 (tp) cc_final: 0.8282 (tp) REVERT: B 641 MET cc_start: 0.8272 (mtt) cc_final: 0.7859 (mmt) REVERT: B 668 ASP cc_start: 0.8278 (t0) cc_final: 0.7988 (t0) REVERT: B 709 TYR cc_start: 0.8946 (t80) cc_final: 0.8678 (t80) REVERT: B 713 MET cc_start: 0.9094 (mmm) cc_final: 0.8764 (mmm) REVERT: B 741 MET cc_start: 0.8898 (ttm) cc_final: 0.8185 (tpp) REVERT: B 748 LEU cc_start: 0.7955 (mt) cc_final: 0.7337 (mp) REVERT: B 789 MET cc_start: 0.8142 (mtt) cc_final: 0.7873 (mtt) REVERT: B 817 TRP cc_start: 0.8721 (m100) cc_final: 0.7964 (m100) REVERT: B 852 MET cc_start: 0.8177 (ptp) cc_final: 0.7833 (mtm) REVERT: B 877 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8022 (mm110) REVERT: B 1148 PHE cc_start: 0.8500 (t80) cc_final: 0.8210 (t80) REVERT: B 1152 ARG cc_start: 0.9058 (ttp-110) cc_final: 0.8709 (ttp-110) REVERT: B 1187 SER cc_start: 0.9245 (t) cc_final: 0.8905 (p) REVERT: B 1213 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9313 (mtmm) REVERT: B 1442 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7032 (mtt180) REVERT: B 1598 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9385 (tp) REVERT: B 1856 GLU cc_start: 0.8876 (tp30) cc_final: 0.8608 (tp30) REVERT: B 1986 MET cc_start: 0.8320 (mtp) cc_final: 0.7911 (mtp) REVERT: J 2089 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8040 (p90) REVERT: J 2192 ASP cc_start: 0.8561 (m-30) cc_final: 0.8299 (m-30) REVERT: T 217 LYS cc_start: 0.9350 (mtpp) cc_final: 0.9113 (mmmm) outliers start: 57 outliers final: 35 residues processed: 219 average time/residue: 0.1570 time to fit residues: 48.6534 Evaluate side-chains 187 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1664 MET Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2000 THR Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2183 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2252 LEU Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 95 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN B1798 GLN J2183 ASN ** J2203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052525 restraints weight = 44671.615| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.06 r_work: 0.2696 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16803 Z= 0.160 Angle : 0.563 10.445 22774 Z= 0.285 Chirality : 0.043 0.202 2551 Planarity : 0.004 0.093 2919 Dihedral : 5.983 54.076 2255 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.40 % Allowed : 10.84 % Favored : 85.76 % 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: 0.93 (0.19), residues: 2029 helix: 1.35 (0.18), residues: 865 sheet: 0.73 (0.27), residues: 367 loop : -0.15 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 728 TYR 0.011 0.001 TYR B1238 PHE 0.009 0.001 PHE B1759 TRP 0.008 0.001 TRP B1432 HIS 0.005 0.001 HIS B 873 Details of bonding type rmsd covalent geometry : bond 0.00366 (16803) covalent geometry : angle 0.56325 (22774) hydrogen bonds : bond 0.04178 ( 730) hydrogen bonds : angle 4.66819 ( 2097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 0.574 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 475 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: B 541 ILE cc_start: 0.9019 (mt) cc_final: 0.8674 (mm) REVERT: B 619 LEU cc_start: 0.8444 (tp) cc_final: 0.8229 (tp) REVERT: B 641 MET cc_start: 0.8250 (mtt) cc_final: 0.7813 (mmt) REVERT: B 668 ASP cc_start: 0.8281 (t0) cc_final: 0.7992 (t0) REVERT: B 709 TYR cc_start: 0.8948 (t80) cc_final: 0.8614 (t80) REVERT: B 713 MET cc_start: 0.9118 (mmm) cc_final: 0.8804 (mmm) REVERT: B 748 LEU cc_start: 0.7966 (mt) cc_final: 0.7381 (mp) REVERT: B 789 MET cc_start: 0.8196 (mtt) cc_final: 0.7888 (ptp) REVERT: B 817 TRP cc_start: 0.8715 (m100) cc_final: 0.7901 (m100) REVERT: B 877 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8089 (mm110) REVERT: B 920 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8863 (tt) REVERT: B 1148 PHE cc_start: 0.8462 (t80) cc_final: 0.8200 (t80) REVERT: B 1152 ARG cc_start: 0.9056 (ttp-110) cc_final: 0.8723 (ttp-110) REVERT: B 1187 SER cc_start: 0.9215 (t) cc_final: 0.8836 (p) REVERT: B 1213 LYS cc_start: 0.9570 (mtpp) cc_final: 0.9319 (mtmm) REVERT: B 1346 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.9106 (t) REVERT: B 1442 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7003 (mtt180) REVERT: B 1856 GLU cc_start: 0.8915 (tp30) cc_final: 0.8668 (tp30) REVERT: B 1986 MET cc_start: 0.8302 (mtp) cc_final: 0.7966 (mtp) REVERT: J 2089 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.8051 (p90) REVERT: J 2192 ASP cc_start: 0.8601 (m-30) cc_final: 0.8333 (m-30) REVERT: T 217 LYS cc_start: 0.9347 (mtpp) cc_final: 0.9137 (mmmm) outliers start: 62 outliers final: 37 residues processed: 214 average time/residue: 0.1587 time to fit residues: 48.5022 Evaluate side-chains 187 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1664 MET Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2183 ASN Chi-restraints excluded: chain J residue 2203 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2252 LEU Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain J residue 2286 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 104 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J2203 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 = 0.3453 r_free = 0.3453 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.052308 restraints weight = 44212.540| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.07 r_work: 0.2693 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16803 Z= 0.179 Angle : 0.561 10.445 22774 Z= 0.285 Chirality : 0.044 0.266 2551 Planarity : 0.004 0.050 2919 Dihedral : 6.006 55.223 2255 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.23 % Allowed : 11.39 % Favored : 85.38 % 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: 0.91 (0.19), residues: 2029 helix: 1.37 (0.18), residues: 866 sheet: 0.66 (0.27), residues: 367 loop : -0.17 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J2266 TYR 0.012 0.001 TYR B1619 PHE 0.009 0.001 PHE B1759 TRP 0.007 0.001 TRP B1432 HIS 0.004 0.001 HIS B 873 Details of bonding type rmsd covalent geometry : bond 0.00416 (16803) covalent geometry : angle 0.56103 (22774) hydrogen bonds : bond 0.03995 ( 730) hydrogen bonds : angle 4.52484 ( 2097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: B 541 ILE cc_start: 0.8928 (mt) cc_final: 0.8569 (mm) REVERT: B 616 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7851 (mp0) REVERT: B 619 LEU cc_start: 0.8429 (tp) cc_final: 0.8224 (tp) REVERT: B 641 MET cc_start: 0.8288 (mtt) cc_final: 0.7841 (mmt) REVERT: B 668 ASP cc_start: 0.8271 (t0) cc_final: 0.8024 (t0) REVERT: B 709 TYR cc_start: 0.8960 (t80) cc_final: 0.8671 (t80) REVERT: B 713 MET cc_start: 0.9104 (mmm) cc_final: 0.8819 (mmm) REVERT: B 748 LEU cc_start: 0.7972 (mt) cc_final: 0.7458 (mp) REVERT: B 789 MET cc_start: 0.8252 (mtt) cc_final: 0.7929 (ptp) REVERT: B 817 TRP cc_start: 0.8613 (m100) cc_final: 0.7876 (m100) REVERT: B 877 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: B 920 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 1148 PHE cc_start: 0.8488 (t80) cc_final: 0.8159 (t80) REVERT: B 1152 ARG cc_start: 0.9054 (ttp-110) cc_final: 0.8710 (ttp-110) REVERT: B 1187 SER cc_start: 0.9169 (t) cc_final: 0.8724 (p) REVERT: B 1213 LYS cc_start: 0.9573 (mtpp) cc_final: 0.9306 (mtmm) REVERT: B 1346 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 1442 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7070 (mtt180) REVERT: B 1856 GLU cc_start: 0.8926 (tp30) cc_final: 0.8662 (tp30) REVERT: B 1913 GLU cc_start: 0.8317 (mp0) cc_final: 0.7906 (mp0) REVERT: B 1986 MET cc_start: 0.8254 (mtp) cc_final: 0.7885 (mtp) REVERT: B 2030 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8892 (tpm170) REVERT: J 2089 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.7990 (p90) REVERT: J 2192 ASP cc_start: 0.8625 (m-30) cc_final: 0.8355 (m-30) REVERT: T 158 HIS cc_start: 0.7904 (m90) cc_final: 0.7662 (m-70) REVERT: T 217 LYS cc_start: 0.9354 (mtpp) cc_final: 0.9153 (mmmm) outliers start: 59 outliers final: 36 residues processed: 202 average time/residue: 0.1482 time to fit residues: 43.2696 Evaluate side-chains 190 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2203 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2252 LEU Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain J residue 2286 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 180 optimal weight: 0.0980 chunk 164 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 HIS B1101 ASN B1447 ASN B1749 GLN ** J2203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052848 restraints weight = 44185.503| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.05 r_work: 0.2706 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16803 Z= 0.137 Angle : 0.543 10.963 22774 Z= 0.275 Chirality : 0.043 0.227 2551 Planarity : 0.004 0.051 2919 Dihedral : 5.925 54.432 2254 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.40 % Allowed : 12.21 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2029 helix: 1.41 (0.18), residues: 866 sheet: 0.59 (0.28), residues: 366 loop : -0.11 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 310 TYR 0.012 0.001 TYR T 155 PHE 0.011 0.001 PHE B1983 TRP 0.009 0.001 TRP B 593 HIS 0.003 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00314 (16803) covalent geometry : angle 0.54329 (22774) hydrogen bonds : bond 0.03684 ( 730) hydrogen bonds : angle 4.36795 ( 2097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: B 541 ILE cc_start: 0.8959 (mt) cc_final: 0.8582 (mm) REVERT: B 551 MET cc_start: 0.9332 (tpp) cc_final: 0.8971 (tpt) REVERT: B 612 ILE cc_start: 0.9190 (mt) cc_final: 0.8887 (mm) REVERT: B 616 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7842 (mp0) REVERT: B 641 MET cc_start: 0.8279 (mtt) cc_final: 0.7800 (mmt) REVERT: B 668 ASP cc_start: 0.8245 (t0) cc_final: 0.8032 (t0) REVERT: B 709 TYR cc_start: 0.8969 (t80) cc_final: 0.8691 (t80) REVERT: B 713 MET cc_start: 0.9127 (mmm) cc_final: 0.8837 (mmm) REVERT: B 748 LEU cc_start: 0.8023 (mt) cc_final: 0.7502 (mp) REVERT: B 789 MET cc_start: 0.8215 (mtt) cc_final: 0.7904 (ptp) REVERT: B 817 TRP cc_start: 0.8657 (m100) cc_final: 0.7751 (m100) REVERT: B 877 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: B 920 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8829 (tt) REVERT: B 1042 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8829 (mm-30) REVERT: B 1148 PHE cc_start: 0.8461 (t80) cc_final: 0.8102 (t80) REVERT: B 1152 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8691 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9589 (mtpp) cc_final: 0.9323 (mtmm) REVERT: B 1346 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9062 (t) REVERT: B 1442 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7077 (mtt180) REVERT: B 1749 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6960 (tm130) REVERT: B 1856 GLU cc_start: 0.8912 (tp30) cc_final: 0.8646 (tp30) REVERT: B 1913 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8045 (mp0) REVERT: B 1986 MET cc_start: 0.8266 (mtp) cc_final: 0.7939 (mtp) REVERT: B 2030 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8885 (tpm170) REVERT: J 2089 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8005 (p90) REVERT: J 2192 ASP cc_start: 0.8617 (m-30) cc_final: 0.8353 (m-30) outliers start: 62 outliers final: 36 residues processed: 208 average time/residue: 0.1449 time to fit residues: 43.6582 Evaluate side-chains 188 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1749 GLN Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2000 THR Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2203 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2252 LEU Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain J residue 2286 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 176 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.0770 chunk 6 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN B1447 ASN ** J2203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.078646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053741 restraints weight = 43466.665| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.01 r_work: 0.2731 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16803 Z= 0.108 Angle : 0.543 11.720 22774 Z= 0.273 Chirality : 0.042 0.204 2551 Planarity : 0.004 0.051 2919 Dihedral : 5.753 54.245 2252 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 2.96 % Allowed : 12.43 % Favored : 84.61 % 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 (0.19), residues: 2029 helix: 1.47 (0.18), residues: 866 sheet: 0.62 (0.28), residues: 367 loop : -0.10 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J2266 TYR 0.016 0.001 TYR B 489 PHE 0.010 0.001 PHE B2094 TRP 0.009 0.001 TRP B 593 HIS 0.003 0.000 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00240 (16803) covalent geometry : angle 0.54303 (22774) hydrogen bonds : bond 0.03442 ( 730) hydrogen bonds : angle 4.23854 ( 2097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: B 541 ILE cc_start: 0.8937 (mt) cc_final: 0.8553 (mm) REVERT: B 551 MET cc_start: 0.9332 (tpp) cc_final: 0.8952 (tpt) REVERT: B 616 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7843 (mp0) REVERT: B 641 MET cc_start: 0.8261 (mtt) cc_final: 0.7789 (mmt) REVERT: B 668 ASP cc_start: 0.8210 (t0) cc_final: 0.7986 (t0) REVERT: B 701 PHE cc_start: 0.9142 (m-80) cc_final: 0.8939 (m-80) REVERT: B 709 TYR cc_start: 0.8956 (t80) cc_final: 0.8716 (t80) REVERT: B 713 MET cc_start: 0.9118 (mmm) cc_final: 0.8814 (mmm) REVERT: B 748 LEU cc_start: 0.8049 (mt) cc_final: 0.7518 (mp) REVERT: B 789 MET cc_start: 0.8156 (mtt) cc_final: 0.7881 (ptp) REVERT: B 817 TRP cc_start: 0.8626 (m100) cc_final: 0.7861 (m100) REVERT: B 877 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: B 920 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8793 (tt) REVERT: B 1043 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8314 (ptp-110) REVERT: B 1148 PHE cc_start: 0.8396 (t80) cc_final: 0.7992 (t80) REVERT: B 1152 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8650 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9567 (mtpp) cc_final: 0.9303 (mtmm) REVERT: B 1346 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9057 (t) REVERT: B 1442 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.7006 (mtt180) REVERT: B 1856 GLU cc_start: 0.8922 (tp30) cc_final: 0.8658 (tp30) REVERT: B 1913 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7957 (mp0) REVERT: B 1986 MET cc_start: 0.8160 (mtp) cc_final: 0.7864 (mtp) REVERT: B 2030 ARG cc_start: 0.9154 (mmm-85) cc_final: 0.8894 (tpm170) REVERT: J 2089 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8023 (p90) REVERT: J 2192 ASP cc_start: 0.8580 (m-30) cc_final: 0.8317 (m-30) REVERT: T 309 LYS cc_start: 0.9211 (mmtm) cc_final: 0.8946 (mmtm) outliers start: 54 outliers final: 34 residues processed: 199 average time/residue: 0.1418 time to fit residues: 41.4126 Evaluate side-chains 182 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1043 ARG Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2000 THR Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 162 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1447 ASN B2012 ASN J2203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.078153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053138 restraints weight = 43444.519| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.01 r_work: 0.2710 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16803 Z= 0.138 Angle : 0.552 11.609 22774 Z= 0.276 Chirality : 0.043 0.193 2551 Planarity : 0.004 0.051 2919 Dihedral : 5.653 54.352 2249 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 3.07 % Allowed : 12.60 % Favored : 84.34 % 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 (0.19), residues: 2029 helix: 1.55 (0.18), residues: 865 sheet: 0.58 (0.28), residues: 367 loop : -0.13 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J2266 TYR 0.021 0.001 TYR T 155 PHE 0.010 0.001 PHE B 782 TRP 0.008 0.001 TRP B 593 HIS 0.011 0.001 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00318 (16803) covalent geometry : angle 0.55215 (22774) hydrogen bonds : bond 0.03459 ( 730) hydrogen bonds : angle 4.22114 ( 2097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: B 541 ILE cc_start: 0.8961 (mt) cc_final: 0.8583 (mm) REVERT: B 551 MET cc_start: 0.9350 (tpp) cc_final: 0.8948 (tpt) REVERT: B 612 ILE cc_start: 0.9160 (mt) cc_final: 0.8903 (mm) REVERT: B 616 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7836 (mp0) REVERT: B 641 MET cc_start: 0.8250 (mtt) cc_final: 0.7762 (mmt) REVERT: B 668 ASP cc_start: 0.8217 (t0) cc_final: 0.7992 (t0) REVERT: B 709 TYR cc_start: 0.8940 (t80) cc_final: 0.8712 (t80) REVERT: B 713 MET cc_start: 0.9129 (mmm) cc_final: 0.8819 (mmm) REVERT: B 748 LEU cc_start: 0.8076 (mt) cc_final: 0.7542 (mp) REVERT: B 789 MET cc_start: 0.8165 (mtt) cc_final: 0.7910 (ptp) REVERT: B 877 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: B 912 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7547 (p0) REVERT: B 1042 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8601 (pt0) REVERT: B 1148 PHE cc_start: 0.8374 (t80) cc_final: 0.7943 (t80) REVERT: B 1152 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8719 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9566 (mtpp) cc_final: 0.9295 (mtmm) REVERT: B 1346 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9049 (t) REVERT: B 1442 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7100 (mtt180) REVERT: B 1856 GLU cc_start: 0.8942 (tp30) cc_final: 0.8672 (tp30) REVERT: B 1913 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7986 (mp0) REVERT: B 1986 MET cc_start: 0.8189 (mtp) cc_final: 0.7916 (mtp) REVERT: J 2089 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.7940 (p90) REVERT: J 2192 ASP cc_start: 0.8590 (m-30) cc_final: 0.8341 (m-30) REVERT: T 309 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8994 (mmtm) outliers start: 56 outliers final: 40 residues processed: 192 average time/residue: 0.1380 time to fit residues: 38.7467 Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 912 ASN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1024 PHE Chi-restraints excluded: chain B residue 1043 ARG Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1787 GLU Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2000 THR Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2203 ASN Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 34 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053141 restraints weight = 44286.703| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.05 r_work: 0.2709 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16803 Z= 0.133 Angle : 0.555 11.900 22774 Z= 0.276 Chirality : 0.043 0.190 2551 Planarity : 0.004 0.056 2919 Dihedral : 5.624 54.587 2249 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 13.42 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.19), residues: 2029 helix: 1.55 (0.18), residues: 865 sheet: 0.56 (0.28), residues: 367 loop : -0.12 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J2266 TYR 0.018 0.001 TYR B 489 PHE 0.009 0.001 PHE B 782 TRP 0.010 0.001 TRP B 593 HIS 0.009 0.001 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00307 (16803) covalent geometry : angle 0.55488 (22774) hydrogen bonds : bond 0.03438 ( 730) hydrogen bonds : angle 4.19866 ( 2097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: B 541 ILE cc_start: 0.8959 (mt) cc_final: 0.8580 (mm) REVERT: B 551 MET cc_start: 0.9359 (tpp) cc_final: 0.8959 (tpt) REVERT: B 612 ILE cc_start: 0.9142 (mt) cc_final: 0.8915 (mm) REVERT: B 616 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7799 (mp0) REVERT: B 641 MET cc_start: 0.8260 (mtt) cc_final: 0.7767 (mmt) REVERT: B 668 ASP cc_start: 0.8217 (t0) cc_final: 0.7987 (t0) REVERT: B 709 TYR cc_start: 0.8946 (t80) cc_final: 0.8715 (t80) REVERT: B 713 MET cc_start: 0.9143 (mmm) cc_final: 0.8837 (mmm) REVERT: B 748 LEU cc_start: 0.8071 (mt) cc_final: 0.7540 (mp) REVERT: B 789 MET cc_start: 0.8172 (mtt) cc_final: 0.7935 (ptp) REVERT: B 877 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: B 912 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 1042 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8585 (pt0) REVERT: B 1148 PHE cc_start: 0.8354 (t80) cc_final: 0.7961 (t80) REVERT: B 1152 ARG cc_start: 0.9019 (ttp-110) cc_final: 0.8682 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9571 (mtpp) cc_final: 0.9308 (mtmm) REVERT: B 1346 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9050 (t) REVERT: B 1442 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7030 (mtt180) REVERT: B 1856 GLU cc_start: 0.8939 (tp30) cc_final: 0.8672 (tp30) REVERT: B 1913 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7985 (mp0) REVERT: B 1986 MET cc_start: 0.8185 (mtp) cc_final: 0.7912 (mtp) REVERT: B 1997 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8678 (pp) REVERT: B 2092 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7225 (pp) REVERT: J 2089 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.7993 (p90) REVERT: T 161 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8339 (ttm110) REVERT: T 309 LYS cc_start: 0.9216 (mmtm) cc_final: 0.9003 (mmtm) outliers start: 49 outliers final: 41 residues processed: 185 average time/residue: 0.1381 time to fit residues: 37.4398 Evaluate side-chains 187 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 912 ASN Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1024 PHE Chi-restraints excluded: chain B residue 1043 ARG Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1447 ASN Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1787 GLU Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1997 LEU Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2000 THR Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain J residue 2286 VAL Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 123 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1749 GLN J2203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053675 restraints weight = 43574.347| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.03 r_work: 0.2725 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16803 Z= 0.112 Angle : 0.550 12.105 22774 Z= 0.275 Chirality : 0.042 0.187 2551 Planarity : 0.004 0.060 2919 Dihedral : 5.554 54.767 2248 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 13.53 % Favored : 83.84 % 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: 1.08 (0.19), residues: 2029 helix: 1.59 (0.18), residues: 865 sheet: 0.68 (0.28), residues: 360 loop : -0.15 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J2266 TYR 0.020 0.001 TYR T 155 PHE 0.010 0.001 PHE B 782 TRP 0.013 0.001 TRP B 593 HIS 0.003 0.000 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00254 (16803) covalent geometry : angle 0.54978 (22774) hydrogen bonds : bond 0.03286 ( 730) hydrogen bonds : angle 4.12880 ( 2097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: B 541 ILE cc_start: 0.8966 (mt) cc_final: 0.8577 (mm) REVERT: B 551 MET cc_start: 0.9360 (tpp) cc_final: 0.8952 (tpt) REVERT: B 612 ILE cc_start: 0.9157 (mt) cc_final: 0.8913 (mm) REVERT: B 616 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7830 (mp0) REVERT: B 641 MET cc_start: 0.8270 (mtt) cc_final: 0.7771 (mmt) REVERT: B 668 ASP cc_start: 0.8216 (t0) cc_final: 0.7990 (t0) REVERT: B 701 PHE cc_start: 0.8734 (m-80) cc_final: 0.8519 (m-80) REVERT: B 713 MET cc_start: 0.9143 (mmm) cc_final: 0.8850 (mmm) REVERT: B 789 MET cc_start: 0.8158 (mtt) cc_final: 0.7925 (ptp) REVERT: B 877 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: B 912 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7552 (p0) REVERT: B 1042 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8567 (pt0) REVERT: B 1148 PHE cc_start: 0.8258 (t80) cc_final: 0.7789 (t80) REVERT: B 1152 ARG cc_start: 0.8965 (ttp-110) cc_final: 0.8643 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9555 (mtpp) cc_final: 0.9296 (mtmm) REVERT: B 1346 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9078 (t) REVERT: B 1856 GLU cc_start: 0.8904 (tp30) cc_final: 0.8612 (tp30) REVERT: B 1913 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7956 (mp0) REVERT: B 1986 MET cc_start: 0.8169 (mtp) cc_final: 0.7893 (mtp) REVERT: B 2092 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7097 (pp) REVERT: J 2089 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.7818 (p90) REVERT: T 161 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8398 (ttm110) REVERT: T 309 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8983 (mmtm) outliers start: 48 outliers final: 37 residues processed: 182 average time/residue: 0.1473 time to fit residues: 39.1373 Evaluate side-chains 181 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 912 ASN Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1024 PHE Chi-restraints excluded: chain B residue 1043 ARG Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1787 GLU Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2039 VAL Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2259 VAL Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 116 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.078680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.053706 restraints weight = 43704.497| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.00 r_work: 0.2728 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16803 Z= 0.116 Angle : 0.551 12.045 22774 Z= 0.274 Chirality : 0.042 0.190 2551 Planarity : 0.004 0.058 2919 Dihedral : 5.492 54.602 2248 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 2.46 % Allowed : 13.69 % Favored : 83.84 % 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: 1.09 (0.19), residues: 2029 helix: 1.61 (0.18), residues: 866 sheet: 0.61 (0.28), residues: 365 loop : -0.11 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J2266 TYR 0.019 0.001 TYR T 155 PHE 0.011 0.001 PHE B 782 TRP 0.013 0.001 TRP B 593 HIS 0.004 0.000 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00264 (16803) covalent geometry : angle 0.55130 (22774) hydrogen bonds : bond 0.03229 ( 730) hydrogen bonds : angle 4.10240 ( 2097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: B 541 ILE cc_start: 0.8945 (mt) cc_final: 0.8560 (mm) REVERT: B 551 MET cc_start: 0.9352 (tpp) cc_final: 0.8950 (tpt) REVERT: B 612 ILE cc_start: 0.9125 (mt) cc_final: 0.8889 (mm) REVERT: B 616 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7789 (mp0) REVERT: B 641 MET cc_start: 0.8267 (mtt) cc_final: 0.7755 (mmt) REVERT: B 668 ASP cc_start: 0.8209 (t0) cc_final: 0.7981 (t0) REVERT: B 701 PHE cc_start: 0.8752 (m-80) cc_final: 0.8536 (m-80) REVERT: B 713 MET cc_start: 0.9089 (mmm) cc_final: 0.8876 (mmm) REVERT: B 789 MET cc_start: 0.8154 (mtt) cc_final: 0.7924 (ptp) REVERT: B 877 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: B 912 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7516 (p0) REVERT: B 1042 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8582 (tt0) REVERT: B 1043 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8013 (ptp-110) REVERT: B 1148 PHE cc_start: 0.8267 (t80) cc_final: 0.7803 (t80) REVERT: B 1152 ARG cc_start: 0.8958 (ttp-110) cc_final: 0.8629 (ttp-110) REVERT: B 1213 LYS cc_start: 0.9569 (mtpp) cc_final: 0.9305 (mtmm) REVERT: B 1346 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9030 (t) REVERT: B 1856 GLU cc_start: 0.8910 (tp30) cc_final: 0.8601 (tp30) REVERT: B 1913 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7957 (mp0) REVERT: B 1986 MET cc_start: 0.8164 (mtp) cc_final: 0.7886 (mtp) REVERT: B 1988 MET cc_start: 0.8543 (mmm) cc_final: 0.8276 (mtt) REVERT: B 1997 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 2092 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6941 (pp) REVERT: J 2089 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.7981 (p90) REVERT: T 161 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8432 (ttm110) outliers start: 45 outliers final: 34 residues processed: 181 average time/residue: 0.1523 time to fit residues: 40.0078 Evaluate side-chains 180 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 517 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 912 ASN Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain B residue 1024 PHE Chi-restraints excluded: chain B residue 1043 ARG Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1435 LEU Chi-restraints excluded: chain B residue 1442 ARG Chi-restraints excluded: chain B residue 1456 VAL Chi-restraints excluded: chain B residue 1482 GLU Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1773 LEU Chi-restraints excluded: chain B residue 1779 ARG Chi-restraints excluded: chain B residue 1787 GLU Chi-restraints excluded: chain B residue 1862 HIS Chi-restraints excluded: chain B residue 1997 LEU Chi-restraints excluded: chain B residue 1999 LEU Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2041 LEU Chi-restraints excluded: chain B residue 2084 LEU Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain J residue 2089 HIS Chi-restraints excluded: chain J residue 2215 THR Chi-restraints excluded: chain J residue 2284 MET Chi-restraints excluded: chain T residue 314 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.079034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053759 restraints weight = 43700.706| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.05 r_work: 0.2728 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16803 Z= 0.112 Angle : 0.559 11.987 22774 Z= 0.278 Chirality : 0.042 0.191 2551 Planarity : 0.004 0.061 2919 Dihedral : 5.403 54.628 2245 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 2.41 % Allowed : 14.18 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.19), residues: 2029 helix: 1.65 (0.18), residues: 858 sheet: 0.59 (0.28), residues: 370 loop : -0.07 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J2266 TYR 0.017 0.001 TYR T 155 PHE 0.012 0.001 PHE B 782 TRP 0.016 0.001 TRP B 593 HIS 0.003 0.000 HIS T 158 Details of bonding type rmsd covalent geometry : bond 0.00256 (16803) covalent geometry : angle 0.55905 (22774) hydrogen bonds : bond 0.03165 ( 730) hydrogen bonds : angle 4.07058 ( 2097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.02 seconds wall clock time: 67 minutes 2.01 seconds (4022.01 seconds total)