Starting phenix.real_space_refine on Thu Feb 5 20:06:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnr_71769/02_2026/9pnr_71769.cif" } resolution = 2.8 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 11931 2.51 5 N 3297 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s 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: 19000 Number of models: 1 Model: "" Number of chains: 1 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: 3.65, per 1000 atoms: 0.19 Number of scatterers: 19000 At special positions: 0 Unit cell: (104.662, 133.87, 164.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3681 8.00 N 3297 7.00 C 11931 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: 1.44 Conformation dependent library (CDL) restraints added in 756.0 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: 122 helices and 20 sheets defined 65.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 3.731A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A1069 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1110 removed outlier: 3.692A pdb=" N ILE A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1099 " --> pdb=" O GLY A1095 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1120 Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 3.627A pdb=" N ARG A1125 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1134 removed outlier: 3.728A pdb=" N ILE A1134 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1162 removed outlier: 4.154A pdb=" N ALA A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A1154 " --> pdb=" O GLN A1150 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1155 " --> pdb=" O THR A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1178 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1199 through 1216 removed outlier: 3.592A pdb=" N LEU A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1229 Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.590A pdb=" N THR A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1286 through 1293 removed outlier: 3.637A pdb=" N GLU A1290 " --> pdb=" O THR A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1334 removed outlier: 3.525A pdb=" N ALA A1327 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A1334 " --> pdb=" O LYS A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1351 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.985A pdb=" N LEU A1369 " --> pdb=" O LYS A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1400 removed outlier: 3.553A pdb=" N LYS A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1377 " --> pdb=" O HIS A1373 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY A1379 " --> pdb=" O LYS A1375 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A1380 " --> pdb=" O SER A1376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1383 " --> pdb=" O GLY A1379 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.091A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1468 removed outlier: 3.856A pdb=" N SER A1458 " --> pdb=" O ASN A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 3.555A pdb=" N MET A1475 " --> pdb=" O VAL A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 3.516A pdb=" N SER A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1486 " --> pdb=" O ASP A1482 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1487 " --> pdb=" O GLU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1506 removed outlier: 3.698A pdb=" N THR A1504 " --> pdb=" O VAL A1500 " (cutoff:3.500A) 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 1525 through 1541 removed outlier: 3.623A pdb=" N LEU A1529 " --> pdb=" O SER A1525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1530 " --> pdb=" O PHE A1526 " (cutoff:3.500A) removed outlier: 3.662A 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: 3.912A 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 1626 removed outlier: 3.528A pdb=" N THR A1613 " --> pdb=" O TYR A1609 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1618 " --> pdb=" O ASN A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.621A 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: 3.718A pdb=" N ASP A1700 " --> pdb=" O GLU A1696 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A1702 " --> pdb=" O MET A1698 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1703 " --> pdb=" O SER A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1719 Processing helix chain 'A' and resid 1720 through 1722 No H-bonds generated for 'chain 'A' and resid 1720 through 1722' Processing helix chain 'A' and resid 1724 through 1744 removed outlier: 3.769A pdb=" N ALA A1728 " --> pdb=" O SER A1724 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.911A 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: 3.618A pdb=" N ASN A1796 " --> pdb=" O GLU A1792 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1801 " --> pdb=" O GLY A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1841 removed outlier: 3.897A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A1841 " --> pdb=" O ALA A1837 " (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 1926 removed outlier: 3.636A pdb=" N MET A1920 " --> pdb=" O GLY A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1936 removed outlier: 3.584A pdb=" N LEU A1933 " --> pdb=" O MET A1929 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A1934 " --> pdb=" O MET A1930 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A1935 " --> pdb=" O GLN A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1972 removed outlier: 4.539A pdb=" N ARG A1962 " --> pdb=" O THR A1958 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1965 " --> pdb=" O SER A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1990 removed outlier: 3.651A pdb=" N SER A1983 " --> pdb=" O ASN A1979 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.538A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) removed outlier: 3.934A 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: 3.841A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 4.057A pdb=" N GLU A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A2031 " --> pdb=" O SER A2027 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A2035 " --> pdb=" O ARG A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2101 removed outlier: 3.504A pdb=" N ASP A2082 " --> pdb=" O GLU A2078 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A2099 " --> pdb=" O ARG A2095 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A2100 " --> pdb=" O LYS A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2148 removed outlier: 3.660A pdb=" N ILE A2147 " --> pdb=" O ASN A2143 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2168 removed outlier: 3.714A pdb=" N ALA A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A2158 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A2159 " --> pdb=" O ALA A2155 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A2163 " --> pdb=" O ALA A2159 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2188 removed outlier: 3.638A pdb=" N ALA A2184 " --> pdb=" O VAL A2180 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A2185 " --> pdb=" O ALA A2181 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A2186 " --> pdb=" O GLU A2182 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2203 Processing helix chain 'A' and resid 2222 through 2244 removed outlier: 3.542A pdb=" N LEU A2230 " --> pdb=" O LEU A2226 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A2231 " --> pdb=" O ILE A2227 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A2235 " --> pdb=" O VAL A2231 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A2238 " --> pdb=" O SER A2234 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A2239 " --> pdb=" O THR A2235 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2267 removed outlier: 3.554A pdb=" N GLU A2264 " --> pdb=" O GLU A2260 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A2265 " --> pdb=" O GLY A2261 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A2267 " --> pdb=" O MET A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2275 through 2294 removed outlier: 3.643A pdb=" N GLU A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A2281 " --> pdb=" O GLU A2277 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A2292 " --> pdb=" O THR A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2318 Processing helix chain 'A' and resid 2318 through 2324 removed outlier: 3.804A pdb=" N LYS A2324 " --> pdb=" O ALA A2320 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2348 Processing helix chain 'A' and resid 2376 through 2382 removed outlier: 3.739A pdb=" N VAL A2380 " --> pdb=" O THR A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2409 removed outlier: 3.729A pdb=" N SER A2399 " --> pdb=" O ASN A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2413 Processing helix chain 'A' and resid 2426 through 2443 removed outlier: 3.568A pdb=" N ALA A2430 " --> pdb=" O ASN A2426 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A2442 " --> pdb=" O VAL A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2468 removed outlier: 3.543A pdb=" N SER A2454 " --> pdb=" O ALA A2450 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A2455 " --> pdb=" O GLN A2451 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A2466 " --> pdb=" O ALA A2462 " (cutoff:3.500A) Processing helix chain 'A' and resid 2474 through 2485 removed outlier: 3.912A pdb=" N GLU A2479 " --> pdb=" O ALA A2475 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A2480 " --> pdb=" O ARG A2476 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2494 Processing helix chain 'A' and resid 2501 through 2517 removed outlier: 4.040A pdb=" N ARG A2505 " --> pdb=" O ASN A2501 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A2514 " --> pdb=" O GLN A2510 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2542 removed outlier: 3.952A pdb=" N THR A2534 " --> pdb=" O SER A2530 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A2541 " --> pdb=" O GLY A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2551 removed outlier: 3.866A pdb=" N ARG A2546 " --> pdb=" O ASN A2542 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A2547 " --> pdb=" O GLU A2543 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2559 Processing helix chain 'A' and resid 2564 through 2585 removed outlier: 3.649A pdb=" N THR A2574 " --> pdb=" O THR A2570 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A2575 " --> pdb=" O ASN A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2587 through 2592 Processing helix chain 'A' and resid 2593 through 2615 removed outlier: 3.564A pdb=" N GLU A2602 " --> pdb=" O ASP A2598 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A2603 " --> pdb=" O ALA A2599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A2611 " --> pdb=" O ALA A2607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A2613 " --> pdb=" O LEU A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2624 through 2641 removed outlier: 3.613A pdb=" N ARG A2639 " --> pdb=" O ASP A2635 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A2640 " --> pdb=" O SER A2636 " (cutoff:3.500A) Processing helix chain 'A' and resid 2665 through 2674 removed outlier: 3.695A pdb=" N LEU A2669 " --> pdb=" O HIS A2665 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A2671 " --> pdb=" O ALA A2667 " (cutoff:3.500A) Processing helix chain 'A' and resid 2681 through 2684 Processing helix chain 'A' and resid 2685 through 2693 removed outlier: 4.039A pdb=" N ALA A2689 " --> pdb=" O GLY A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2708 removed outlier: 3.955A pdb=" N PHE A2699 " --> pdb=" O VAL A2695 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A2701 " --> pdb=" O GLN A2697 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A2702 " --> pdb=" O PRO A2698 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A2705 " --> pdb=" O ASP A2701 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2736 removed outlier: 3.508A pdb=" N LEU A2719 " --> pdb=" O ASN A2715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A2722 " --> pdb=" O ASP A2718 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A2725 " --> pdb=" O LYS A2721 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A2727 " --> pdb=" O VAL A2723 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A2728 " --> pdb=" O LYS A2724 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A2729 " --> pdb=" O SER A2725 " (cutoff:3.500A) removed outlier: 3.586A 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 removed outlier: 3.731A pdb=" N GLU A2772 " --> pdb=" O VAL A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2775 through 2784 removed outlier: 3.534A pdb=" N ARG A2780 " --> pdb=" O MET A2776 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A2784 " --> pdb=" O ARG A2780 " (cutoff:3.500A) Processing helix chain 'A' and resid 2785 through 2805 removed outlier: 3.734A pdb=" N VAL A2789 " --> pdb=" O SER A2785 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2825 removed outlier: 3.649A pdb=" N ILE A2823 " --> pdb=" O ALA A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2841 removed outlier: 3.631A pdb=" N ARG A2840 " --> pdb=" O HIS A2836 " (cutoff:3.500A) Processing helix chain 'A' and resid 2853 through 2867 removed outlier: 3.727A 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 GLU A2879 " --> pdb=" O ASP A2875 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A2882 " --> pdb=" O SER A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2907 removed outlier: 3.563A pdb=" N MET A2895 " --> pdb=" O SER A2891 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A2901 " --> pdb=" O GLY A2897 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A2902 " --> pdb=" O GLN A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2909 through 2914 removed outlier: 3.686A pdb=" N LEU A2914 " --> pdb=" O ASN A2910 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2941 removed outlier: 3.810A pdb=" N LYS A2941 " --> pdb=" O LYS A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3021 removed outlier: 3.578A pdb=" N ARG A3016 " --> pdb=" O PRO A3012 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A3019 " --> pdb=" O GLU A3015 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A3020 " --> pdb=" O ARG A3016 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3057 removed outlier: 3.792A pdb=" N HIS A3055 " --> pdb=" O MET A3052 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3101 removed outlier: 3.585A pdb=" N GLY A3067 " --> pdb=" O ALA A3063 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A3075 " --> pdb=" O GLY A3071 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A3083 " --> pdb=" O ALA A3079 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A3084 " --> pdb=" O GLN A3080 " (cutoff:3.500A) Processing helix chain 'A' and resid 3102 through 3106 removed outlier: 3.893A pdb=" N LYS A3105 " --> pdb=" O SER A3102 " (cutoff:3.500A) Processing helix chain 'A' and resid 3117 through 3126 Processing helix chain 'A' and resid 3128 through 3139 removed outlier: 3.569A pdb=" N LYS A3134 " --> pdb=" O GLU A3130 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A3138 " --> pdb=" O LYS A3134 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3155 removed outlier: 3.659A pdb=" N ASP A3153 " --> pdb=" O ASP A3149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A3154 " --> pdb=" O MET A3150 " (cutoff:3.500A) Processing helix chain 'A' and resid 3173 through 3188 removed outlier: 3.903A pdb=" N LYS A3182 " --> pdb=" O ASP A3178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A3183 " --> pdb=" O THR A3179 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A3185 " --> pdb=" O LYS A3181 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A3186 " --> pdb=" O LYS A3182 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3197 removed outlier: 3.561A pdb=" N VAL A3195 " --> pdb=" O LYS A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3203 through 3207 removed outlier: 3.919A pdb=" N VAL A3207 " --> pdb=" O GLN A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3209 through 3236 removed outlier: 3.643A pdb=" N VAL A3213 " --> pdb=" O ASP A3209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A3214 " --> pdb=" O ALA A3210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A3215 " --> pdb=" O LYS A3211 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A3220 " --> pdb=" O VAL A3216 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A3221 " --> pdb=" O LYS A3217 " (cutoff:3.500A) Proline residue: A3222 - end of helix removed outlier: 3.629A pdb=" N ILE A3230 " --> pdb=" O PHE A3226 " (cutoff:3.500A) Processing helix chain 'A' and resid 3239 through 3273 removed outlier: 3.830A pdb=" N ILE A3243 " --> pdb=" O PRO A3239 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A3245 " --> pdb=" O LYS A3241 " (cutoff:3.500A) Proline residue: A3248 - end of helix removed outlier: 3.625A pdb=" N TYR A3257 " --> pdb=" O GLU A3253 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A3258 " --> pdb=" O ILE A3254 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A3259 " --> pdb=" O ASN A3255 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A3263 " --> pdb=" O LYS A3259 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A3264 " --> pdb=" O SER A3260 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A3266 " --> pdb=" O LEU A3262 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A3268 " --> pdb=" O GLN A3264 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA A3269 " --> pdb=" O ILE A3265 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A3270 " --> pdb=" O ASP A3266 " (cutoff:3.500A) Processing helix chain 'A' and resid 3277 through 3297 removed outlier: 3.931A pdb=" N VAL A3281 " --> pdb=" O ASN A3277 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A3297 " --> pdb=" O ASP A3293 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3307 removed outlier: 3.533A pdb=" N ILE A3304 " --> pdb=" O ILE A3300 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A3307 " --> pdb=" O LEU A3303 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3311 removed outlier: 3.908A pdb=" N SER A3311 " --> pdb=" O GLU A3308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3308 through 3311' Processing helix chain 'A' and resid 3321 through 3327 removed outlier: 3.603A pdb=" N ALA A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) Processing helix chain 'A' and resid 3328 through 3338 removed outlier: 3.601A pdb=" N LEU A3336 " --> pdb=" O TYR A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3341 through 3346 Processing helix chain 'A' and resid 3347 through 3351 Processing helix chain 'A' and resid 3357 through 3385 removed outlier: 3.633A pdb=" N GLN A3361 " --> pdb=" O THR A3357 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A3364 " --> pdb=" O PHE A3360 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A3373 " --> pdb=" O TYR A3369 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A3376 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A3385 " --> pdb=" O ASP A3381 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3398 removed outlier: 3.879A pdb=" N LEU A3394 " --> pdb=" O SER A3390 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A3398 " --> pdb=" O LEU A3394 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3407 removed outlier: 3.680A pdb=" N ARG A3406 " --> pdb=" O ASN A3403 " (cutoff:3.500A) Processing helix chain 'A' and resid 3417 through 3441 removed outlier: 3.788A pdb=" N TRP A3422 " --> pdb=" O MET A3418 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A3429 " --> pdb=" O ASN A3425 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A3439 " --> pdb=" O MET A3435 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3449 removed outlier: 3.539A pdb=" N SER A3445 " --> pdb=" O ASN A3441 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A3449 " --> pdb=" O SER A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3467 through 3475 removed outlier: 3.804A pdb=" N MET A3471 " --> pdb=" O ASN A3467 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A3472 " --> pdb=" O MET A3468 " (cutoff:3.500A) removed outlier: 3.958A 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 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: 4.242A 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: 6.886A 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 removed outlier: 3.565A pdb=" N LEU A1944 " --> pdb=" O ASN A1951 " (cutoff:3.500A) 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 1882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1891 through 1894 Processing sheet with id=AB6, first strand: chain 'A' and resid 2126 through 2127 removed outlier: 6.459A pdb=" N LYS A2171 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A2218 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 6.391A 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: 7.426A pdb=" N LYS A2964 " --> pdb=" O THR A2952 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR A2952 " --> pdb=" O LYS A2964 " (cutoff:3.500A) removed outlier: 6.457A 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: 3.574A 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: 4.176A pdb=" N GLY A3006 " --> pdb=" O GLN A3046 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A3034 " --> pdb=" O VAL A3042 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR A3044 " --> pdb=" O MET A3032 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A3032 " --> pdb=" O TYR A3044 " (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 979 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 1.96 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: 6412 1.34 - 1.46: 3995 1.46 - 1.58: 8713 1.58 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 19302 Sorted by residual: bond pdb=" CB ASN A3255 " pdb=" CG ASN A3255 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" CB GLU A1725 " pdb=" CG GLU A1725 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB LYS A2589 " pdb=" CG LYS A2589 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB MET A2223 " pdb=" CG MET A2223 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CA ASN A3255 " pdb=" CB ASN A3255 " ideal model delta sigma weight residual 1.529 1.543 -0.014 1.55e-02 4.16e+03 7.75e-01 ... (remaining 19297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25922 2.16 - 4.33: 142 4.33 - 6.49: 21 6.49 - 8.66: 1 8.66 - 10.82: 1 Bond angle restraints: 26087 Sorted by residual: angle pdb=" CB MET A2223 " pdb=" CG MET A2223 " pdb=" SD MET A2223 " ideal model delta sigma weight residual 112.70 123.52 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET A1930 " pdb=" CG MET A1930 " pdb=" SD MET A1930 " ideal model delta sigma weight residual 112.70 104.11 8.59 3.00e+00 1.11e-01 8.20e+00 angle pdb=" CA GLU A1725 " pdb=" CB GLU A1725 " pdb=" CG GLU A1725 " ideal model delta sigma weight residual 114.10 119.25 -5.15 2.00e+00 2.50e-01 6.64e+00 angle pdb=" CB LYS A2589 " pdb=" CG LYS A2589 " pdb=" CD LYS A2589 " ideal model delta sigma weight residual 111.30 117.07 -5.77 2.30e+00 1.89e-01 6.30e+00 angle pdb=" N VAL A3450 " pdb=" CA VAL A3450 " pdb=" C VAL A3450 " ideal model delta sigma weight residual 111.62 109.67 1.95 7.90e-01 1.60e+00 6.08e+00 ... (remaining 26082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 10128 17.44 - 34.88: 1272 34.88 - 52.33: 351 52.33 - 69.77: 84 69.77 - 87.21: 18 Dihedral angle restraints: 11853 sinusoidal: 4758 harmonic: 7095 Sorted by residual: dihedral pdb=" CA PHE A2614 " pdb=" C PHE A2614 " pdb=" N TYR A2615 " pdb=" CA TYR A2615 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A3122 " pdb=" CB ASP A3122 " pdb=" CG ASP A3122 " pdb=" OD1 ASP A3122 " ideal model delta sinusoidal sigma weight residual -30.00 -87.01 57.01 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP A2616 " pdb=" CB ASP A2616 " pdb=" CG ASP A2616 " pdb=" OD1 ASP A2616 " ideal model delta sinusoidal sigma weight residual -30.00 -86.28 56.28 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 11850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1867 0.026 - 0.052: 698 0.052 - 0.078: 277 0.078 - 0.104: 88 0.104 - 0.130: 43 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CA THR A1247 " pdb=" N THR A1247 " pdb=" C THR A1247 " pdb=" CB THR A1247 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A2933 " pdb=" N ILE A2933 " pdb=" C ILE A2933 " pdb=" CB ILE A2933 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-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 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 2970 not shown) Planarity restraints: 3400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1429 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A1430 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1430 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1430 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2616 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ASP A2616 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP A2616 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A2617 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A2694 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C LYS A2694 " -0.022 2.00e-02 2.50e+03 pdb=" O LYS A2694 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A2695 " 0.008 2.00e-02 2.50e+03 ... (remaining 3397 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3294 2.76 - 3.30: 17817 3.30 - 3.83: 28934 3.83 - 4.37: 34797 4.37 - 4.90: 60682 Nonbonded interactions: 145524 Sorted by model distance: nonbonded pdb=" O PRO A3030 " pdb=" OG SER A3047 " model vdw 2.228 3.040 nonbonded pdb=" O GLY A2761 " pdb=" OG1 THR A2765 " model vdw 2.255 3.040 nonbonded pdb=" O SER A3310 " pdb=" OG SER A3310 " model vdw 2.266 3.040 nonbonded pdb=" N GLU A3331 " pdb=" OE1 GLU A3331 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP A2071 " pdb=" OG SER A2073 " model vdw 2.285 3.040 ... (remaining 145519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.320 Find NCS groups from input model: 0.210 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:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 19302 Z= 0.075 Angle : 0.413 10.820 26087 Z= 0.214 Chirality : 0.035 0.130 2973 Planarity : 0.003 0.035 3400 Dihedral : 16.988 87.209 7269 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.37 % Allowed : 24.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2435 helix: -0.14 (0.13), residues: 1360 sheet: -0.02 (0.54), residues: 91 loop : -0.58 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3319 TYR 0.012 0.001 TYR A1013 PHE 0.018 0.001 PHE A2297 TRP 0.005 0.001 TRP A3166 HIS 0.002 0.000 HIS A1373 Details of bonding type rmsd covalent geometry : bond 0.00163 (19302) covalent geometry : angle 0.41308 (26087) hydrogen bonds : bond 0.32808 ( 979) hydrogen bonds : angle 7.06167 ( 2775) *********************** 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 183 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.718 Fit side-chains REVERT: A 1067 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8804 (mm) REVERT: A 1499 MET cc_start: 0.8349 (tpp) cc_final: 0.7963 (mmm) REVERT: A 1542 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 1928 MET cc_start: 0.9219 (mmm) cc_final: 0.8806 (tpp) REVERT: A 1963 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7362 (mmpt) REVERT: A 2141 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8430 (pp) REVERT: A 2144 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5273 (tp) REVERT: A 2162 GLN cc_start: 0.7068 (tm-30) cc_final: 0.6560 (tm-30) REVERT: A 2163 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7989 (mmtt) REVERT: A 2247 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: A 2362 ASN cc_start: 0.7665 (m-40) cc_final: 0.6796 (t0) REVERT: A 2372 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8429 (mmt90) REVERT: A 2424 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7964 (ttp80) REVERT: A 2584 MET cc_start: 0.8208 (mtm) cc_final: 0.7777 (mtp) REVERT: A 2844 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 3019 LYS cc_start: 0.8889 (pptt) cc_final: 0.8374 (ptpp) REVERT: A 3075 GLU cc_start: 0.8504 (tt0) cc_final: 0.8276 (tt0) REVERT: A 3182 LYS cc_start: 0.8662 (pttt) cc_final: 0.8417 (ptmt) REVERT: A 3297 ARG cc_start: 0.8703 (mtm180) cc_final: 0.8484 (mtm110) REVERT: A 3465 GLN cc_start: 0.8411 (mp10) cc_final: 0.7767 (mm-40) REVERT: A 3485 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6590 (tm-30) outliers start: 28 outliers final: 18 residues processed: 179 average time/residue: 0.6612 time to fit residues: 131.0089 Evaluate side-chains 175 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1963 LYS Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2124 VAL Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2294 SER Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2987 ASN Chi-restraints excluded: chain A residue 3127 MET Chi-restraints excluded: chain A residue 3175 SER Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3485 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.0030 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1895 ASN A2143 ASN A2318 ASN A2442 GLN A2444 HIS A2983 GLN A3225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079916 restraints weight = 36896.682| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.85 r_work: 0.3035 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19302 Z= 0.138 Angle : 0.515 5.452 26087 Z= 0.283 Chirality : 0.038 0.144 2973 Planarity : 0.004 0.037 3400 Dihedral : 4.734 59.703 2671 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.18 % Allowed : 21.15 % Favored : 75.67 % 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: 0.48 (0.17), residues: 2435 helix: 0.99 (0.14), residues: 1389 sheet: 0.06 (0.55), residues: 93 loop : -0.56 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1101 TYR 0.017 0.001 TYR A1144 PHE 0.016 0.001 PHE A2614 TRP 0.010 0.001 TRP A2696 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00254 (19302) covalent geometry : angle 0.51543 (26087) hydrogen bonds : bond 0.07489 ( 979) hydrogen bonds : angle 4.55087 ( 2775) *********************** 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 231 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 0.681 Fit side-chains REVERT: A 1041 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: A 1067 LEU cc_start: 0.9187 (tm) cc_final: 0.8816 (mt) REVERT: A 1499 MET cc_start: 0.8093 (tpp) cc_final: 0.7832 (mmm) REVERT: A 1928 MET cc_start: 0.8894 (mmm) cc_final: 0.8664 (tpp) REVERT: A 2141 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8417 (pp) REVERT: A 2162 GLN cc_start: 0.6807 (tm-30) cc_final: 0.6295 (tm-30) REVERT: A 2163 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7855 (mmtt) REVERT: A 2210 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8428 (t0) REVERT: A 2223 MET cc_start: 0.7122 (tpp) cc_final: 0.6821 (tpt) REVERT: A 2362 ASN cc_start: 0.7648 (m-40) cc_final: 0.6747 (t0) REVERT: A 2372 ARG cc_start: 0.8735 (mmt90) cc_final: 0.8392 (mmt90) REVERT: A 2424 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7844 (ttp80) REVERT: A 2844 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 2894 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7364 (t80) REVERT: A 3164 ASP cc_start: 0.8107 (t0) cc_final: 0.7881 (t0) REVERT: A 3182 LYS cc_start: 0.8539 (pttt) cc_final: 0.8239 (pptt) REVERT: A 3255 ASN cc_start: 0.7651 (t0) cc_final: 0.7432 (t0) REVERT: A 3256 GLN cc_start: 0.7810 (pt0) cc_final: 0.7154 (pm20) REVERT: A 3297 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8272 (ptp-110) REVERT: A 3298 MET cc_start: 0.7726 (mtm) cc_final: 0.7507 (mtm) REVERT: A 3465 GLN cc_start: 0.8422 (mp10) cc_final: 0.7823 (mm-40) outliers start: 65 outliers final: 20 residues processed: 218 average time/residue: 0.6454 time to fit residues: 157.4151 Evaluate side-chains 177 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2695 VAL 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 3240 VAL Chi-restraints excluded: chain A residue 3260 SER Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 195 optimal weight: 0.0980 chunk 218 optimal weight: 5.9990 chunk 209 optimal weight: 0.0870 chunk 59 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 224 optimal weight: 0.0170 chunk 175 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2292 HIS A2733 GLN A2983 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082190 restraints weight = 36941.119| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.82 r_work: 0.3088 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19302 Z= 0.106 Angle : 0.436 6.237 26087 Z= 0.234 Chirality : 0.037 0.131 2973 Planarity : 0.003 0.037 3400 Dihedral : 3.798 59.417 2639 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.22 % Allowed : 21.35 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2435 helix: 1.56 (0.14), residues: 1405 sheet: 0.06 (0.55), residues: 93 loop : -0.64 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2126 TYR 0.021 0.001 TYR A1144 PHE 0.018 0.001 PHE A3372 TRP 0.007 0.001 TRP A1215 HIS 0.002 0.001 HIS A1727 Details of bonding type rmsd covalent geometry : bond 0.00199 (19302) covalent geometry : angle 0.43565 (26087) hydrogen bonds : bond 0.05525 ( 979) hydrogen bonds : angle 3.94663 ( 2775) *********************** 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 239 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.712 Fit side-chains REVERT: A 1041 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: A 1067 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8820 (mt) REVERT: A 1499 MET cc_start: 0.8180 (tpp) cc_final: 0.7813 (mmm) REVERT: A 1542 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 1928 MET cc_start: 0.8724 (mmm) cc_final: 0.8357 (tpp) REVERT: A 2075 MET cc_start: 0.8704 (mtt) cc_final: 0.8408 (mtm) REVERT: A 2141 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 2162 GLN cc_start: 0.6858 (tm-30) cc_final: 0.6410 (tm-30) REVERT: A 2163 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7968 (mmtm) REVERT: A 2210 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 2223 MET cc_start: 0.6997 (tpp) cc_final: 0.6705 (tpt) REVERT: A 2277 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: A 2362 ASN cc_start: 0.7594 (m-40) cc_final: 0.6720 (t0) REVERT: A 2372 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8167 (mmt90) REVERT: A 2844 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 2894 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 3164 ASP cc_start: 0.8058 (t0) cc_final: 0.7727 (t0) REVERT: A 3182 LYS cc_start: 0.8541 (pttt) cc_final: 0.8200 (ptmt) REVERT: A 3256 GLN cc_start: 0.7789 (pt0) cc_final: 0.7165 (pm20) REVERT: A 3297 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8218 (ptp-110) REVERT: A 3298 MET cc_start: 0.7676 (mtm) cc_final: 0.7453 (mtm) REVERT: A 3465 GLN cc_start: 0.8381 (mp10) cc_final: 0.7830 (mm-40) outliers start: 66 outliers final: 20 residues processed: 223 average time/residue: 0.6297 time to fit residues: 156.4497 Evaluate side-chains 180 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1359 MET Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3344 VAL Chi-restraints excluded: chain A residue 3384 LYS Chi-restraints excluded: chain A residue 3415 MET Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 169 optimal weight: 0.0470 chunk 170 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2983 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081863 restraints weight = 36765.496| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.83 r_work: 0.3079 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19302 Z= 0.105 Angle : 0.436 5.413 26087 Z= 0.233 Chirality : 0.037 0.175 2973 Planarity : 0.003 0.036 3400 Dihedral : 3.712 59.959 2635 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.08 % Allowed : 22.08 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2435 helix: 1.80 (0.14), residues: 1401 sheet: 0.04 (0.56), residues: 86 loop : -0.61 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3319 TYR 0.017 0.001 TYR A1144 PHE 0.019 0.001 PHE A3372 TRP 0.006 0.001 TRP A2347 HIS 0.004 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00215 (19302) covalent geometry : angle 0.43642 (26087) hydrogen bonds : bond 0.05013 ( 979) hydrogen bonds : angle 3.80416 ( 2775) *********************** 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 223 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8806 (mm) REVERT: A 1212 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: A 1499 MET cc_start: 0.8191 (tpp) cc_final: 0.7828 (mmm) REVERT: A 1542 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 1569 MET cc_start: 0.8595 (mtm) cc_final: 0.8394 (mtt) REVERT: A 1667 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: A 1928 MET cc_start: 0.8728 (mmm) cc_final: 0.8367 (tpp) REVERT: A 2075 MET cc_start: 0.8650 (mtt) cc_final: 0.8364 (mtm) REVERT: A 2141 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 2162 GLN cc_start: 0.6830 (tm-30) cc_final: 0.6439 (tm-30) REVERT: A 2210 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 2223 MET cc_start: 0.7051 (tpp) cc_final: 0.6803 (tpt) REVERT: A 2277 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: A 2362 ASN cc_start: 0.7618 (m-40) cc_final: 0.6665 (t0) REVERT: A 2372 ARG cc_start: 0.8745 (mmt90) cc_final: 0.8164 (mmt90) REVERT: A 2844 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 2894 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 3019 LYS cc_start: 0.8800 (pptt) cc_final: 0.8390 (ptpp) REVERT: A 3164 ASP cc_start: 0.8137 (t0) cc_final: 0.7766 (t0) REVERT: A 3182 LYS cc_start: 0.8692 (pttt) cc_final: 0.8342 (ptmt) REVERT: A 3256 GLN cc_start: 0.7779 (pt0) cc_final: 0.7177 (pm20) REVERT: A 3297 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8369 (mtm110) REVERT: A 3298 MET cc_start: 0.7670 (mtm) cc_final: 0.7408 (mtm) REVERT: A 3465 GLN cc_start: 0.8390 (mp10) cc_final: 0.7836 (mm-40) outliers start: 63 outliers final: 33 residues processed: 206 average time/residue: 0.6542 time to fit residues: 150.8889 Evaluate side-chains 192 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1359 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 2030 GLU Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2776 MET Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2964 LYS Chi-restraints excluded: chain A residue 3075 GLU Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3129 ILE Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3234 ILE Chi-restraints excluded: chain A residue 3344 VAL Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 137 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 161 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2983 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077394 restraints weight = 37083.808| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.82 r_work: 0.2999 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19302 Z= 0.194 Angle : 0.514 6.946 26087 Z= 0.275 Chirality : 0.041 0.156 2973 Planarity : 0.004 0.038 3400 Dihedral : 3.959 58.628 2634 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.62 % Allowed : 21.69 % Favored : 74.69 % 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: 0.99 (0.17), residues: 2435 helix: 1.61 (0.14), residues: 1402 sheet: 0.03 (0.55), residues: 92 loop : -0.72 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2424 TYR 0.015 0.001 TYR A1144 PHE 0.024 0.002 PHE A3372 TRP 0.007 0.001 TRP A3422 HIS 0.005 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00459 (19302) covalent geometry : angle 0.51425 (26087) hydrogen bonds : bond 0.06938 ( 979) hydrogen bonds : angle 4.06757 ( 2775) *********************** 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 228 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8795 (mm) REVERT: A 1212 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8184 (tp30) REVERT: A 1499 MET cc_start: 0.8257 (tpp) cc_final: 0.7962 (mmm) REVERT: A 1542 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 1569 MET cc_start: 0.8722 (mtm) cc_final: 0.8499 (mtt) REVERT: A 1667 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8213 (mtmm) REVERT: A 1928 MET cc_start: 0.8897 (mmm) cc_final: 0.8474 (tpp) REVERT: A 2141 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8335 (pp) REVERT: A 2162 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6558 (tm-30) REVERT: A 2210 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8439 (t0) REVERT: A 2223 MET cc_start: 0.7189 (tpp) cc_final: 0.6915 (tpt) REVERT: A 2277 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: A 2362 ASN cc_start: 0.7959 (m-40) cc_final: 0.7153 (t0) REVERT: A 2372 ARG cc_start: 0.8754 (mmt90) cc_final: 0.8205 (mmt90) REVERT: A 2844 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 3164 ASP cc_start: 0.8142 (t0) cc_final: 0.7728 (t0) REVERT: A 3182 LYS cc_start: 0.8602 (pttt) cc_final: 0.8256 (ptmt) REVERT: A 3297 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8213 (ptp-110) REVERT: A 3465 GLN cc_start: 0.8364 (mp10) cc_final: 0.7790 (mm-40) outliers start: 74 outliers final: 39 residues processed: 214 average time/residue: 0.6234 time to fit residues: 151.6437 Evaluate side-chains 196 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2180 VAL Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2829 ASN Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2985 VAL Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3344 VAL Chi-restraints excluded: chain A residue 3468 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2983 GLN 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 = 0.105101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078886 restraints weight = 36735.237| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.80 r_work: 0.3025 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19302 Z= 0.140 Angle : 0.471 6.206 26087 Z= 0.252 Chirality : 0.039 0.149 2973 Planarity : 0.003 0.038 3400 Dihedral : 3.928 59.460 2634 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 22.62 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2435 helix: 1.70 (0.14), residues: 1402 sheet: -0.13 (0.56), residues: 86 loop : -0.74 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3319 TYR 0.015 0.001 TYR A1144 PHE 0.020 0.001 PHE A3372 TRP 0.006 0.001 TRP A3422 HIS 0.004 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00320 (19302) covalent geometry : angle 0.47150 (26087) hydrogen bonds : bond 0.05905 ( 979) hydrogen bonds : angle 3.91340 ( 2775) *********************** 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 220 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8826 (mt) REVERT: A 1212 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: A 1499 MET cc_start: 0.8238 (tpp) cc_final: 0.7921 (mmm) REVERT: A 1542 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 1667 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8222 (mtmm) REVERT: A 1928 MET cc_start: 0.8889 (mmm) cc_final: 0.8497 (tpp) REVERT: A 2141 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 2162 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 2210 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8428 (t0) REVERT: A 2223 MET cc_start: 0.7135 (tpp) cc_final: 0.6890 (tpt) REVERT: A 2277 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: A 2344 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7903 (tttm) REVERT: A 2362 ASN cc_start: 0.7951 (m-40) cc_final: 0.7156 (t0) REVERT: A 2372 ARG cc_start: 0.8765 (mmt90) cc_final: 0.8231 (mmt90) REVERT: A 2424 ARG cc_start: 0.8227 (ttp-110) cc_final: 0.7918 (ttp80) REVERT: A 2589 LYS cc_start: 0.8472 (mppt) cc_final: 0.8179 (ptmm) REVERT: A 2844 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 2894 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 3019 LYS cc_start: 0.8737 (pptt) cc_final: 0.8297 (ptpp) REVERT: A 3164 ASP cc_start: 0.8173 (t0) cc_final: 0.7757 (t0) REVERT: A 3182 LYS cc_start: 0.8733 (pttt) cc_final: 0.8382 (ptmt) REVERT: A 3256 GLN cc_start: 0.7921 (pt0) cc_final: 0.7423 (pp30) REVERT: A 3297 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8226 (ptp-110) REVERT: A 3298 MET cc_start: 0.7763 (mtm) cc_final: 0.7394 (mtt) REVERT: A 3465 GLN cc_start: 0.8421 (mp10) cc_final: 0.7866 (mm-40) outliers start: 62 outliers final: 35 residues processed: 207 average time/residue: 0.6756 time to fit residues: 156.0266 Evaluate side-chains 195 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1432 SER Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2030 GLU Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2344 LYS Chi-restraints excluded: chain A residue 2373 SER Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2985 VAL Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3149 ASP Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3344 VAL Chi-restraints excluded: chain A residue 3430 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2983 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077922 restraints weight = 37102.825| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.82 r_work: 0.2988 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19302 Z= 0.167 Angle : 0.497 6.517 26087 Z= 0.265 Chirality : 0.039 0.152 2973 Planarity : 0.003 0.039 3400 Dihedral : 3.991 59.213 2634 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.52 % Allowed : 22.37 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2435 helix: 1.65 (0.14), residues: 1402 sheet: -0.19 (0.55), residues: 86 loop : -0.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3319 TYR 0.015 0.001 TYR A1144 PHE 0.022 0.001 PHE A3372 TRP 0.007 0.001 TRP A3422 HIS 0.005 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00390 (19302) covalent geometry : angle 0.49711 (26087) hydrogen bonds : bond 0.06335 ( 979) hydrogen bonds : angle 3.96539 ( 2775) *********************** 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 228 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 156 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8812 (mt) REVERT: A 1212 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: A 1499 MET cc_start: 0.8230 (tpp) cc_final: 0.7896 (mmm) REVERT: A 1542 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 1667 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8232 (mtmm) REVERT: A 1725 GLU cc_start: 0.8018 (tp30) cc_final: 0.7797 (tp30) REVERT: A 1729 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: A 1928 MET cc_start: 0.8912 (mmm) cc_final: 0.8496 (tpp) REVERT: A 2141 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8328 (pp) REVERT: A 2162 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 2169 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: A 2210 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8450 (t0) REVERT: A 2223 MET cc_start: 0.7176 (tpp) cc_final: 0.6928 (tpt) REVERT: A 2277 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: A 2362 ASN cc_start: 0.7976 (m-40) cc_final: 0.7170 (t0) REVERT: A 2372 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8235 (mmt90) REVERT: A 2844 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 2894 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7369 (t80) REVERT: A 3164 ASP cc_start: 0.8188 (t0) cc_final: 0.7778 (t0) REVERT: A 3182 LYS cc_start: 0.8741 (pttt) cc_final: 0.8390 (ptmt) REVERT: A 3256 GLN cc_start: 0.7717 (pt0) cc_final: 0.7270 (pp30) REVERT: A 3297 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8225 (ptp-110) REVERT: A 3298 MET cc_start: 0.7767 (mtm) cc_final: 0.7402 (mtt) REVERT: A 3418 MET cc_start: 0.8179 (tpp) cc_final: 0.7905 (tpp) REVERT: A 3465 GLN cc_start: 0.8379 (mp10) cc_final: 0.7823 (mm-40) outliers start: 72 outliers final: 43 residues processed: 217 average time/residue: 0.5899 time to fit residues: 144.1184 Evaluate side-chains 206 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1432 SER Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1717 MET Chi-restraints excluded: chain A residue 1729 GLU Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2099 VAL Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2180 VAL Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2373 SER Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2985 VAL Chi-restraints excluded: chain A residue 3098 ILE Chi-restraints excluded: chain A residue 3129 ILE Chi-restraints excluded: chain A residue 3149 ASP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3260 SER Chi-restraints excluded: chain A residue 3344 VAL Chi-restraints excluded: chain A residue 3430 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 239 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 138 optimal weight: 0.0030 chunk 158 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1721 GLN A2143 ASN A2983 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.106278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080024 restraints weight = 36729.948| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.82 r_work: 0.3053 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19302 Z= 0.110 Angle : 0.458 7.058 26087 Z= 0.243 Chirality : 0.037 0.143 2973 Planarity : 0.003 0.038 3400 Dihedral : 3.863 59.939 2634 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 23.64 % Favored : 73.86 % 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: 1.88 (0.14), residues: 1399 sheet: -0.18 (0.55), residues: 86 loop : -0.71 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3319 TYR 0.017 0.001 TYR A1144 PHE 0.017 0.001 PHE A3372 TRP 0.006 0.001 TRP A2347 HIS 0.004 0.001 HIS A1727 Details of bonding type rmsd covalent geometry : bond 0.00238 (19302) covalent geometry : angle 0.45825 (26087) hydrogen bonds : bond 0.05001 ( 979) hydrogen bonds : angle 3.74605 ( 2775) *********************** 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 213 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 1212 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: A 1499 MET cc_start: 0.8220 (tpp) cc_final: 0.7945 (mmm) REVERT: A 1542 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 1667 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8213 (mtmm) REVERT: A 1721 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: A 1928 MET cc_start: 0.8823 (mmm) cc_final: 0.8423 (tpp) REVERT: A 2141 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 2162 GLN cc_start: 0.6948 (tm-30) cc_final: 0.6597 (tm-30) REVERT: A 2210 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 2223 MET cc_start: 0.7063 (tpp) cc_final: 0.6834 (tpt) REVERT: A 2277 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: A 2344 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7885 (tttm) REVERT: A 2362 ASN cc_start: 0.7928 (m-40) cc_final: 0.7153 (t0) REVERT: A 2372 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8243 (mmt90) REVERT: A 2424 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7908 (ttp80) REVERT: A 2589 LYS cc_start: 0.8598 (mppt) cc_final: 0.8264 (ptmm) REVERT: A 2844 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 2894 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7397 (t80) REVERT: A 3019 LYS cc_start: 0.8735 (pptt) cc_final: 0.8266 (ptpp) REVERT: A 3164 ASP cc_start: 0.8173 (t0) cc_final: 0.7752 (t0) REVERT: A 3182 LYS cc_start: 0.8714 (pttt) cc_final: 0.8358 (ptmt) REVERT: A 3297 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8378 (mtm110) REVERT: A 3418 MET cc_start: 0.8053 (tpp) cc_final: 0.7829 (tpp) REVERT: A 3465 GLN cc_start: 0.8416 (mp10) cc_final: 0.7851 (mm-40) outliers start: 51 outliers final: 28 residues processed: 204 average time/residue: 0.6332 time to fit residues: 144.2040 Evaluate side-chains 198 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1432 SER Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1721 GLN Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2344 LYS Chi-restraints excluded: chain A residue 2373 SER Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 3149 ASP Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 108 optimal weight: 0.9980 chunk 195 optimal weight: 0.1980 chunk 6 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1721 GLN A2983 GLN A3256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081109 restraints weight = 36513.426| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.81 r_work: 0.3062 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19302 Z= 0.102 Angle : 0.462 8.226 26087 Z= 0.243 Chirality : 0.037 0.142 2973 Planarity : 0.003 0.037 3400 Dihedral : 3.777 59.937 2634 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.59 % Allowed : 23.64 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2435 helix: 2.02 (0.14), residues: 1400 sheet: -0.13 (0.55), residues: 86 loop : -0.69 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3319 TYR 0.017 0.001 TYR A1144 PHE 0.017 0.001 PHE A3372 TRP 0.006 0.001 TRP A2347 HIS 0.003 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00217 (19302) covalent geometry : angle 0.46167 (26087) hydrogen bonds : bond 0.04576 ( 979) hydrogen bonds : angle 3.62802 ( 2775) *********************** 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 217 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8823 (mt) REVERT: A 1212 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8184 (tp30) REVERT: A 1499 MET cc_start: 0.8208 (tpp) cc_final: 0.7911 (mmm) REVERT: A 1667 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: A 1928 MET cc_start: 0.8709 (mmm) cc_final: 0.8381 (tpp) REVERT: A 2141 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 2162 GLN cc_start: 0.6935 (tm-30) cc_final: 0.6590 (tm-30) REVERT: A 2169 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: A 2210 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8250 (t0) REVERT: A 2223 MET cc_start: 0.7007 (tpp) cc_final: 0.6806 (tpt) REVERT: A 2277 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: A 2344 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7868 (tttm) REVERT: A 2362 ASN cc_start: 0.7722 (m-40) cc_final: 0.6920 (t0) REVERT: A 2372 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8229 (mmt90) REVERT: A 2424 ARG cc_start: 0.8205 (ttp-110) cc_final: 0.7891 (ttp80) REVERT: A 2432 MET cc_start: 0.7565 (mtp) cc_final: 0.7337 (mtt) REVERT: A 2844 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 2894 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7387 (t80) REVERT: A 3019 LYS cc_start: 0.8776 (pptt) cc_final: 0.8319 (ptpp) REVERT: A 3164 ASP cc_start: 0.8137 (t0) cc_final: 0.7731 (t0) REVERT: A 3182 LYS cc_start: 0.8698 (pttt) cc_final: 0.8339 (ptmt) REVERT: A 3297 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8255 (ptp-110) REVERT: A 3309 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5642 (t80) REVERT: A 3465 GLN cc_start: 0.8413 (mp10) cc_final: 0.7845 (mm-40) outliers start: 53 outliers final: 31 residues processed: 206 average time/residue: 0.6427 time to fit residues: 148.0682 Evaluate side-chains 199 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1432 SER Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2099 VAL Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2169 ASP Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2344 LYS Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2776 MET Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 3149 ASP Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3260 SER Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 242 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 54 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2143 ASN A2983 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080921 restraints weight = 36691.366| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.80 r_work: 0.3057 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19302 Z= 0.108 Angle : 0.468 9.861 26087 Z= 0.245 Chirality : 0.037 0.147 2973 Planarity : 0.003 0.037 3400 Dihedral : 3.756 59.894 2634 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.20 % Allowed : 24.04 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2435 helix: 2.03 (0.14), residues: 1407 sheet: -0.09 (0.55), residues: 86 loop : -0.71 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3319 TYR 0.017 0.001 TYR A1144 PHE 0.018 0.001 PHE A3372 TRP 0.006 0.001 TRP A2347 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00237 (19302) covalent geometry : angle 0.46774 (26087) hydrogen bonds : bond 0.04645 ( 979) hydrogen bonds : angle 3.61702 ( 2775) ********************** 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: 45 poor density : 162 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 1067 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 1212 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: A 1499 MET cc_start: 0.8242 (tpp) cc_final: 0.7849 (mmm) REVERT: A 1667 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: A 1928 MET cc_start: 0.8763 (mmm) cc_final: 0.8529 (tpp) REVERT: A 2141 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8411 (pp) REVERT: A 2162 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6623 (tm-30) REVERT: A 2210 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 2277 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: A 2344 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7900 (tttm) REVERT: A 2362 ASN cc_start: 0.7714 (m-40) cc_final: 0.6900 (t0) REVERT: A 2372 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8224 (mmt90) REVERT: A 2424 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7888 (ttp80) REVERT: A 2432 MET cc_start: 0.7511 (mtp) cc_final: 0.7298 (mtt) REVERT: A 2844 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 2894 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7392 (t80) REVERT: A 3019 LYS cc_start: 0.8847 (pptt) cc_final: 0.8314 (ptpp) REVERT: A 3164 ASP cc_start: 0.8141 (t0) cc_final: 0.7732 (t0) REVERT: A 3182 LYS cc_start: 0.8686 (pttt) cc_final: 0.8327 (ptmt) REVERT: A 3297 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8282 (ptp-110) REVERT: A 3309 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5822 (t80) REVERT: A 3465 GLN cc_start: 0.8423 (mp10) cc_final: 0.7860 (mm-40) outliers start: 45 outliers final: 33 residues processed: 199 average time/residue: 0.6527 time to fit residues: 144.6432 Evaluate side-chains 201 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1432 SER Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1667 LYS Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1862 SER Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1904 MET Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2030 GLU Chi-restraints excluded: chain A residue 2133 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2158 LEU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2210 ASN Chi-restraints excluded: chain A residue 2277 GLU Chi-restraints excluded: chain A residue 2334 MET Chi-restraints excluded: chain A residue 2344 LYS Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2507 TYR Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2554 VAL Chi-restraints excluded: chain A residue 2556 LYS Chi-restraints excluded: chain A residue 2624 ASN Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2769 VAL Chi-restraints excluded: chain A residue 2776 MET Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2923 VAL Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 3149 ASP Chi-restraints excluded: chain A residue 3230 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3251 THR Chi-restraints excluded: chain A residue 3260 SER Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3466 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 224 optimal weight: 0.0370 chunk 119 optimal weight: 0.0270 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 HIS A2983 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.080291 restraints weight = 36881.880| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.82 r_work: 0.3059 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19302 Z= 0.116 Angle : 0.470 11.159 26087 Z= 0.246 Chirality : 0.038 0.146 2973 Planarity : 0.003 0.038 3400 Dihedral : 3.770 59.790 2634 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.20 % Allowed : 24.04 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2435 helix: 2.02 (0.14), residues: 1406 sheet: -0.10 (0.55), residues: 86 loop : -0.71 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1750 TYR 0.016 0.001 TYR A1144 PHE 0.021 0.001 PHE A3372 TRP 0.006 0.001 TRP A2347 HIS 0.003 0.001 HIS A2759 Details of bonding type rmsd covalent geometry : bond 0.00260 (19302) covalent geometry : angle 0.46952 (26087) hydrogen bonds : bond 0.04790 ( 979) hydrogen bonds : angle 3.63658 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4989.60 seconds wall clock time: 86 minutes 7.04 seconds (5167.04 seconds total)