Starting phenix.real_space_refine on Thu Feb 5 21:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnw_71774/02_2026/9pnw_71774.map" } resolution = 2.9 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= 0.003 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 91 5.16 5 C 12117 2.51 5 N 3375 2.21 5 O 3790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19392 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 19000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2443, 19000 Classifications: {'peptide': 2443} Link IDs: {'PTRANS': 84, 'TRANS': 2358} Chain breaks: 3 Time building chain proxies: 4.29, per 1000 atoms: 0.22 Number of scatterers: 19392 At special positions: 0 Unit cell: (103.445, 133.87, 165.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 P 19 15.00 O 3790 8.00 N 3375 7.00 C 12117 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: 1.62 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 20 sheets defined 64.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1070 removed outlier: 3.820A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1069 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1110 removed outlier: 4.231A pdb=" N LYS A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A1096 " --> pdb=" O HIS A1092 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1120 removed outlier: 3.765A pdb=" N ALA A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A1120 " --> pdb=" O ARG A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 3.633A pdb=" N ARG A1125 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP A1126 " --> pdb=" O ALA A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1126' Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 4.109A pdb=" N LEU A1131 " --> pdb=" O GLY A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1163 removed outlier: 3.530A pdb=" N LEU A1154 " --> pdb=" O GLN A1150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1155 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A1162 " --> pdb=" O GLN A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.728A pdb=" N THR A1196 " --> pdb=" O GLN A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 removed outlier: 3.716A pdb=" N LYS A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1229 removed outlier: 3.544A pdb=" N LYS A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1246 Processing helix chain 'A' and resid 1279 through 1283 Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1322 through 1334 removed outlier: 3.637A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1351 removed outlier: 3.537A pdb=" N GLN A1345 " --> pdb=" O THR A1341 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A1346 " --> pdb=" O PRO A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.625A pdb=" N LEU A1369 " --> pdb=" O LYS A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1400 removed outlier: 3.628A pdb=" N LYS A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A1379 " --> pdb=" O LYS A1375 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A1380 " --> pdb=" O SER A1376 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A1397 " --> pdb=" O SER A1393 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.629A pdb=" N THR A1407 " --> pdb=" O ASP A1404 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1404 through 1408' Processing helix chain 'A' and resid 1435 through 1438 removed outlier: 3.545A pdb=" N GLU A1438 " --> pdb=" O LEU A1435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1435 through 1438' Processing helix chain 'A' and resid 1455 through 1468 removed outlier: 3.643A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 3.850A pdb=" N SER A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1486 " --> pdb=" O ASP A1482 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1487 " --> pdb=" O GLU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1506 Processing helix chain 'A' and resid 1511 through 1521 Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1527 through 1541 removed outlier: 3.572A pdb=" N VAL A1540 " --> pdb=" O SER A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1569 Processing helix chain 'A' and resid 1575 through 1584 removed outlier: 3.730A pdb=" N LYS A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1603 Processing helix chain 'A' and resid 1607 through 1627 removed outlier: 3.941A pdb=" N TYR A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.567A pdb=" N PHE A1647 " --> pdb=" O LEU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1675 Processing helix chain 'A' and resid 1678 through 1708 removed outlier: 3.549A pdb=" N ASP A1700 " --> pdb=" O GLU A1696 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A1707 " --> pdb=" O LYS A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1718 Processing helix chain 'A' and resid 1719 through 1722 removed outlier: 3.596A pdb=" N ALA A1722 " --> pdb=" O GLY A1719 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1719 through 1722' Processing helix chain 'A' and resid 1724 through 1743 removed outlier: 3.542A pdb=" N GLU A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.913A pdb=" N TYR A1772 " --> pdb=" O PRO A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1790 Processing helix chain 'A' and resid 1790 through 1803 removed outlier: 3.575A pdb=" N THR A1801 " --> pdb=" O GLY A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1840 removed outlier: 3.783A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A1832 " --> pdb=" O PHE A1828 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A1833 " --> pdb=" O LYS A1829 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1862 Processing helix chain 'A' and resid 1863 through 1867 Processing helix chain 'A' and resid 1915 through 1925 Processing helix chain 'A' and resid 1926 through 1936 removed outlier: 3.550A pdb=" N MET A1930 " --> pdb=" O ASP A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1972 removed outlier: 4.073A pdb=" N ARG A1962 " --> pdb=" O THR A1958 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A1963 " --> pdb=" O ASP A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1990 removed outlier: 3.641A pdb=" N SER A1983 " --> pdb=" O ASN A1979 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.700A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A1996 " --> pdb=" O PHE A1993 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1992 through 1996' Processing helix chain 'A' and resid 1997 through 2009 removed outlier: 4.353A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.665A pdb=" N ILE A2029 " --> pdb=" O ALA A2025 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A2048 " --> pdb=" O HIS A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2101 removed outlier: 3.904A pdb=" N ASP A2082 " --> pdb=" O GLU A2078 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A2083 " --> pdb=" O GLN A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2142 through 2146 removed outlier: 3.824A pdb=" N LYS A2146 " --> pdb=" O ASN A2143 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2168 removed outlier: 4.715A pdb=" N THR A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A2158 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A2159 " --> pdb=" O ALA A2155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2188 removed outlier: 3.642A pdb=" N ALA A2184 " --> pdb=" O VAL A2180 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A2185 " --> pdb=" O ALA A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2203 removed outlier: 3.520A pdb=" N GLN A2201 " --> pdb=" O MET A2197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A2202 " --> pdb=" O GLU A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2244 removed outlier: 3.652A pdb=" N ILE A2227 " --> pdb=" O MET A2223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A2228 " --> pdb=" O GLU A2224 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A2234 " --> pdb=" O LEU A2230 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A2238 " --> pdb=" O SER A2234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A2239 " --> pdb=" O THR A2235 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2265 removed outlier: 3.648A pdb=" N ALA A2255 " --> pdb=" O THR A2251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A2265 " --> pdb=" O GLY A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2275 through 2294 removed outlier: 3.644A pdb=" N GLU A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A2288 " --> pdb=" O ASP A2284 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A2293 " --> pdb=" O ILE A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2318 Processing helix chain 'A' and resid 2318 through 2323 Processing helix chain 'A' and resid 2329 through 2348 removed outlier: 3.898A pdb=" N LYS A2336 " --> pdb=" O VAL A2332 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A2344 " --> pdb=" O GLN A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2382 removed outlier: 3.721A pdb=" N VAL A2380 " --> pdb=" O THR A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2410 through 2413 Processing helix chain 'A' and resid 2426 through 2443 removed outlier: 3.616A pdb=" N ALA A2430 " --> pdb=" O ASN A2426 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A2442 " --> pdb=" O VAL A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2470 Processing helix chain 'A' and resid 2471 through 2473 No H-bonds generated for 'chain 'A' and resid 2471 through 2473' Processing helix chain 'A' and resid 2474 through 2486 removed outlier: 3.580A pdb=" N GLU A2479 " --> pdb=" O ALA A2475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A2483 " --> pdb=" O GLU A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2494 Processing helix chain 'A' and resid 2501 through 2517 removed outlier: 3.923A pdb=" N ARG A2505 " --> pdb=" O ASN A2501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A2508 " --> pdb=" O ASP A2504 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A2514 " --> pdb=" O GLN A2510 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2540 removed outlier: 3.689A pdb=" N THR A2534 " --> pdb=" O SER A2530 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2550 removed outlier: 3.565A pdb=" N ILE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2559 Processing helix chain 'A' and resid 2564 through 2585 removed outlier: 3.971A pdb=" N VAL A2576 " --> pdb=" O ALA A2572 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A2583 " --> pdb=" O SER A2579 " (cutoff:3.500A) Processing helix chain 'A' and resid 2593 through 2615 Processing helix chain 'A' and resid 2624 through 2641 removed outlier: 3.668A pdb=" N LEU A2640 " --> pdb=" O SER A2636 " (cutoff:3.500A) Processing helix chain 'A' and resid 2665 through 2674 removed outlier: 3.541A pdb=" N LEU A2669 " --> pdb=" O HIS A2665 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A2672 " --> pdb=" O LYS A2668 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A2673 " --> pdb=" O LEU A2669 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A2674 " --> pdb=" O THR A2670 " (cutoff:3.500A) Processing helix chain 'A' and resid 2681 through 2684 Processing helix chain 'A' and resid 2685 through 2693 removed outlier: 3.887A pdb=" N ALA A2689 " --> pdb=" O GLY A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2708 removed outlier: 3.624A pdb=" N PHE A2699 " --> pdb=" O VAL A2695 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A2702 " --> pdb=" O PRO A2698 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A2705 " --> pdb=" O ASP A2701 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2736 removed outlier: 3.580A pdb=" N SER A2725 " --> pdb=" O LYS A2721 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A2728 " --> pdb=" O LYS A2724 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A2736 " --> pdb=" O GLN A2732 " (cutoff:3.500A) Processing helix chain 'A' and resid 2737 through 2744 Processing helix chain 'A' and resid 2751 through 2763 Processing helix chain 'A' and resid 2766 through 2773 Processing helix chain 'A' and resid 2775 through 2785 removed outlier: 3.595A pdb=" N LEU A2783 " --> pdb=" O ILE A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2785 through 2805 removed outlier: 4.048A pdb=" N VAL A2789 " --> pdb=" O SER A2785 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A2790 " --> pdb=" O SER A2786 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A2798 " --> pdb=" O SER A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2825 removed outlier: 3.543A pdb=" N ILE A2823 " --> pdb=" O ALA A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2841 removed outlier: 3.666A pdb=" N ARG A2840 " --> pdb=" O HIS A2836 " (cutoff:3.500A) Processing helix chain 'A' and resid 2853 through 2867 removed outlier: 3.594A pdb=" N GLU A2867 " --> pdb=" O LEU A2863 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2884 removed outlier: 3.511A pdb=" N LEU A2876 " --> pdb=" O SER A2872 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2907 removed outlier: 3.548A pdb=" N PHE A2890 " --> pdb=" O GLU A2886 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A2897 " --> pdb=" O ALA A2893 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A2905 " --> pdb=" O GLU A2901 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A2906 " --> pdb=" O GLU A2902 " (cutoff:3.500A) Processing helix chain 'A' and resid 2909 through 2914 removed outlier: 3.616A pdb=" N LEU A2914 " --> pdb=" O ASN A2910 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2943 removed outlier: 3.938A pdb=" N LYS A2941 " --> pdb=" O LYS A2937 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A2942 " --> pdb=" O GLU A2938 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A2943 " --> pdb=" O PHE A2939 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3021 removed outlier: 3.515A pdb=" N ARG A3016 " --> pdb=" O PRO A3012 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A3019 " --> pdb=" O GLU A3015 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A3020 " --> pdb=" O ARG A3016 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3057 Processing helix chain 'A' and resid 3061 through 3101 removed outlier: 3.576A pdb=" N GLY A3067 " --> pdb=" O ALA A3063 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A3075 " --> pdb=" O GLY A3071 " (cutoff:3.500A) Processing helix chain 'A' and resid 3102 through 3106 removed outlier: 3.853A pdb=" N LYS A3105 " --> pdb=" O SER A3102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A3106 " --> pdb=" O ALA A3103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3102 through 3106' Processing helix chain 'A' and resid 3117 through 3126 removed outlier: 3.596A pdb=" N ALA A3123 " --> pdb=" O VAL A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3128 through 3139 removed outlier: 3.528A pdb=" N LYS A3134 " --> pdb=" O GLU A3130 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A3138 " --> pdb=" O LYS A3134 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3155 removed outlier: 3.529A pdb=" N ASP A3153 " --> pdb=" O ASP A3149 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A3154 " --> pdb=" O MET A3150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A3155 " --> pdb=" O LEU A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3156 through 3159 removed outlier: 3.588A pdb=" N ALA A3159 " --> pdb=" O GLY A3156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3156 through 3159' Processing helix chain 'A' and resid 3173 through 3188 removed outlier: 3.520A pdb=" N ASP A3178 " --> pdb=" O PRO A3174 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A3182 " --> pdb=" O ASP A3178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A3186 " --> pdb=" O LYS A3182 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3197 Processing helix chain 'A' and resid 3209 through 3236 removed outlier: 3.801A pdb=" N VAL A3213 " --> pdb=" O ASP A3209 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A3214 " --> pdb=" O ALA A3210 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A3215 " --> pdb=" O LYS A3211 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A3220 " --> pdb=" O VAL A3216 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A3221 " --> pdb=" O LYS A3217 " (cutoff:3.500A) Proline residue: A3222 - end of helix removed outlier: 3.531A pdb=" N ILE A3230 " --> pdb=" O PHE A3226 " (cutoff:3.500A) Processing helix chain 'A' and resid 3239 through 3266 removed outlier: 3.706A pdb=" N ILE A3243 " --> pdb=" O PRO A3239 " (cutoff:3.500A) Proline residue: A3248 - end of helix removed outlier: 3.793A pdb=" N ARG A3263 " --> pdb=" O LYS A3259 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A3264 " --> pdb=" O SER A3260 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A3266 " --> pdb=" O LEU A3262 " (cutoff:3.500A) Processing helix chain 'A' and resid 3266 through 3274 Processing helix chain 'A' and resid 3277 through 3297 removed outlier: 3.936A pdb=" N VAL A3281 " --> pdb=" O ASN A3277 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A3283 " --> pdb=" O ASN A3279 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A3289 " --> pdb=" O LYS A3285 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A3294 " --> pdb=" O SER A3290 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A3295 " --> pdb=" O ILE A3291 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3307 Processing helix chain 'A' and resid 3318 through 3320 No H-bonds generated for 'chain 'A' and resid 3318 through 3320' Processing helix chain 'A' and resid 3321 through 3327 removed outlier: 3.820A pdb=" N ALA A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) Processing helix chain 'A' and resid 3328 through 3338 Processing helix chain 'A' and resid 3341 through 3346 Processing helix chain 'A' and resid 3347 through 3351 removed outlier: 3.743A pdb=" N ALA A3351 " --> pdb=" O GLY A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3385 removed outlier: 3.650A pdb=" N GLN A3361 " --> pdb=" O THR A3357 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A3364 " --> pdb=" O PHE A3360 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A3373 " --> pdb=" O TYR A3369 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A3383 " --> pdb=" O TYR A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3398 Processing helix chain 'A' and resid 3403 through 3407 removed outlier: 3.725A pdb=" N ARG A3406 " --> pdb=" O ASN A3403 " (cutoff:3.500A) Processing helix chain 'A' and resid 3417 through 3441 removed outlier: 3.946A pdb=" N TRP A3422 " --> pdb=" O MET A3418 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A3438 " --> pdb=" O ALA A3434 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A3439 " --> pdb=" O MET A3435 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3449 removed outlier: 3.509A pdb=" N SER A3445 " --> pdb=" O ASN A3441 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A3449 " --> pdb=" O SER A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3467 through 3473 removed outlier: 3.620A pdb=" N ALA A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3493 through 3500 Processing sheet with id=AA1, first strand: chain 'A' and resid 1035 through 1036 removed outlier: 3.621A pdb=" N SER A1218 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1136 through 1137 Processing sheet with id=AA3, first strand: chain 'A' and resid 1249 through 1253 Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1302 removed outlier: 4.259A pdb=" N PHE A1301 " --> pdb=" O HIS A1411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1312 through 1313 removed outlier: 7.015A pdb=" N VAL A1319 " --> pdb=" O GLN A1313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AA7, first strand: chain 'A' and resid 1414 through 1416 Processing sheet with id=AA8, first strand: chain 'A' and resid 1445 through 1447 Processing sheet with id=AA9, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AB1, first strand: chain 'A' and resid 1587 through 1589 Processing sheet with id=AB2, first strand: chain 'A' and resid 1745 through 1750 Processing sheet with id=AB3, first strand: chain 'A' and resid 1870 through 1871 Processing sheet with id=AB4, first strand: chain 'A' and resid 1881 through 1884 Processing sheet with id=AB5, first strand: chain 'A' and resid 1891 through 1894 removed outlier: 3.534A pdb=" N ALA A1893 " --> pdb=" O VAL A1902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2126 through 2127 removed outlier: 6.436A pdb=" N LYS A2171 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A2218 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A2173 " --> pdb=" O LEU A2218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2930 through 2935 removed outlier: 3.509A pdb=" N ASN A2930 " --> pdb=" O SER A2969 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS A2964 " --> pdb=" O THR A2952 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR A2952 " --> pdb=" O LYS A2964 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A2966 " --> pdb=" O ILE A2950 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2988 through 2989 removed outlier: 3.729A pdb=" N VAL A2992 " --> pdb=" O ALA A2989 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3006 through 3008 removed outlier: 4.187A pdb=" N GLY A3006 " --> pdb=" O GLN A3046 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A3046 " --> pdb=" O GLY A3006 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A3043 " --> pdb=" O ILE A3034 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 3108 through 3110 Processing sheet with id=AC2, first strand: chain 'A' and resid 3161 through 3162 1003 hydrogen bonds defined for protein. 2865 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: 5.01 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6455 1.34 - 1.46: 3291 1.46 - 1.58: 9778 1.58 - 1.70: 37 1.70 - 1.82: 182 Bond restraints: 19743 Sorted by residual: bond pdb=" CB LYS A3096 " pdb=" CG LYS A3096 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN A2254 " pdb=" CG GLN A2254 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CG LYS A3096 " pdb=" CD LYS A3096 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CG LYS A2694 " pdb=" CD LYS A2694 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.67e-01 bond pdb=" CA LYS A1751 " pdb=" CB LYS A1751 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.06e-01 ... (remaining 19738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 26569 2.20 - 4.39: 161 4.39 - 6.59: 26 6.59 - 8.78: 6 8.78 - 10.98: 3 Bond angle restraints: 26765 Sorted by residual: angle pdb=" CA GLN A2254 " pdb=" CB GLN A2254 " pdb=" CG GLN A2254 " ideal model delta sigma weight residual 114.10 121.66 -7.56 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CB MET A2223 " pdb=" CG MET A2223 " pdb=" SD MET A2223 " ideal model delta sigma weight residual 112.70 123.68 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB LYS A3096 " pdb=" CG LYS A3096 " pdb=" CD LYS A3096 " ideal model delta sigma weight residual 111.30 119.60 -8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N MET A3456 " pdb=" CA MET A3456 " pdb=" C MET A3456 " ideal model delta sigma weight residual 114.56 109.97 4.59 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C THR A2591 " pdb=" N ASN A2592 " pdb=" CA ASN A2592 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 ... (remaining 26760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 10992 26.27 - 52.55: 944 52.55 - 78.82: 123 78.82 - 105.10: 12 105.10 - 131.37: 1 Dihedral angle restraints: 12072 sinusoidal: 4977 harmonic: 7095 Sorted by residual: dihedral pdb=" C4' DC B 5 " pdb=" C3' DC B 5 " pdb=" O3' DC B 5 " pdb=" P DA B 6 " ideal model delta sinusoidal sigma weight residual 220.00 88.63 131.37 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" CA ASN A1768 " pdb=" CB ASN A1768 " pdb=" CG ASN A1768 " pdb=" OD1 ASN A1768 " ideal model delta sinusoidal sigma weight residual 120.00 -166.80 -73.20 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LEU A2832 " pdb=" C LEU A2832 " pdb=" N ARG A2833 " pdb=" CA ARG A2833 " ideal model delta harmonic sigma weight residual -180.00 -163.85 -16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 12069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2172 0.032 - 0.064: 665 0.064 - 0.096: 144 0.096 - 0.128: 66 0.128 - 0.160: 2 Chirality restraints: 3049 Sorted by residual: chirality pdb=" CA ASN A2592 " pdb=" N ASN A2592 " pdb=" C ASN A2592 " pdb=" CB ASN A2592 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA LYS A1751 " pdb=" N LYS A1751 " pdb=" C LYS A1751 " pdb=" CB LYS A1751 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A2173 " pdb=" N ILE A2173 " pdb=" C ILE A2173 " pdb=" CB ILE A2173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 3046 not shown) Planarity restraints: 3419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2076 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A2077 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2620 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A2621 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A2621 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A2621 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1429 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A1430 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1430 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1430 " -0.021 5.00e-02 4.00e+02 ... (remaining 3416 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1174 2.74 - 3.28: 19333 3.28 - 3.82: 30244 3.82 - 4.36: 36023 4.36 - 4.90: 62548 Nonbonded interactions: 149322 Sorted by model distance: nonbonded pdb=" O MET A1566 " pdb=" OG1 THR A1570 " model vdw 2.196 3.040 nonbonded pdb=" O GLY A2761 " pdb=" OG1 THR A2765 " model vdw 2.210 3.040 nonbonded pdb=" OD2 ASP A2993 " pdb=" OG1 THR A2996 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A3007 " pdb=" O VAL A3460 " model vdw 2.259 3.120 nonbonded pdb=" O SER A3310 " pdb=" OG SER A3310 " model vdw 2.266 3.040 ... (remaining 149317 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.200 Find NCS groups from input model: 0.300 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:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.002 0.038 19743 Z= 0.079 Angle : 0.438 10.979 26765 Z= 0.224 Chirality : 0.035 0.160 3049 Planarity : 0.003 0.046 3419 Dihedral : 18.112 131.373 7488 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.18 % Allowed : 27.65 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2435 helix: 0.37 (0.14), residues: 1378 sheet: 0.14 (0.53), residues: 93 loop : -0.47 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2960 TYR 0.011 0.001 TYR A1013 PHE 0.008 0.001 PHE A1117 TRP 0.004 0.000 TRP A2347 HIS 0.001 0.000 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00173 (19743) covalent geometry : angle 0.43756 (26765) hydrogen bonds : bond 0.32519 ( 1003) hydrogen bonds : angle 7.10536 ( 2865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 134 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 1057 GLN cc_start: 0.7729 (pp30) cc_final: 0.7243 (pp30) REVERT: A 1252 ASN cc_start: 0.7517 (m110) cc_final: 0.6832 (p0) REVERT: A 1469 ASP cc_start: 0.8767 (t0) cc_final: 0.8450 (t0) REVERT: A 1533 MET cc_start: 0.8368 (tpp) cc_final: 0.7796 (tpt) REVERT: A 1549 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8433 (t) REVERT: A 1667 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: A 1827 MET cc_start: 0.8580 (tpp) cc_final: 0.8296 (mmm) REVERT: A 1871 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: A 2018 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 2135 ILE cc_start: 0.8640 (mt) cc_final: 0.8354 (mm) REVERT: A 2146 LYS cc_start: 0.8378 (pmtt) cc_final: 0.8051 (tppt) REVERT: A 2160 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: A 2205 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 2210 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.7806 (t0) REVERT: A 2257 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: A 2265 GLN cc_start: 0.8075 (mp10) cc_final: 0.7764 (mp10) REVERT: A 2284 ASP cc_start: 0.8185 (m-30) cc_final: 0.7868 (m-30) REVERT: A 2344 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8224 (tppp) REVERT: A 2362 ASN cc_start: 0.8539 (p0) cc_final: 0.8124 (p0) REVERT: A 2420 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 2787 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8533 (tptt) REVERT: A 2868 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8704 (mt) REVERT: A 2886 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8477 (tp30) REVERT: A 2964 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8502 (mtpp) REVERT: A 3010 ASP cc_start: 0.8245 (t0) cc_final: 0.7907 (t0) REVERT: A 3019 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8424 (pmtt) REVERT: A 3105 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8628 (tppp) REVERT: A 3263 ARG cc_start: 0.7549 (mmm160) cc_final: 0.6905 (tpm170) outliers start: 65 outliers final: 41 residues processed: 195 average time/residue: 0.5951 time to fit residues: 131.1497 Evaluate side-chains 188 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1283 SER Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1491 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1597 ASN Chi-restraints excluded: chain A residue 1601 SER Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2073 SER Chi-restraints excluded: chain A residue 2099 VAL Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2160 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2213 ASP Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2344 LYS Chi-restraints excluded: chain A residue 2373 SER Chi-restraints excluded: chain A residue 2420 GLU Chi-restraints excluded: chain A residue 2549 ILE Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2570 THR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2616 ASP Chi-restraints excluded: chain A residue 2716 VAL Chi-restraints excluded: chain A residue 2723 VAL Chi-restraints excluded: chain A residue 2787 LYS Chi-restraints excluded: chain A residue 2816 LYS Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2886 GLU Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3105 LYS Chi-restraints excluded: chain A residue 3130 GLU Chi-restraints excluded: chain A residue 3260 SER Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3389 SER Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1503 ASN A1768 ASN A2065 GLN A2210 ASN A2292 HIS A2318 ASN ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2402 ASN A2697 GLN ** A2700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 GLN A3225 ASN ** A3485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068699 restraints weight = 41321.646| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.85 r_work: 0.2991 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19743 Z= 0.178 Angle : 0.545 6.992 26765 Z= 0.296 Chirality : 0.040 0.176 3049 Planarity : 0.004 0.044 3419 Dihedral : 10.511 133.534 2952 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.25 % Allowed : 25.50 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2435 helix: 1.18 (0.14), residues: 1430 sheet: 0.06 (0.51), residues: 95 loop : -0.58 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2142 TYR 0.014 0.001 TYR A1388 PHE 0.016 0.001 PHE A1392 TRP 0.010 0.001 TRP A3422 HIS 0.006 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00392 (19743) covalent geometry : angle 0.54523 (26765) hydrogen bonds : bond 0.07808 ( 1003) hydrogen bonds : angle 4.68701 ( 2865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 141 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7934 (p90) REVERT: A 1252 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7279 (p0) REVERT: A 1279 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 1289 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: A 1343 MET cc_start: 0.8911 (tpt) cc_final: 0.8301 (tpt) REVERT: A 1475 MET cc_start: 0.9077 (ptp) cc_final: 0.8820 (ptm) REVERT: A 1567 MET cc_start: 0.8892 (mmm) cc_final: 0.8686 (tpt) REVERT: A 1667 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8639 (mttm) REVERT: A 1883 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: A 2160 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: A 2191 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8383 (pp20) REVERT: A 2257 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: A 2264 GLU cc_start: 0.9284 (tt0) cc_final: 0.8942 (tp30) REVERT: A 2265 GLN cc_start: 0.7933 (mp10) cc_final: 0.7636 (mp10) REVERT: A 2284 ASP cc_start: 0.8136 (m-30) cc_final: 0.7772 (m-30) REVERT: A 2362 ASN cc_start: 0.8651 (p0) cc_final: 0.8151 (p0) REVERT: A 2432 MET cc_start: 0.8395 (ttm) cc_final: 0.8180 (mtp) REVERT: A 2507 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 2559 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8964 (mtpp) REVERT: A 2787 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7877 (tptt) REVERT: A 2840 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8349 (mtm-85) REVERT: A 2894 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 3015 GLU cc_start: 0.8041 (pp20) cc_final: 0.7836 (pp20) REVERT: A 3019 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8488 (pmtt) REVERT: A 3263 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7126 (tpm170) REVERT: A 3297 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (ptp-110) REVERT: A 3384 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7705 (mppt) outliers start: 87 outliers final: 30 residues processed: 214 average time/residue: 0.6036 time to fit residues: 145.1641 Evaluate side-chains 175 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1983 SER Chi-restraints excluded: chain A residue 2099 VAL Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2160 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2218 LEU Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2288 THR Chi-restraints excluded: chain A residue 2321 LEU Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2385 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2559 LYS Chi-restraints excluded: chain A residue 2723 VAL Chi-restraints excluded: chain A residue 2787 LYS Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 3002 THR Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3075 GLU Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3297 ARG Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3436 SER Chi-restraints excluded: chain A residue 3465 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.0270 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 HIS A2983 GLN A3107 GLN ** A3485 GLN ** 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 = 0.3562 r_free = 0.3562 target = 0.094591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070757 restraints weight = 41284.079| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.88 r_work: 0.3006 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19743 Z= 0.119 Angle : 0.464 6.693 26765 Z= 0.248 Chirality : 0.038 0.165 3049 Planarity : 0.003 0.043 3419 Dihedral : 9.773 133.554 2870 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.57 % Allowed : 25.94 % Favored : 70.49 % 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: 1.15 (0.17), residues: 2435 helix: 1.70 (0.14), residues: 1426 sheet: 0.01 (0.50), residues: 95 loop : -0.62 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1750 TYR 0.012 0.001 TYR A1013 PHE 0.015 0.001 PHE A1117 TRP 0.006 0.001 TRP A2347 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00239 (19743) covalent geometry : angle 0.46401 (26765) hydrogen bonds : bond 0.06198 ( 1003) hydrogen bonds : angle 4.19216 ( 2865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7965 (p90) REVERT: A 1252 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7165 (p0) REVERT: A 1279 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: A 1382 ARG cc_start: 0.8599 (tpp-160) cc_final: 0.8160 (ptm160) REVERT: A 1475 MET cc_start: 0.8948 (ptp) cc_final: 0.8709 (ptm) REVERT: A 1567 MET cc_start: 0.8841 (mmm) cc_final: 0.8543 (tpt) REVERT: A 1696 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7834 (tp30) REVERT: A 2057 MET cc_start: 0.8509 (mtp) cc_final: 0.8297 (ttm) REVERT: A 2075 MET cc_start: 0.8902 (mtp) cc_final: 0.8666 (mtp) REVERT: A 2160 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: A 2191 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: A 2257 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: A 2264 GLU cc_start: 0.9244 (tt0) cc_final: 0.8995 (tp30) REVERT: A 2265 GLN cc_start: 0.7988 (mp10) cc_final: 0.7292 (mp10) REVERT: A 2284 ASP cc_start: 0.8104 (m-30) cc_final: 0.7773 (m-30) REVERT: A 2362 ASN cc_start: 0.8592 (p0) cc_final: 0.8093 (p0) REVERT: A 2507 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 2886 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: A 2983 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7515 (pp30) REVERT: A 3019 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8438 (pmtt) REVERT: A 3263 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7276 (tpm170) REVERT: A 3384 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7496 (mptm) outliers start: 73 outliers final: 22 residues processed: 197 average time/residue: 0.5812 time to fit residues: 128.6685 Evaluate side-chains 164 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1983 SER Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2160 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2222 SER Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2620 THR Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2886 GLU Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3428 ILE Chi-restraints excluded: chain A residue 3465 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 207 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 127 optimal weight: 0.0870 chunk 244 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2983 GLN A3440 ASN ** A3485 GLN ** 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 = 0.3535 r_free = 0.3535 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068959 restraints weight = 41348.285| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.97 r_work: 0.2975 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19743 Z= 0.164 Angle : 0.493 6.783 26765 Z= 0.262 Chirality : 0.039 0.172 3049 Planarity : 0.003 0.046 3419 Dihedral : 9.726 133.435 2858 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.15 % Allowed : 25.60 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2435 helix: 1.75 (0.14), residues: 1428 sheet: -0.05 (0.50), residues: 95 loop : -0.66 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2142 TYR 0.013 0.001 TYR A2966 PHE 0.015 0.001 PHE A1392 TRP 0.007 0.001 TRP A3422 HIS 0.004 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00377 (19743) covalent geometry : angle 0.49289 (26765) hydrogen bonds : bond 0.06444 ( 1003) hydrogen bonds : angle 4.15034 ( 2865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 139 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7951 (p90) REVERT: A 1057 GLN cc_start: 0.8013 (pp30) cc_final: 0.7618 (pp30) REVERT: A 1160 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (tpt-90) REVERT: A 1252 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7169 (p0) REVERT: A 1279 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: A 1289 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: A 1382 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8194 (ptm160) REVERT: A 1475 MET cc_start: 0.8831 (ptp) cc_final: 0.8547 (ptm) REVERT: A 1567 MET cc_start: 0.8839 (mmm) cc_final: 0.8615 (tpt) REVERT: A 1696 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7804 (tp30) REVERT: A 1787 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7528 (tp) REVERT: A 2075 MET cc_start: 0.8877 (mtp) cc_final: 0.8616 (mtp) REVERT: A 2160 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8769 (mp0) REVERT: A 2191 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8278 (pp20) REVERT: A 2205 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 2223 MET cc_start: 0.7737 (tpp) cc_final: 0.7525 (tpt) REVERT: A 2257 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: A 2264 GLU cc_start: 0.9241 (tt0) cc_final: 0.8959 (tp30) REVERT: A 2265 GLN cc_start: 0.7954 (mp10) cc_final: 0.7545 (mp10) REVERT: A 2284 ASP cc_start: 0.8108 (m-30) cc_final: 0.7771 (m-30) REVERT: A 2347 TRP cc_start: 0.8363 (m-90) cc_final: 0.7784 (m-90) REVERT: A 2362 ASN cc_start: 0.8575 (p0) cc_final: 0.8085 (p0) REVERT: A 2507 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7863 (t80) REVERT: A 2886 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: A 2894 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.6278 (t80) REVERT: A 3019 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8405 (pmtt) REVERT: A 3263 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7283 (tpm170) REVERT: A 3297 ARG cc_start: 0.8285 (ptp-110) cc_final: 0.8064 (ptp-110) REVERT: A 3384 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7426 (mptm) outliers start: 85 outliers final: 35 residues processed: 208 average time/residue: 0.7073 time to fit residues: 165.3811 Evaluate side-chains 181 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2160 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2385 THR Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2448 MET Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2620 THR Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2886 GLU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2402 ASN A2983 GLN ** A3485 GLN ** 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 = 0.3533 r_free = 0.3533 target = 0.092847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068930 restraints weight = 41445.982| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.89 r_work: 0.2970 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19743 Z= 0.164 Angle : 0.491 6.390 26765 Z= 0.261 Chirality : 0.039 0.162 3049 Planarity : 0.003 0.047 3419 Dihedral : 9.760 133.329 2857 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.54 % Allowed : 25.60 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2435 helix: 1.80 (0.14), residues: 1431 sheet: 0.05 (0.50), residues: 94 loop : -0.68 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2142 TYR 0.013 0.001 TYR A2966 PHE 0.015 0.001 PHE A1392 TRP 0.007 0.001 TRP A3422 HIS 0.004 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00379 (19743) covalent geometry : angle 0.49065 (26765) hydrogen bonds : bond 0.06347 ( 1003) hydrogen bonds : angle 4.08471 ( 2865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 138 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7926 (p90) REVERT: A 1132 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 1160 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (tpt-90) REVERT: A 1252 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7214 (p0) REVERT: A 1279 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: A 1289 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: A 1343 MET cc_start: 0.8760 (tpt) cc_final: 0.8090 (tpt) REVERT: A 1382 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8218 (ptm160) REVERT: A 1567 MET cc_start: 0.8862 (mmm) cc_final: 0.8625 (tpt) REVERT: A 1618 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: A 1696 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7866 (tp30) REVERT: A 1787 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (tp) REVERT: A 2075 MET cc_start: 0.8915 (mtp) cc_final: 0.8670 (mtp) REVERT: A 2160 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: A 2191 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: A 2205 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 2223 MET cc_start: 0.7701 (tpp) cc_final: 0.7475 (tpt) REVERT: A 2257 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: A 2264 GLU cc_start: 0.9230 (tt0) cc_final: 0.8955 (tp30) REVERT: A 2265 GLN cc_start: 0.7941 (mp10) cc_final: 0.7515 (mp10) REVERT: A 2284 ASP cc_start: 0.8141 (m-30) cc_final: 0.7804 (m-30) REVERT: A 2347 TRP cc_start: 0.8390 (m-90) cc_final: 0.7944 (m-90) REVERT: A 2362 ASN cc_start: 0.8629 (p0) cc_final: 0.8109 (p0) REVERT: A 2507 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7914 (t80) REVERT: A 2840 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (mtm-85) REVERT: A 2868 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 2886 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 2894 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6358 (t80) REVERT: A 2964 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8490 (mtpp) REVERT: A 2983 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: A 3019 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8418 (pmtt) REVERT: A 3150 MET cc_start: 0.8158 (mtm) cc_final: 0.7957 (ttm) REVERT: A 3263 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7292 (tpm170) REVERT: A 3384 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7435 (mptm) outliers start: 93 outliers final: 48 residues processed: 219 average time/residue: 0.6456 time to fit residues: 159.3611 Evaluate side-chains 204 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1618 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2160 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2385 THR Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2448 MET Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2620 THR Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2886 GLU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3002 THR Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3101 SER Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3294 SER Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3428 ILE Chi-restraints excluded: chain A residue 3436 SER Chi-restraints excluded: chain A residue 3465 GLN Chi-restraints excluded: chain A residue 3480 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 101 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2983 GLN A3055 HIS ** A3485 GLN ** 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 = 0.3522 r_free = 0.3522 target = 0.091935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067982 restraints weight = 41320.184| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.89 r_work: 0.2950 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19743 Z= 0.207 Angle : 0.528 6.987 26765 Z= 0.279 Chirality : 0.040 0.187 3049 Planarity : 0.004 0.048 3419 Dihedral : 9.826 133.185 2857 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.89 % Allowed : 25.45 % Favored : 69.66 % 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: 1.12 (0.17), residues: 2435 helix: 1.71 (0.14), residues: 1432 sheet: 0.01 (0.51), residues: 94 loop : -0.73 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3297 TYR 0.015 0.001 TYR A2966 PHE 0.018 0.001 PHE A1392 TRP 0.008 0.001 TRP A3422 HIS 0.005 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00489 (19743) covalent geometry : angle 0.52758 (26765) hydrogen bonds : bond 0.06826 ( 1003) hydrogen bonds : angle 4.16270 ( 2865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 134 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7990 (p90) REVERT: A 1160 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8278 (tpt-90) REVERT: A 1252 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7297 (p0) REVERT: A 1279 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: A 1289 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: A 1343 MET cc_start: 0.8860 (tpt) cc_final: 0.8303 (tpt) REVERT: A 1382 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8273 (ptm160) REVERT: A 1567 MET cc_start: 0.8908 (mmm) cc_final: 0.8676 (tpt) REVERT: A 1618 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8206 (tp30) REVERT: A 1696 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7924 (tp30) REVERT: A 1787 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 2075 MET cc_start: 0.8934 (mtp) cc_final: 0.8593 (mtp) REVERT: A 2191 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (pp20) REVERT: A 2205 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8219 (mm) REVERT: A 2257 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: A 2264 GLU cc_start: 0.9208 (tt0) cc_final: 0.8951 (tp30) REVERT: A 2265 GLN cc_start: 0.7957 (mp10) cc_final: 0.7513 (mp10) REVERT: A 2284 ASP cc_start: 0.8206 (m-30) cc_final: 0.7858 (m-30) REVERT: A 2347 TRP cc_start: 0.8568 (m-90) cc_final: 0.8195 (m-90) REVERT: A 2362 ASN cc_start: 0.8720 (p0) cc_final: 0.8187 (p0) REVERT: A 2507 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 2611 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: A 2840 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (mtm-85) REVERT: A 2868 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 2886 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: A 2894 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6494 (t80) REVERT: A 2964 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8627 (mtpp) REVERT: A 3019 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8475 (pmtt) REVERT: A 3263 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7292 (tpm170) REVERT: A 3384 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7617 (mppt) outliers start: 100 outliers final: 53 residues processed: 215 average time/residue: 0.6725 time to fit residues: 163.1626 Evaluate side-chains 206 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 134 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1618 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1644 MET Chi-restraints excluded: chain A residue 1671 THR Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2189 VAL Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2288 THR Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2385 THR Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2611 ARG Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2886 GLU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 3002 THR Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3101 SER Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3294 SER Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3436 SER Chi-restraints excluded: chain A residue 3480 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 147 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2983 GLN ** A3485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070716 restraints weight = 41154.434| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.88 r_work: 0.3003 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19743 Z= 0.117 Angle : 0.462 6.902 26765 Z= 0.245 Chirality : 0.038 0.172 3049 Planarity : 0.003 0.047 3419 Dihedral : 9.679 133.341 2854 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.81 % Allowed : 26.48 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2435 helix: 1.99 (0.14), residues: 1429 sheet: 0.01 (0.50), residues: 96 loop : -0.69 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3297 TYR 0.011 0.001 TYR A1013 PHE 0.010 0.001 PHE A1392 TRP 0.006 0.001 TRP A3422 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00252 (19743) covalent geometry : angle 0.46181 (26765) hydrogen bonds : bond 0.05258 ( 1003) hydrogen bonds : angle 3.85026 ( 2865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 144 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8041 (p90) REVERT: A 1021 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 1057 GLN cc_start: 0.8055 (pp30) cc_final: 0.7633 (pp30) REVERT: A 1252 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7293 (p0) REVERT: A 1279 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: A 1289 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 1382 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8353 (ptm160) REVERT: A 1567 MET cc_start: 0.8896 (mmm) cc_final: 0.8597 (tpt) REVERT: A 1618 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: A 1696 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7929 (tp30) REVERT: A 1787 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (tp) REVERT: A 1982 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 2075 MET cc_start: 0.8936 (mtp) cc_final: 0.8619 (mtp) REVERT: A 2191 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8345 (pp20) REVERT: A 2205 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8201 (mm) REVERT: A 2257 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: A 2265 GLN cc_start: 0.7930 (mp10) cc_final: 0.7255 (mp10) REVERT: A 2284 ASP cc_start: 0.8179 (m-30) cc_final: 0.7848 (m-30) REVERT: A 2347 TRP cc_start: 0.8430 (m-90) cc_final: 0.8003 (m-90) REVERT: A 2362 ASN cc_start: 0.8674 (p0) cc_final: 0.8166 (p0) REVERT: A 2507 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7831 (t80) REVERT: A 2840 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8375 (mtm-85) REVERT: A 2894 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.6483 (t80) REVERT: A 2964 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8652 (mtpp) REVERT: A 2983 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: A 3019 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (pmtt) REVERT: A 3263 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7337 (tpm170) REVERT: A 3384 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7450 (mptm) outliers start: 78 outliers final: 31 residues processed: 209 average time/residue: 0.7242 time to fit residues: 169.6007 Evaluate side-chains 187 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1422 MET Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1618 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1952 ILE Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3101 SER Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3428 ILE Chi-restraints excluded: chain A residue 3436 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 182 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2983 GLN ** A3485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070279 restraints weight = 41401.287| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.89 r_work: 0.3015 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19743 Z= 0.131 Angle : 0.493 10.453 26765 Z= 0.256 Chirality : 0.038 0.161 3049 Planarity : 0.003 0.048 3419 Dihedral : 9.628 133.232 2852 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.47 % Allowed : 26.92 % Favored : 69.61 % 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: 1.41 (0.17), residues: 2435 helix: 2.01 (0.14), residues: 1431 sheet: -0.08 (0.50), residues: 96 loop : -0.70 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3297 TYR 0.012 0.001 TYR A1013 PHE 0.020 0.001 PHE A3372 TRP 0.007 0.001 TRP A3422 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00294 (19743) covalent geometry : angle 0.49325 (26765) hydrogen bonds : bond 0.05401 ( 1003) hydrogen bonds : angle 3.84823 ( 2865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 140 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8050 (p90) REVERT: A 1021 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 1057 GLN cc_start: 0.8065 (pp30) cc_final: 0.7619 (pp30) REVERT: A 1252 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 1279 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: A 1289 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: A 1382 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8326 (ptm160) REVERT: A 1567 MET cc_start: 0.8906 (mmm) cc_final: 0.8601 (tpt) REVERT: A 1618 GLU cc_start: 0.8655 (tp30) cc_final: 0.8415 (tp30) REVERT: A 1667 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: A 1696 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7934 (tp30) REVERT: A 1787 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 1982 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 2075 MET cc_start: 0.8901 (mtp) cc_final: 0.8563 (mtp) REVERT: A 2191 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: A 2205 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 2257 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8736 (mp0) REVERT: A 2265 GLN cc_start: 0.7964 (mp10) cc_final: 0.7535 (mp10) REVERT: A 2284 ASP cc_start: 0.8212 (m-30) cc_final: 0.7858 (m-30) REVERT: A 2347 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8071 (m-90) REVERT: A 2362 ASN cc_start: 0.8672 (p0) cc_final: 0.8138 (p0) REVERT: A 2507 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 2840 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8388 (mtm-85) REVERT: A 2868 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8652 (mt) REVERT: A 2894 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 2964 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: A 3019 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8499 (pmtt) REVERT: A 3263 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7338 (tpm170) REVERT: A 3384 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7460 (mptm) outliers start: 71 outliers final: 35 residues processed: 199 average time/residue: 0.7002 time to fit residues: 156.8570 Evaluate side-chains 192 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1952 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2347 TRP Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3101 SER Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3383 VAL Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3428 ILE Chi-restraints excluded: chain A residue 3436 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 178 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 229 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2983 GLN ** A3485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070111 restraints weight = 40863.679| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.86 r_work: 0.3005 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19743 Z= 0.137 Angle : 0.502 9.588 26765 Z= 0.261 Chirality : 0.039 0.216 3049 Planarity : 0.003 0.048 3419 Dihedral : 9.633 133.126 2852 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.37 % Allowed : 27.16 % Favored : 69.47 % 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: 1.41 (0.17), residues: 2435 helix: 2.01 (0.14), residues: 1433 sheet: -0.12 (0.50), residues: 96 loop : -0.70 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3297 TYR 0.012 0.001 TYR A1013 PHE 0.013 0.001 PHE A1392 TRP 0.007 0.001 TRP A3422 HIS 0.004 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00313 (19743) covalent geometry : angle 0.50157 (26765) hydrogen bonds : bond 0.05466 ( 1003) hydrogen bonds : angle 3.84618 ( 2865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 139 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8053 (p90) REVERT: A 1057 GLN cc_start: 0.8068 (pp30) cc_final: 0.7612 (pp30) REVERT: A 1252 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 1279 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: A 1289 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: A 1382 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8344 (ptm160) REVERT: A 1567 MET cc_start: 0.8905 (mmm) cc_final: 0.8607 (tpt) REVERT: A 1618 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: A 1667 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: A 1696 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7932 (tp30) REVERT: A 1787 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 1982 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 2066 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (p0) REVERT: A 2075 MET cc_start: 0.8899 (mtp) cc_final: 0.8560 (mtp) REVERT: A 2191 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: A 2205 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 2257 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: A 2265 GLN cc_start: 0.8006 (mp10) cc_final: 0.7584 (mp10) REVERT: A 2284 ASP cc_start: 0.8214 (m-30) cc_final: 0.7859 (m-30) REVERT: A 2347 TRP cc_start: 0.8470 (m-90) cc_final: 0.8012 (m-90) REVERT: A 2362 ASN cc_start: 0.8679 (p0) cc_final: 0.8168 (p0) REVERT: A 2507 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7908 (t80) REVERT: A 2771 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8945 (mmm160) REVERT: A 2840 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8382 (mtm-85) REVERT: A 2868 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8638 (mt) REVERT: A 2894 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 2964 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8657 (mtpp) REVERT: A 2983 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7567 (pp30) REVERT: A 3019 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8508 (pmtt) REVERT: A 3263 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7406 (tpm170) REVERT: A 3384 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7513 (mptm) outliers start: 69 outliers final: 39 residues processed: 197 average time/residue: 0.7164 time to fit residues: 158.6950 Evaluate side-chains 198 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1618 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1952 ILE Chi-restraints excluded: chain A residue 2066 ASN Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2771 ARG Chi-restraints excluded: chain A residue 2840 ARG Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3019 LYS Chi-restraints excluded: chain A residue 3075 GLU Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3101 SER Chi-restraints excluded: chain A residue 3130 GLU Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3383 VAL Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3428 ILE Chi-restraints excluded: chain A residue 3436 SER Chi-restraints excluded: chain A residue 3480 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 83 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2594 GLN A2983 GLN ** A3485 GLN ** 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 = 0.3570 r_free = 0.3570 target = 0.094803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071047 restraints weight = 41168.812| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.88 r_work: 0.3011 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19743 Z= 0.114 Angle : 0.492 9.499 26765 Z= 0.254 Chirality : 0.038 0.184 3049 Planarity : 0.003 0.048 3419 Dihedral : 9.601 133.141 2852 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.27 % Allowed : 27.31 % Favored : 69.42 % 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: 1.51 (0.17), residues: 2435 helix: 2.09 (0.14), residues: 1436 sheet: -0.21 (0.50), residues: 96 loop : -0.66 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3297 TYR 0.012 0.001 TYR A1013 PHE 0.011 0.001 PHE A1392 TRP 0.007 0.001 TRP A3422 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00246 (19743) covalent geometry : angle 0.49159 (26765) hydrogen bonds : bond 0.04997 ( 1003) hydrogen bonds : angle 3.76070 ( 2865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8063 (p90) REVERT: A 1021 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7889 (t0) REVERT: A 1057 GLN cc_start: 0.8064 (pp30) cc_final: 0.7621 (pp30) REVERT: A 1252 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7284 (p0) REVERT: A 1279 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: A 1289 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: A 1382 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8356 (ptm160) REVERT: A 1533 MET cc_start: 0.8095 (tpp) cc_final: 0.7502 (tpt) REVERT: A 1567 MET cc_start: 0.8902 (mmm) cc_final: 0.8601 (tpt) REVERT: A 1618 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: A 1667 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8569 (mttm) REVERT: A 1696 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7920 (tp30) REVERT: A 1787 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7575 (tp) REVERT: A 1827 MET cc_start: 0.8483 (tpp) cc_final: 0.8176 (mmm) REVERT: A 1982 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 2075 MET cc_start: 0.8886 (mtp) cc_final: 0.8549 (mtp) REVERT: A 2191 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: A 2205 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 2257 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: A 2265 GLN cc_start: 0.8081 (mp10) cc_final: 0.7670 (mp10) REVERT: A 2284 ASP cc_start: 0.8192 (m-30) cc_final: 0.7848 (m-30) REVERT: A 2347 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.7941 (m-90) REVERT: A 2362 ASN cc_start: 0.8646 (p0) cc_final: 0.8118 (p0) REVERT: A 2507 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7719 (t80) REVERT: A 2771 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8947 (mmm160) REVERT: A 2868 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 2894 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 2964 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8662 (mtpp) REVERT: A 3263 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7457 (tpm170) REVERT: A 3384 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7324 (mptm) outliers start: 67 outliers final: 35 residues processed: 195 average time/residue: 0.6986 time to fit residues: 152.8043 Evaluate side-chains 190 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1618 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1644 MET Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1952 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2191 GLU Chi-restraints excluded: chain A residue 2205 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain A residue 2316 LEU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2347 TRP Chi-restraints excluded: chain A residue 2369 ILE Chi-restraints excluded: chain A residue 2415 THR Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2595 ASP Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2728 SER Chi-restraints excluded: chain A residue 2771 ARG Chi-restraints excluded: chain A residue 2868 LEU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3075 GLU Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3308 GLU Chi-restraints excluded: chain A residue 3383 VAL Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 210 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 243 optimal weight: 0.0770 chunk 23 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2594 GLN A2983 GLN A2984 ASN A3104 ASN ** A3485 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.095778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072135 restraints weight = 40879.177| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.87 r_work: 0.3033 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19743 Z= 0.107 Angle : 0.492 9.321 26765 Z= 0.253 Chirality : 0.038 0.159 3049 Planarity : 0.003 0.048 3419 Dihedral : 9.511 133.154 2848 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 27.94 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.17), residues: 2435 helix: 2.19 (0.14), residues: 1431 sheet: -0.34 (0.50), residues: 97 loop : -0.65 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3297 TYR 0.011 0.001 TYR A1013 PHE 0.024 0.001 PHE A3372 TRP 0.008 0.001 TRP A3422 HIS 0.003 0.000 HIS A3091 Details of bonding type rmsd covalent geometry : bond 0.00226 (19743) covalent geometry : angle 0.49210 (26765) hydrogen bonds : bond 0.04553 ( 1003) hydrogen bonds : angle 3.67569 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5551.12 seconds wall clock time: 95 minutes 37.41 seconds (5737.41 seconds total)