Starting phenix.real_space_refine on Thu Feb 5 09:53:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci3_45609/02_2026/9ci3_45609.cif" } resolution = 3.96 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 90 5.16 5 C 10115 2.51 5 N 2734 2.21 5 O 2983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 15926 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1909 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 4, 'TRANS': 232} Chain: "B" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1935 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "A" Number of atoms: 12054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 12054 Classifications: {'peptide': 1521} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1450} Chain breaks: 9 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.18 Number of scatterers: 15926 At special positions: 0 Unit cell: (98.01, 134.46, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 4 15.00 O 2983 8.00 N 2734 7.00 C 10115 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 700.1 milliseconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 18 sheets defined 42.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.538A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 38 through 71 removed outlier: 3.613A pdb=" N ARG C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 107 Processing helix chain 'C' and resid 116 through 138 removed outlier: 3.713A pdb=" N VAL C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 165 Processing helix chain 'C' and resid 169 through 186 Processing helix chain 'C' and resid 189 through 206 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.770A pdb=" N THR C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 234 removed outlier: 3.947A pdb=" N LYS C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.754A pdb=" N MET B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 74 removed outlier: 3.799A pdb=" N ARG B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 107 Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 140 through 165 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 189 through 208 removed outlier: 3.529A pdb=" N GLU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 235 removed outlier: 3.702A pdb=" N ASP B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.771A pdb=" N GLN A1002 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.511A pdb=" N GLU A1011 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A1012 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1013 " --> pdb=" O LEU A1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1013' Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.564A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 3.536A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 removed outlier: 3.924A pdb=" N TRP A1244 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1266 Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.584A pdb=" N MET A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1347 through 1355 removed outlier: 3.505A pdb=" N GLN A1353 " --> pdb=" O THR A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1402 Processing helix chain 'A' and resid 1404 through 1409 Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1426 through 1431 removed outlier: 3.764A pdb=" N ALA A1430 " --> pdb=" O ALA A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1465 through 1473 removed outlier: 3.888A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1539 removed outlier: 4.054A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 4.198A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A1605 " --> pdb=" O LYS A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 removed outlier: 4.274A pdb=" N GLU A1654 " --> pdb=" O PHE A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1713 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1828 through 1835 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.910A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1925 removed outlier: 3.612A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1962 Processing helix chain 'A' and resid 1963 through 1966 Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2017 through 2026 removed outlier: 3.581A pdb=" N ALA A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A2026 " --> pdb=" O GLN A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2046 removed outlier: 3.635A pdb=" N ARG A2045 " --> pdb=" O PRO A2041 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A2046 " --> pdb=" O GLU A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2051 through 2069 removed outlier: 3.984A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2078 removed outlier: 3.855A pdb=" N VAL A2074 " --> pdb=" O GLY A2070 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A2078 " --> pdb=" O VAL A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2088 removed outlier: 3.997A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2116 removed outlier: 3.938A pdb=" N GLU A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 4.562A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2135 through 2139' Processing helix chain 'A' and resid 2278 through 2281 removed outlier: 3.963A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2278 through 2281' Processing helix chain 'A' and resid 2389 through 2394 Processing helix chain 'A' and resid 2500 through 2521 removed outlier: 3.850A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A2517 " --> pdb=" O VAL A2513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2527 Processing sheet with id=AA1, first strand: chain 'A' and resid 986 through 988 removed outlier: 7.336A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 7.368A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A1112 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A1135 " --> pdb=" O LEU A1112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 7.022A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1332 removed outlier: 3.530A pdb=" N GLN A1521 " --> pdb=" O TYR A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1336 through 1337 removed outlier: 3.698A pdb=" N LEU A1390 " --> pdb=" O TRP A1376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1339 through 1340 removed outlier: 3.664A pdb=" N VAL A1418 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A1447 " --> pdb=" O ILE A1482 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP A1484 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AA8, first strand: chain 'A' and resid 1740 through 1743 removed outlier: 6.613A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1813 " --> pdb=" O ILE A1692 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A1696 " --> pdb=" O LYS A1809 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 removed outlier: 3.636A pdb=" N VAL A1841 " --> pdb=" O ILE A1850 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 3.865A pdb=" N MET A1944 " --> pdb=" O GLY A1939 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1953 through 1954 removed outlier: 3.870A pdb=" N GLY A1953 " --> pdb=" O LEU A2002 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 5.412A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A2473 " --> pdb=" O VAL A2457 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2155 through 2156 removed outlier: 6.489A pdb=" N GLY A2177 " --> pdb=" O VAL A2194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 3.562A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A2212 " --> pdb=" O LEU A2207 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A2219 " --> pdb=" O THR A2223 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR A2223 " --> pdb=" O THR A2219 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A2224 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2250 removed outlier: 3.947A pdb=" N VAL A2265 " --> pdb=" O ALA A2273 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A2273 " --> pdb=" O VAL A2265 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR A2267 " --> pdb=" O LYS A2271 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A2274 " --> pdb=" O LYS A2289 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A2289 " --> pdb=" O ILE A2274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 7.048A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A2315 " --> pdb=" O PHE A2326 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A2319 " --> pdb=" O LYS A2322 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A2325 " --> pdb=" O LYS A2334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.838A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 6.742A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A2435 " --> pdb=" O ILE A2427 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.61 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: 5186 1.34 - 1.46: 3224 1.46 - 1.58: 7664 1.58 - 1.70: 11 1.70 - 1.83: 138 Bond restraints: 16223 Sorted by residual: bond pdb=" N ILE A2498 " pdb=" CA ILE A2498 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" N ASN A2499 " pdb=" CA ASN A2499 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.92e+00 bond pdb=" N LEU A2500 " pdb=" CA LEU A2500 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.41e-02 5.03e+03 7.62e+00 bond pdb=" N VAL A2138 " pdb=" CA VAL A2138 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.25e+00 bond pdb=" N PHE A 940 " pdb=" CA PHE A 940 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 ... (remaining 16218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 21632 2.79 - 5.58: 251 5.58 - 8.36: 45 8.36 - 11.15: 13 11.15 - 13.94: 6 Bond angle restraints: 21947 Sorted by residual: angle pdb=" CA PRO A 938 " pdb=" N PRO A 938 " pdb=" CD PRO A 938 " ideal model delta sigma weight residual 112.00 98.06 13.94 1.40e+00 5.10e-01 9.91e+01 angle pdb=" C PRO A 938 " pdb=" CA PRO A 938 " pdb=" CB PRO A 938 " ideal model delta sigma weight residual 111.56 123.18 -11.62 1.65e+00 3.67e-01 4.96e+01 angle pdb=" N PRO A 938 " pdb=" CA PRO A 938 " pdb=" CB PRO A 938 " ideal model delta sigma weight residual 103.25 96.25 7.00 1.05e+00 9.07e-01 4.45e+01 angle pdb=" N ARG A2142 " pdb=" CA ARG A2142 " pdb=" C ARG A2142 " ideal model delta sigma weight residual 107.88 116.77 -8.89 1.41e+00 5.03e-01 3.98e+01 angle pdb=" CA LEU A2500 " pdb=" C LEU A2500 " pdb=" N PRO A2501 " ideal model delta sigma weight residual 118.44 128.11 -9.67 1.59e+00 3.96e-01 3.70e+01 ... (remaining 21942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8670 17.92 - 35.83: 1006 35.83 - 53.75: 218 53.75 - 71.67: 34 71.67 - 89.59: 16 Dihedral angle restraints: 9944 sinusoidal: 4060 harmonic: 5884 Sorted by residual: dihedral pdb=" CD ARG A2142 " pdb=" NE ARG A2142 " pdb=" CZ ARG A2142 " pdb=" NH1 ARG A2142 " ideal model delta sinusoidal sigma weight residual 0.00 -62.12 62.12 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CA TYR A1419 " pdb=" C TYR A1419 " pdb=" N ASP A1420 " pdb=" CA ASP A1420 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" C PRO A 938 " pdb=" N PRO A 938 " pdb=" CA PRO A 938 " pdb=" CB PRO A 938 " ideal model delta harmonic sigma weight residual -120.70 -131.63 10.93 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 9941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2291 0.082 - 0.165: 202 0.165 - 0.247: 14 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 2509 Sorted by residual: chirality pdb=" CA PRO A 938 " pdb=" N PRO A 938 " pdb=" C PRO A 938 " pdb=" CB PRO A 938 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA CYS A2139 " pdb=" N CYS A2139 " pdb=" C CYS A2139 " pdb=" CB CYS A2139 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU C 226 " pdb=" CB LEU C 226 " pdb=" CD1 LEU C 226 " pdb=" CD2 LEU C 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2506 not shown) Planarity restraints: 2788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2142 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.16e+02 pdb=" NE ARG A2142 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A2142 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A2142 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2142 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 937 " -0.080 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 938 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1244 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A1244 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A1244 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1244 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A1244 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1244 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A1244 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1244 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1244 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1244 " -0.013 2.00e-02 2.50e+03 ... (remaining 2785 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 285 2.64 - 3.21: 15666 3.21 - 3.77: 25569 3.77 - 4.34: 34156 4.34 - 4.90: 53984 Nonbonded interactions: 129660 Sorted by model distance: nonbonded pdb=" O LEU C 225 " pdb=" ND2 ASN C 229 " model vdw 2.081 3.120 nonbonded pdb=" NH1 ARG A2456 " pdb=" OH TYR A2475 " model vdw 2.112 3.120 nonbonded pdb=" OG1 THR A1491 " pdb=" OE1 GLU A1492 " model vdw 2.118 3.040 nonbonded pdb=" O ASN A1068 " pdb=" ND2 ASN A1093 " model vdw 2.152 3.120 nonbonded pdb=" O SER A2213 " pdb=" OG1 THR A2229 " model vdw 2.165 3.040 ... (remaining 129655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 0 through 236) selection = chain 'C' } 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 group one per residue 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 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 : 0.007 0.811 16224 Z= 0.663 Angle : 0.821 13.939 21947 Z= 0.441 Chirality : 0.047 0.411 2509 Planarity : 0.010 0.439 2788 Dihedral : 15.930 89.585 6114 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.37 % Favored : 92.48 % Rotamer: Outliers : 1.87 % Allowed : 17.17 % Favored : 80.96 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.28 % 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: -1.32 (0.19), residues: 1968 helix: 0.56 (0.19), residues: 730 sheet: -1.69 (0.34), residues: 243 loop : -1.80 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1731 TYR 0.021 0.002 TYR B 49 PHE 0.021 0.002 PHE A1401 TRP 0.060 0.002 TRP A1244 HIS 0.009 0.001 HIS A1929 Details of bonding type rmsd covalent geometry : bond 0.00357 (16223) covalent geometry : angle 0.82114 (21947) hydrogen bonds : bond 0.19539 ( 670) hydrogen bonds : angle 7.63996 ( 1908) Misc. bond : bond 0.81132 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 TRP cc_start: 0.8126 (t60) cc_final: 0.7176 (t-100) REVERT: C 182 PHE cc_start: 0.7972 (t80) cc_final: 0.7644 (t80) REVERT: B 56 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7388 (mmt-90) REVERT: B 122 PHE cc_start: 0.7991 (t80) cc_final: 0.7545 (t80) REVERT: B 165 MET cc_start: 0.7126 (mmt) cc_final: 0.6857 (mmt) REVERT: B 166 GLN cc_start: 0.7161 (pp30) cc_final: 0.6852 (pp30) REVERT: A 986 SER cc_start: 0.6201 (p) cc_final: 0.5917 (m) REVERT: A 1148 PHE cc_start: 0.5652 (t80) cc_final: 0.5054 (m-80) REVERT: A 1256 LYS cc_start: 0.7541 (mmmm) cc_final: 0.7077 (mmmm) REVERT: A 1268 GLU cc_start: 0.7707 (pm20) cc_final: 0.7359 (pm20) REVERT: A 1320 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7277 (mmm-85) REVERT: A 1375 ASP cc_start: 0.7144 (t0) cc_final: 0.6497 (m-30) REVERT: A 1432 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7421 (mttm) REVERT: A 1507 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 1529 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6927 (mt-10) REVERT: A 1552 ARG cc_start: 0.6896 (mmm160) cc_final: 0.6546 (tpt90) REVERT: A 1599 GLU cc_start: 0.7575 (pt0) cc_final: 0.7218 (pt0) REVERT: A 1603 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4265 (tp) REVERT: A 1699 TYR cc_start: 0.6576 (m-80) cc_final: 0.6118 (m-80) REVERT: A 1747 TYR cc_start: 0.8014 (p90) cc_final: 0.7783 (p90) REVERT: A 1788 MET cc_start: 0.7454 (tpp) cc_final: 0.7236 (tpp) REVERT: A 1790 GLU cc_start: 0.7717 (tt0) cc_final: 0.6963 (tt0) REVERT: A 1827 LEU cc_start: 0.8012 (tp) cc_final: 0.7790 (tp) REVERT: A 1877 PHE cc_start: 0.6809 (t80) cc_final: 0.4654 (t80) REVERT: A 2168 TRP cc_start: 0.6833 (m100) cc_final: 0.6200 (m-10) REVERT: A 2267 THR cc_start: 0.3141 (OUTLIER) cc_final: 0.2545 (p) REVERT: A 2458 MET cc_start: 0.4823 (tpt) cc_final: 0.4210 (tpt) REVERT: A 2498 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7605 (pp) REVERT: A 2514 ARG cc_start: 0.5050 (tpt170) cc_final: 0.3737 (mmm160) outliers start: 33 outliers final: 21 residues processed: 317 average time/residue: 0.1244 time to fit residues: 57.5744 Evaluate side-chains 309 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 938 PRO Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1758 HIS Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2397 MET Chi-restraints excluded: chain A residue 2436 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2498 ILE Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN A1021 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN ** A1586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.220096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.183392 restraints weight = 31105.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189099 restraints weight = 18385.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.193300 restraints weight = 12412.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.195989 restraints weight = 9093.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.198069 restraints weight = 7159.796| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 16224 Z= 0.175 Angle : 0.715 11.553 21947 Z= 0.361 Chirality : 0.046 0.244 2509 Planarity : 0.006 0.154 2788 Dihedral : 7.060 59.324 2217 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 3.23 % Allowed : 16.37 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.33 (0.19), residues: 1968 helix: 0.60 (0.19), residues: 757 sheet: -2.03 (0.31), residues: 260 loop : -1.79 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 57 TYR 0.024 0.002 TYR A1332 PHE 0.022 0.002 PHE A1401 TRP 0.045 0.002 TRP A1244 HIS 0.008 0.001 HIS A1574 Details of bonding type rmsd covalent geometry : bond 0.00383 (16223) covalent geometry : angle 0.71462 (21947) hydrogen bonds : bond 0.04774 ( 670) hydrogen bonds : angle 5.83423 ( 1908) Misc. bond : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 MET cc_start: 0.6619 (ptm) cc_final: 0.6338 (ptm) REVERT: C 32 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7051 (mm-30) REVERT: C 60 TRP cc_start: 0.8114 (t60) cc_final: 0.7267 (t-100) REVERT: C 61 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7677 (mtp85) REVERT: C 183 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: C 223 MET cc_start: 0.7819 (tpp) cc_final: 0.7539 (tpp) REVERT: B 51 ASN cc_start: 0.8125 (m-40) cc_final: 0.7898 (t0) REVERT: B 122 PHE cc_start: 0.7943 (t80) cc_final: 0.7080 (t80) REVERT: B 126 MET cc_start: 0.7409 (mtm) cc_final: 0.6753 (mtm) REVERT: B 132 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7216 (ttp-110) REVERT: B 143 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.7077 (ttt-90) REVERT: B 164 HIS cc_start: 0.6586 (t-90) cc_final: 0.6303 (t-90) REVERT: B 165 MET cc_start: 0.7284 (mmt) cc_final: 0.6812 (mmt) REVERT: B 166 GLN cc_start: 0.7295 (pp30) cc_final: 0.7001 (pp30) REVERT: A 986 SER cc_start: 0.6385 (p) cc_final: 0.6068 (m) REVERT: A 1014 GLU cc_start: 0.6406 (mp0) cc_final: 0.5969 (mt-10) REVERT: A 1068 ASN cc_start: 0.6814 (t0) cc_final: 0.5901 (t0) REVERT: A 1148 PHE cc_start: 0.5758 (t80) cc_final: 0.5134 (m-80) REVERT: A 1244 TRP cc_start: 0.5980 (m-90) cc_final: 0.5437 (m-90) REVERT: A 1256 LYS cc_start: 0.7477 (mmmm) cc_final: 0.6965 (mmmm) REVERT: A 1268 GLU cc_start: 0.7785 (pm20) cc_final: 0.7403 (pm20) REVERT: A 1320 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7298 (mmm-85) REVERT: A 1375 ASP cc_start: 0.6835 (t0) cc_final: 0.6501 (m-30) REVERT: A 1432 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7266 (mttm) REVERT: A 1507 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 1516 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 1529 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 1552 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6831 (tpt90) REVERT: A 1599 GLU cc_start: 0.7501 (pt0) cc_final: 0.7184 (pt0) REVERT: A 1603 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.4512 (tp) REVERT: A 1690 ILE cc_start: 0.7335 (pt) cc_final: 0.6944 (tp) REVERT: A 1827 LEU cc_start: 0.8021 (tp) cc_final: 0.7738 (tp) REVERT: A 1944 MET cc_start: 0.6823 (pmm) cc_final: 0.6556 (pmm) REVERT: A 1947 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4677 (mtm) REVERT: A 1977 HIS cc_start: 0.6675 (m90) cc_final: 0.6071 (m170) REVERT: A 2155 MET cc_start: 0.7264 (ppp) cc_final: 0.6971 (tmm) REVERT: A 2264 LEU cc_start: 0.5290 (mp) cc_final: 0.5047 (mt) REVERT: A 2267 THR cc_start: 0.3478 (OUTLIER) cc_final: 0.3208 (p) REVERT: A 2324 PHE cc_start: 0.6274 (p90) cc_final: 0.5894 (p90) REVERT: A 2417 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6496 (mm) REVERT: A 2420 GLN cc_start: 0.5549 (tt0) cc_final: 0.4977 (tt0) REVERT: A 2458 MET cc_start: 0.5483 (tpt) cc_final: 0.4532 (tpt) REVERT: A 2514 ARG cc_start: 0.5347 (tpt170) cc_final: 0.4738 (tpt170) outliers start: 57 outliers final: 29 residues processed: 337 average time/residue: 0.1199 time to fit residues: 60.2339 Evaluate side-chains 315 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1431 MET Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1523 ILE Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2436 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2475 TYR Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 0.0270 chunk 142 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1333 ASN ** A1586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.220228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.183290 restraints weight = 31177.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188972 restraints weight = 18549.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193043 restraints weight = 12541.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.195839 restraints weight = 9274.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.197861 restraints weight = 7295.525| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16224 Z= 0.148 Angle : 0.680 10.745 21947 Z= 0.340 Chirality : 0.045 0.211 2509 Planarity : 0.005 0.142 2788 Dihedral : 6.229 59.874 2189 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 3.40 % Allowed : 18.30 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1968 helix: 0.64 (0.19), residues: 757 sheet: -2.19 (0.31), residues: 259 loop : -1.88 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2523 TYR 0.016 0.001 TYR A1332 PHE 0.016 0.001 PHE A1401 TRP 0.028 0.002 TRP A2496 HIS 0.009 0.001 HIS A2206 Details of bonding type rmsd covalent geometry : bond 0.00329 (16223) covalent geometry : angle 0.68002 (21947) hydrogen bonds : bond 0.04359 ( 670) hydrogen bonds : angle 5.55193 ( 1908) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7042 (mm-30) REVERT: C 60 TRP cc_start: 0.8146 (t60) cc_final: 0.7421 (t-100) REVERT: C 61 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7617 (mtp85) REVERT: C 126 MET cc_start: 0.7372 (mmt) cc_final: 0.7157 (tpp) REVERT: B 28 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7708 (mmmt) REVERT: B 51 ASN cc_start: 0.8086 (m-40) cc_final: 0.7669 (t0) REVERT: B 122 PHE cc_start: 0.7914 (t80) cc_final: 0.7416 (t80) REVERT: B 132 ARG cc_start: 0.7521 (ttp-110) cc_final: 0.7183 (ttp-110) REVERT: B 143 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.7012 (ttt-90) REVERT: B 165 MET cc_start: 0.7281 (mmt) cc_final: 0.6681 (mmt) REVERT: B 166 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6963 (pp30) REVERT: B 223 MET cc_start: 0.8419 (ttt) cc_final: 0.8187 (ttt) REVERT: A 986 SER cc_start: 0.6450 (p) cc_final: 0.6122 (m) REVERT: A 1014 GLU cc_start: 0.6576 (mp0) cc_final: 0.5902 (mt-10) REVERT: A 1068 ASN cc_start: 0.7425 (t0) cc_final: 0.7179 (t0) REVERT: A 1148 PHE cc_start: 0.5897 (t80) cc_final: 0.5249 (m-80) REVERT: A 1244 TRP cc_start: 0.5956 (m-90) cc_final: 0.5488 (m-90) REVERT: A 1268 GLU cc_start: 0.7817 (pm20) cc_final: 0.7407 (pm20) REVERT: A 1269 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.5850 (t160) REVERT: A 1320 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.7290 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.5601 (tpt170) REVERT: A 1375 ASP cc_start: 0.6715 (t0) cc_final: 0.6382 (m-30) REVERT: A 1425 GLN cc_start: 0.7534 (tm-30) cc_final: 0.6787 (mm110) REVERT: A 1432 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7219 (mttm) REVERT: A 1529 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6791 (mt-10) REVERT: A 1599 GLU cc_start: 0.7453 (pt0) cc_final: 0.7120 (pt0) REVERT: A 1603 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4388 (tp) REVERT: A 1710 ASN cc_start: 0.7852 (t0) cc_final: 0.7583 (t0) REVERT: A 1827 LEU cc_start: 0.8057 (tp) cc_final: 0.7655 (tp) REVERT: A 1831 MET cc_start: 0.5077 (ppp) cc_final: 0.4267 (ptp) REVERT: A 1858 ASP cc_start: 0.7626 (p0) cc_final: 0.7317 (p0) REVERT: A 2064 TYR cc_start: 0.8010 (t80) cc_final: 0.7457 (t80) REVERT: A 2108 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5547 (tp30) REVERT: A 2137 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5353 (tt) REVERT: A 2155 MET cc_start: 0.7211 (ppp) cc_final: 0.5991 (ppp) REVERT: A 2248 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7276 (pp) REVERT: A 2267 THR cc_start: 0.3254 (OUTLIER) cc_final: 0.3023 (p) REVERT: A 2420 GLN cc_start: 0.5518 (tt0) cc_final: 0.5159 (tt0) REVERT: A 2500 LEU cc_start: 0.4815 (OUTLIER) cc_final: 0.3598 (pt) REVERT: A 2504 VAL cc_start: 0.5780 (p) cc_final: 0.5523 (p) REVERT: A 2514 ARG cc_start: 0.5183 (tpt170) cc_final: 0.4773 (tpt170) outliers start: 60 outliers final: 34 residues processed: 345 average time/residue: 0.1134 time to fit residues: 58.4478 Evaluate side-chains 339 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2436 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2475 TYR Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 75 optimal weight: 0.0270 chunk 162 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 188 optimal weight: 0.0170 chunk 137 optimal weight: 0.5980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1043 HIS ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.221539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.185299 restraints weight = 31219.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.190916 restraints weight = 18517.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.195004 restraints weight = 12494.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.197803 restraints weight = 9228.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.199668 restraints weight = 7280.066| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16224 Z= 0.122 Angle : 0.662 10.751 21947 Z= 0.327 Chirality : 0.044 0.204 2509 Planarity : 0.005 0.133 2788 Dihedral : 5.793 57.934 2186 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 3.63 % Allowed : 19.04 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.26 (0.19), residues: 1968 helix: 0.75 (0.19), residues: 753 sheet: -2.10 (0.31), residues: 268 loop : -1.79 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.027 0.001 TYR B 49 PHE 0.014 0.001 PHE A2326 TRP 0.030 0.002 TRP A2496 HIS 0.005 0.001 HIS A2206 Details of bonding type rmsd covalent geometry : bond 0.00268 (16223) covalent geometry : angle 0.66201 (21947) hydrogen bonds : bond 0.03971 ( 670) hydrogen bonds : angle 5.24926 ( 1908) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7029 (mm-30) REVERT: C 60 TRP cc_start: 0.8201 (t60) cc_final: 0.7582 (t-100) REVERT: C 61 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7628 (mtp85) REVERT: B 20 TYR cc_start: 0.7109 (m-80) cc_final: 0.6298 (m-10) REVERT: B 51 ASN cc_start: 0.8036 (m-40) cc_final: 0.7605 (t0) REVERT: B 122 PHE cc_start: 0.7844 (t80) cc_final: 0.6905 (t80) REVERT: B 126 MET cc_start: 0.7407 (mtm) cc_final: 0.6765 (mtm) REVERT: B 132 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7134 (ttp-110) REVERT: B 165 MET cc_start: 0.7140 (mmt) cc_final: 0.6890 (mmt) REVERT: B 166 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6953 (pp30) REVERT: B 223 MET cc_start: 0.8361 (ttt) cc_final: 0.8136 (ttt) REVERT: A 986 SER cc_start: 0.6430 (OUTLIER) cc_final: 0.6100 (m) REVERT: A 1014 GLU cc_start: 0.6602 (mp0) cc_final: 0.5852 (mt-10) REVERT: A 1084 THR cc_start: 0.1668 (OUTLIER) cc_final: 0.0560 (p) REVERT: A 1148 PHE cc_start: 0.5865 (t80) cc_final: 0.5264 (m-80) REVERT: A 1180 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5676 (tp) REVERT: A 1244 TRP cc_start: 0.5913 (m-10) cc_final: 0.5476 (m-90) REVERT: A 1256 LYS cc_start: 0.7567 (mmmm) cc_final: 0.7033 (mmmm) REVERT: A 1268 GLU cc_start: 0.7741 (pm20) cc_final: 0.7333 (pm20) REVERT: A 1269 ASN cc_start: 0.6258 (OUTLIER) cc_final: 0.5799 (t160) REVERT: A 1320 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.7243 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.5566 (tpt170) REVERT: A 1432 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7108 (mttp) REVERT: A 1516 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 1521 GLN cc_start: 0.7227 (tt0) cc_final: 0.6857 (tt0) REVERT: A 1529 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6755 (mt-10) REVERT: A 1599 GLU cc_start: 0.7421 (pt0) cc_final: 0.7058 (pt0) REVERT: A 1603 LEU cc_start: 0.4788 (OUTLIER) cc_final: 0.4561 (tp) REVERT: A 1690 ILE cc_start: 0.7336 (pt) cc_final: 0.7007 (tp) REVERT: A 1788 MET cc_start: 0.7273 (tpp) cc_final: 0.6959 (mmm) REVERT: A 1814 TYR cc_start: 0.5978 (p90) cc_final: 0.5516 (p90) REVERT: A 1827 LEU cc_start: 0.8024 (tp) cc_final: 0.7583 (tp) REVERT: A 1858 ASP cc_start: 0.7555 (p0) cc_final: 0.7254 (p0) REVERT: A 1914 LEU cc_start: 0.7253 (pt) cc_final: 0.6730 (mm) REVERT: A 1974 ILE cc_start: 0.7745 (mt) cc_final: 0.7496 (mt) REVERT: A 2064 TYR cc_start: 0.7989 (t80) cc_final: 0.7415 (t80) REVERT: A 2108 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5409 (tp30) REVERT: A 2137 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5141 (tt) REVERT: A 2264 LEU cc_start: 0.4817 (mp) cc_final: 0.3181 (pp) REVERT: A 2417 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6848 (mm) REVERT: A 2420 GLN cc_start: 0.5538 (tt0) cc_final: 0.5164 (tt0) REVERT: A 2458 MET cc_start: 0.5432 (tpt) cc_final: 0.4354 (tpt) REVERT: A 2459 MET cc_start: 0.7074 (pmm) cc_final: 0.6449 (tpt) REVERT: A 2498 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7418 (pp) REVERT: A 2500 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.3308 (pt) REVERT: A 2514 ARG cc_start: 0.5284 (tpt170) cc_final: 0.4857 (tpt170) outliers start: 64 outliers final: 41 residues processed: 340 average time/residue: 0.1142 time to fit residues: 57.8817 Evaluate side-chains 343 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1407 HIS Chi-restraints excluded: chain A residue 1431 MET Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1945 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 195 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 163 optimal weight: 0.0570 chunk 186 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1730 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.220101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.183228 restraints weight = 31183.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.188819 restraints weight = 18650.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.192931 restraints weight = 12729.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.195737 restraints weight = 9419.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.197702 restraints weight = 7476.789| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16224 Z= 0.139 Angle : 0.667 10.233 21947 Z= 0.332 Chirality : 0.045 0.196 2509 Planarity : 0.005 0.126 2788 Dihedral : 5.386 53.297 2177 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.01 % Favored : 92.89 % Rotamer: Outliers : 4.02 % Allowed : 20.23 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.30 (0.19), residues: 1968 helix: 0.74 (0.19), residues: 756 sheet: -2.14 (0.31), residues: 258 loop : -1.84 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 61 TYR 0.027 0.001 TYR B 49 PHE 0.016 0.001 PHE A2326 TRP 0.029 0.002 TRP A2496 HIS 0.014 0.001 HIS A1043 Details of bonding type rmsd covalent geometry : bond 0.00305 (16223) covalent geometry : angle 0.66654 (21947) hydrogen bonds : bond 0.03953 ( 670) hydrogen bonds : angle 5.18890 ( 1908) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 TRP cc_start: 0.8247 (t60) cc_final: 0.7646 (t-100) REVERT: C 61 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7624 (mtp85) REVERT: C 126 MET cc_start: 0.7616 (tpp) cc_final: 0.7371 (tpp) REVERT: C 166 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: B 51 ASN cc_start: 0.7973 (m-40) cc_final: 0.7645 (t0) REVERT: B 122 PHE cc_start: 0.7870 (t80) cc_final: 0.6902 (t80) REVERT: B 126 MET cc_start: 0.7387 (mtm) cc_final: 0.6674 (mtm) REVERT: B 132 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7131 (ttp-110) REVERT: B 164 HIS cc_start: 0.6378 (t-90) cc_final: 0.6039 (m-70) REVERT: B 165 MET cc_start: 0.7128 (mmt) cc_final: 0.6691 (mmt) REVERT: B 166 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7023 (pp30) REVERT: B 217 LYS cc_start: 0.6598 (pttm) cc_final: 0.5903 (pttm) REVERT: B 223 MET cc_start: 0.8413 (ttt) cc_final: 0.8180 (ttt) REVERT: A 986 SER cc_start: 0.6701 (OUTLIER) cc_final: 0.6379 (m) REVERT: A 1014 GLU cc_start: 0.6682 (mp0) cc_final: 0.5921 (mt-10) REVERT: A 1148 PHE cc_start: 0.6047 (t80) cc_final: 0.5426 (m-80) REVERT: A 1180 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5513 (tp) REVERT: A 1256 LYS cc_start: 0.7592 (mmmm) cc_final: 0.7031 (mmmm) REVERT: A 1268 GLU cc_start: 0.7791 (pm20) cc_final: 0.7371 (pm20) REVERT: A 1269 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.5855 (t160) REVERT: A 1320 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7243 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.5562 (tpt170) REVERT: A 1407 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7337 (m-70) REVERT: A 1425 GLN cc_start: 0.7450 (tp40) cc_final: 0.6900 (mm-40) REVERT: A 1432 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7303 (mttp) REVERT: A 1521 GLN cc_start: 0.7268 (tt0) cc_final: 0.6939 (tt0) REVERT: A 1529 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6792 (mt-10) REVERT: A 1599 GLU cc_start: 0.7401 (pt0) cc_final: 0.7018 (pt0) REVERT: A 1603 LEU cc_start: 0.5072 (OUTLIER) cc_final: 0.4661 (tp) REVERT: A 1690 ILE cc_start: 0.7337 (pt) cc_final: 0.7074 (tp) REVERT: A 1699 TYR cc_start: 0.6700 (m-80) cc_final: 0.6162 (m-80) REVERT: A 1728 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7368 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: A 1788 MET cc_start: 0.7295 (tpp) cc_final: 0.6967 (mmm) REVERT: A 1811 TRP cc_start: 0.7605 (m100) cc_final: 0.6870 (m-10) REVERT: A 1814 TYR cc_start: 0.6054 (p90) cc_final: 0.5585 (p90) REVERT: A 1827 LEU cc_start: 0.8022 (tp) cc_final: 0.7515 (tp) REVERT: A 1831 MET cc_start: 0.4880 (ppp) cc_final: 0.4113 (ptp) REVERT: A 1838 ASP cc_start: 0.7370 (p0) cc_final: 0.7105 (p0) REVERT: A 1858 ASP cc_start: 0.7556 (p0) cc_final: 0.7270 (p0) REVERT: A 1914 LEU cc_start: 0.7399 (pt) cc_final: 0.6992 (mm) REVERT: A 1973 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7530 (tpp-160) REVERT: A 1974 ILE cc_start: 0.7918 (mt) cc_final: 0.7666 (mt) REVERT: A 2064 TYR cc_start: 0.8008 (t80) cc_final: 0.7485 (t80) REVERT: A 2108 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5508 (tp30) REVERT: A 2137 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5178 (tt) REVERT: A 2167 ILE cc_start: 0.7730 (tp) cc_final: 0.7493 (tp) REVERT: A 2168 TRP cc_start: 0.7343 (m100) cc_final: 0.6860 (m-10) REVERT: A 2192 GLU cc_start: 0.6653 (pt0) cc_final: 0.5899 (tp30) REVERT: A 2264 LEU cc_start: 0.5153 (mp) cc_final: 0.3623 (pp) REVERT: A 2300 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7912 (mm) REVERT: A 2420 GLN cc_start: 0.5687 (tt0) cc_final: 0.5327 (tt0) REVERT: A 2459 MET cc_start: 0.6724 (pmm) cc_final: 0.6341 (pmm) REVERT: A 2500 LEU cc_start: 0.4598 (OUTLIER) cc_final: 0.2576 (pt) REVERT: A 2514 ARG cc_start: 0.5559 (tpt170) cc_final: 0.5064 (tpt170) outliers start: 71 outliers final: 42 residues processed: 346 average time/residue: 0.1238 time to fit residues: 62.7617 Evaluate side-chains 352 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1407 HIS Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.9980 chunk 82 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 70 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN A1062 ASN ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1684 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.217890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.180393 restraints weight = 30748.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.186131 restraints weight = 18287.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.190288 restraints weight = 12356.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.193078 restraints weight = 9153.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.195128 restraints weight = 7278.021| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16224 Z= 0.164 Angle : 0.692 13.809 21947 Z= 0.346 Chirality : 0.045 0.199 2509 Planarity : 0.005 0.120 2788 Dihedral : 5.498 57.014 2177 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 4.31 % Allowed : 20.91 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.42 (0.19), residues: 1968 helix: 0.62 (0.19), residues: 773 sheet: -2.06 (0.32), residues: 256 loop : -1.98 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1983 TYR 0.024 0.002 TYR B 49 PHE 0.021 0.002 PHE A1401 TRP 0.037 0.002 TRP C 233 HIS 0.006 0.001 HIS A1574 Details of bonding type rmsd covalent geometry : bond 0.00358 (16223) covalent geometry : angle 0.69202 (21947) hydrogen bonds : bond 0.04090 ( 670) hydrogen bonds : angle 5.21487 ( 1908) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.2932 (mmm) cc_final: 0.1323 (mmm) REVERT: C 60 TRP cc_start: 0.8347 (t60) cc_final: 0.7987 (t-100) REVERT: C 61 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7722 (mtp85) REVERT: C 126 MET cc_start: 0.7524 (tpp) cc_final: 0.7307 (tpp) REVERT: C 223 MET cc_start: 0.7877 (tpp) cc_final: 0.7375 (mpp) REVERT: B 108 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6448 (mm) REVERT: B 122 PHE cc_start: 0.7917 (t80) cc_final: 0.6924 (t80) REVERT: B 126 MET cc_start: 0.7482 (mtm) cc_final: 0.6860 (mtm) REVERT: B 132 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7098 (ttp-110) REVERT: B 164 HIS cc_start: 0.6388 (t-90) cc_final: 0.6063 (m-70) REVERT: B 165 MET cc_start: 0.7134 (mmt) cc_final: 0.6645 (mmt) REVERT: B 223 MET cc_start: 0.8425 (ttt) cc_final: 0.8211 (ttt) REVERT: A 986 SER cc_start: 0.6945 (OUTLIER) cc_final: 0.6621 (m) REVERT: A 1014 GLU cc_start: 0.6927 (mp0) cc_final: 0.6193 (mt-10) REVERT: A 1148 PHE cc_start: 0.6268 (t80) cc_final: 0.5530 (m-80) REVERT: A 1180 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5657 (tp) REVERT: A 1256 LYS cc_start: 0.7596 (mmmm) cc_final: 0.7249 (mtmt) REVERT: A 1268 GLU cc_start: 0.7798 (pm20) cc_final: 0.7390 (pm20) REVERT: A 1269 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.5965 (t160) REVERT: A 1334 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.5819 (tpt170) REVERT: A 1371 ILE cc_start: 0.7336 (pt) cc_final: 0.7040 (mp) REVERT: A 1379 GLN cc_start: 0.8094 (pm20) cc_final: 0.7860 (pm20) REVERT: A 1388 LEU cc_start: 0.7756 (pp) cc_final: 0.7532 (tp) REVERT: A 1412 ARG cc_start: 0.6901 (ptp-110) cc_final: 0.6649 (ptm160) REVERT: A 1418 VAL cc_start: 0.6235 (m) cc_final: 0.5384 (p) REVERT: A 1425 GLN cc_start: 0.7547 (tp40) cc_final: 0.7020 (mm-40) REVERT: A 1432 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7537 (mttp) REVERT: A 1439 LYS cc_start: 0.7521 (tppt) cc_final: 0.7247 (tppt) REVERT: A 1529 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6671 (mt-10) REVERT: A 1581 VAL cc_start: 0.7717 (p) cc_final: 0.7251 (t) REVERT: A 1599 GLU cc_start: 0.7414 (pt0) cc_final: 0.7080 (pt0) REVERT: A 1603 LEU cc_start: 0.5180 (OUTLIER) cc_final: 0.4894 (tp) REVERT: A 1651 LYS cc_start: 0.7925 (ptpt) cc_final: 0.7570 (mmmt) REVERT: A 1690 ILE cc_start: 0.7415 (pt) cc_final: 0.7194 (tp) REVERT: A 1699 TYR cc_start: 0.6737 (m-80) cc_final: 0.6189 (m-80) REVERT: A 1728 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7367 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: A 1742 TRP cc_start: 0.7743 (m-90) cc_final: 0.7494 (m-90) REVERT: A 1811 TRP cc_start: 0.7698 (m100) cc_final: 0.7323 (m-10) REVERT: A 1838 ASP cc_start: 0.7528 (p0) cc_final: 0.7107 (p0) REVERT: A 1914 LEU cc_start: 0.7624 (pt) cc_final: 0.7387 (mm) REVERT: A 1947 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.3952 (mtm) REVERT: A 1973 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7455 (tpp-160) REVERT: A 1974 ILE cc_start: 0.8068 (mt) cc_final: 0.7797 (mt) REVERT: A 2064 TYR cc_start: 0.8015 (t80) cc_final: 0.7562 (t80) REVERT: A 2108 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5774 (tp30) REVERT: A 2264 LEU cc_start: 0.5823 (mp) cc_final: 0.4234 (pp) REVERT: A 2289 LYS cc_start: 0.7512 (mptt) cc_final: 0.7181 (mptt) REVERT: A 2300 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 2371 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7256 (Cg_exo) REVERT: A 2420 GLN cc_start: 0.5807 (tt0) cc_final: 0.5369 (tt0) REVERT: A 2436 LEU cc_start: 0.7356 (mm) cc_final: 0.7149 (mm) REVERT: A 2459 MET cc_start: 0.6621 (pmm) cc_final: 0.5148 (pmm) REVERT: A 2498 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7611 (pp) REVERT: A 2500 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.3119 (pt) REVERT: A 2505 GLN cc_start: 0.7349 (pt0) cc_final: 0.6528 (pp30) REVERT: A 2514 ARG cc_start: 0.5852 (tpt170) cc_final: 0.5465 (tpt170) outliers start: 76 outliers final: 48 residues processed: 355 average time/residue: 0.1242 time to fit residues: 65.2756 Evaluate side-chains 356 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1758 HIS Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 106 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 0.0670 chunk 87 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN A1251 HIS ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.219147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.180695 restraints weight = 31110.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.186580 restraints weight = 18515.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.190467 restraints weight = 12544.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.193395 restraints weight = 9355.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.195091 restraints weight = 7456.724| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16224 Z= 0.148 Angle : 0.701 15.288 21947 Z= 0.345 Chirality : 0.045 0.202 2509 Planarity : 0.005 0.116 2788 Dihedral : 5.397 53.452 2177 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 3.91 % Allowed : 21.81 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.42 (0.19), residues: 1968 helix: 0.59 (0.19), residues: 771 sheet: -2.07 (0.31), residues: 272 loop : -1.93 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1866 TYR 0.019 0.002 TYR B 20 PHE 0.017 0.001 PHE A1401 TRP 0.033 0.002 TRP C 233 HIS 0.005 0.001 HIS A1574 Details of bonding type rmsd covalent geometry : bond 0.00329 (16223) covalent geometry : angle 0.70097 (21947) hydrogen bonds : bond 0.03919 ( 670) hydrogen bonds : angle 5.16267 ( 1908) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.2910 (mmm) cc_final: 0.1262 (mmm) REVERT: C 60 TRP cc_start: 0.8255 (t60) cc_final: 0.7962 (t-100) REVERT: C 61 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7792 (mtp85) REVERT: C 126 MET cc_start: 0.7522 (tpp) cc_final: 0.7321 (tpp) REVERT: C 134 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7390 (mt) REVERT: C 166 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: C 223 MET cc_start: 0.7813 (tpp) cc_final: 0.7401 (mpp) REVERT: B 28 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7557 (ttpt) REVERT: B 108 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6327 (mm) REVERT: B 122 PHE cc_start: 0.7933 (t80) cc_final: 0.6940 (t80) REVERT: B 126 MET cc_start: 0.7441 (mtm) cc_final: 0.6832 (mtm) REVERT: B 132 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.6627 (ttp-110) REVERT: B 165 MET cc_start: 0.6983 (mmt) cc_final: 0.6754 (mmt) REVERT: B 223 MET cc_start: 0.8373 (ttt) cc_final: 0.8136 (ttt) REVERT: A 986 SER cc_start: 0.6944 (OUTLIER) cc_final: 0.6655 (m) REVERT: A 1014 GLU cc_start: 0.6929 (mp0) cc_final: 0.6080 (mt-10) REVERT: A 1068 ASN cc_start: 0.8140 (t0) cc_final: 0.7430 (t0) REVERT: A 1148 PHE cc_start: 0.6401 (t80) cc_final: 0.5638 (m-80) REVERT: A 1180 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5639 (tp) REVERT: A 1244 TRP cc_start: 0.6048 (m-10) cc_final: 0.5556 (m-90) REVERT: A 1256 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7237 (mtmt) REVERT: A 1268 GLU cc_start: 0.7762 (pm20) cc_final: 0.7356 (pm20) REVERT: A 1269 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.5897 (t160) REVERT: A 1320 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7170 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.5537 (tpt170) REVERT: A 1371 ILE cc_start: 0.7313 (pt) cc_final: 0.7028 (mp) REVERT: A 1412 ARG cc_start: 0.6859 (ptp-110) cc_final: 0.6651 (ptm160) REVERT: A 1425 GLN cc_start: 0.7517 (tp40) cc_final: 0.7002 (mm-40) REVERT: A 1432 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7466 (mmtt) REVERT: A 1439 LYS cc_start: 0.7515 (tppt) cc_final: 0.7288 (tppt) REVERT: A 1521 GLN cc_start: 0.7339 (tt0) cc_final: 0.6974 (tt0) REVERT: A 1581 VAL cc_start: 0.7747 (p) cc_final: 0.7226 (t) REVERT: A 1599 GLU cc_start: 0.7395 (pt0) cc_final: 0.7068 (pt0) REVERT: A 1690 ILE cc_start: 0.7333 (pt) cc_final: 0.7103 (tp) REVERT: A 1699 TYR cc_start: 0.6723 (m-80) cc_final: 0.6190 (m-80) REVERT: A 1728 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7382 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: A 1742 TRP cc_start: 0.7759 (m-90) cc_final: 0.7501 (m-90) REVERT: A 1811 TRP cc_start: 0.7644 (m100) cc_final: 0.6879 (m-10) REVERT: A 1838 ASP cc_start: 0.7547 (p0) cc_final: 0.7126 (p0) REVERT: A 1947 MET cc_start: 0.4188 (OUTLIER) cc_final: 0.3627 (mtm) REVERT: A 1973 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7482 (tpp-160) REVERT: A 1974 ILE cc_start: 0.8194 (mt) cc_final: 0.7951 (mt) REVERT: A 2001 LEU cc_start: 0.8094 (mp) cc_final: 0.7894 (tp) REVERT: A 2064 TYR cc_start: 0.8072 (t80) cc_final: 0.7664 (t80) REVERT: A 2108 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5803 (tp30) REVERT: A 2192 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5972 (tp30) REVERT: A 2264 LEU cc_start: 0.6182 (mp) cc_final: 0.4580 (pp) REVERT: A 2289 LYS cc_start: 0.7580 (mptt) cc_final: 0.7317 (mptt) REVERT: A 2300 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7863 (mm) REVERT: A 2371 PRO cc_start: 0.7484 (Cg_endo) cc_final: 0.7230 (Cg_exo) REVERT: A 2420 GLN cc_start: 0.5864 (tt0) cc_final: 0.5639 (tt0) REVERT: A 2436 LEU cc_start: 0.7380 (mm) cc_final: 0.7173 (mm) REVERT: A 2459 MET cc_start: 0.6178 (pmm) cc_final: 0.5457 (pmm) REVERT: A 2470 MET cc_start: 0.7281 (ppp) cc_final: 0.7032 (tmm) REVERT: A 2498 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7591 (pp) REVERT: A 2500 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.3317 (pt) outliers start: 69 outliers final: 51 residues processed: 351 average time/residue: 0.1243 time to fit residues: 64.3888 Evaluate side-chains 360 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 295 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2192 GLU Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Chi-restraints excluded: chain A residue 2500 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 192 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1684 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.219496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.180727 restraints weight = 31352.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186543 restraints weight = 18856.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.190646 restraints weight = 12875.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.193410 restraints weight = 9619.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.195455 restraints weight = 7733.133| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16224 Z= 0.139 Angle : 0.703 17.213 21947 Z= 0.344 Chirality : 0.045 0.193 2509 Planarity : 0.005 0.113 2788 Dihedral : 5.314 55.329 2175 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.11 % Favored : 92.78 % Rotamer: Outliers : 3.74 % Allowed : 23.29 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1968 helix: 0.60 (0.19), residues: 772 sheet: -2.10 (0.31), residues: 273 loop : -1.91 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.018 0.002 TYR A1747 PHE 0.026 0.001 PHE A1908 TRP 0.036 0.002 TRP C 233 HIS 0.005 0.001 HIS A1972 Details of bonding type rmsd covalent geometry : bond 0.00307 (16223) covalent geometry : angle 0.70284 (21947) hydrogen bonds : bond 0.03845 ( 670) hydrogen bonds : angle 5.11816 ( 1908) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 305 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3055 (mmm) cc_final: 0.1369 (mmm) REVERT: C 23 MET cc_start: 0.6227 (ptm) cc_final: 0.5932 (ptm) REVERT: C 60 TRP cc_start: 0.8275 (t60) cc_final: 0.8008 (t-100) REVERT: C 61 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7804 (mtp85) REVERT: C 134 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7397 (mt) REVERT: C 166 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: C 223 MET cc_start: 0.7794 (tpp) cc_final: 0.7300 (mpp) REVERT: B 28 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7489 (ttpt) REVERT: B 51 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7746 (t160) REVERT: B 122 PHE cc_start: 0.7880 (t80) cc_final: 0.6864 (t80) REVERT: B 126 MET cc_start: 0.7450 (mtm) cc_final: 0.6799 (mtm) REVERT: B 132 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.6651 (ttp-110) REVERT: B 165 MET cc_start: 0.6991 (mmt) cc_final: 0.6489 (mmt) REVERT: B 217 LYS cc_start: 0.6691 (pttm) cc_final: 0.6491 (pttm) REVERT: B 223 MET cc_start: 0.8333 (ttt) cc_final: 0.8131 (ttt) REVERT: A 986 SER cc_start: 0.6979 (OUTLIER) cc_final: 0.6703 (m) REVERT: A 1014 GLU cc_start: 0.6995 (mp0) cc_final: 0.6139 (mt-10) REVERT: A 1042 LEU cc_start: 0.6727 (pt) cc_final: 0.6451 (pt) REVERT: A 1068 ASN cc_start: 0.8138 (t0) cc_final: 0.7533 (t0) REVERT: A 1148 PHE cc_start: 0.6479 (t80) cc_final: 0.5718 (m-80) REVERT: A 1180 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5540 (tp) REVERT: A 1244 TRP cc_start: 0.5976 (m-10) cc_final: 0.5425 (m-90) REVERT: A 1256 LYS cc_start: 0.7559 (mmmm) cc_final: 0.7243 (mtmt) REVERT: A 1268 GLU cc_start: 0.7740 (pm20) cc_final: 0.7317 (pm20) REVERT: A 1269 ASN cc_start: 0.6318 (OUTLIER) cc_final: 0.5857 (t160) REVERT: A 1320 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7212 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.5727 (tpt170) REVERT: A 1338 MET cc_start: 0.6274 (mtm) cc_final: 0.6045 (mtm) REVERT: A 1371 ILE cc_start: 0.7277 (pt) cc_final: 0.7001 (mp) REVERT: A 1407 HIS cc_start: 0.7518 (m-70) cc_final: 0.7125 (m-70) REVERT: A 1412 ARG cc_start: 0.6796 (ptp-110) cc_final: 0.6586 (ptp-110) REVERT: A 1432 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7508 (mmtt) REVERT: A 1439 LYS cc_start: 0.7524 (tppt) cc_final: 0.7301 (tppt) REVERT: A 1581 VAL cc_start: 0.7696 (p) cc_final: 0.7252 (t) REVERT: A 1599 GLU cc_start: 0.7381 (pt0) cc_final: 0.7061 (pt0) REVERT: A 1646 MET cc_start: 0.7940 (ppp) cc_final: 0.7606 (ppp) REVERT: A 1651 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7491 (mmmt) REVERT: A 1690 ILE cc_start: 0.7365 (pt) cc_final: 0.7163 (tp) REVERT: A 1699 TYR cc_start: 0.6710 (m-80) cc_final: 0.6162 (m-80) REVERT: A 1728 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7432 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: A 1811 TRP cc_start: 0.7683 (m100) cc_final: 0.6885 (m-10) REVERT: A 1838 ASP cc_start: 0.7569 (p0) cc_final: 0.7182 (p0) REVERT: A 1947 MET cc_start: 0.4141 (OUTLIER) cc_final: 0.3664 (mtm) REVERT: A 1952 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7597 (mmtt) REVERT: A 1973 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7795 (tpp-160) REVERT: A 1974 ILE cc_start: 0.8313 (mt) cc_final: 0.8071 (mt) REVERT: A 2064 TYR cc_start: 0.8091 (t80) cc_final: 0.7674 (t80) REVERT: A 2108 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5849 (tp30) REVERT: A 2264 LEU cc_start: 0.6311 (mp) cc_final: 0.4623 (pp) REVERT: A 2289 LYS cc_start: 0.7615 (mptt) cc_final: 0.7297 (mptt) REVERT: A 2300 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7877 (mm) REVERT: A 2371 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7206 (Cg_exo) REVERT: A 2420 GLN cc_start: 0.6071 (tt0) cc_final: 0.5646 (tt0) REVERT: A 2459 MET cc_start: 0.6185 (pmm) cc_final: 0.5056 (pmm) REVERT: A 2498 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7794 (pp) REVERT: A 2514 ARG cc_start: 0.6228 (tpt170) cc_final: 0.5928 (tpt170) outliers start: 66 outliers final: 52 residues processed: 346 average time/residue: 0.1225 time to fit residues: 62.2477 Evaluate side-chains 362 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1379 GLN Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2343 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 12 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 160 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.219651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180506 restraints weight = 31290.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.187956 restraints weight = 19576.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.193692 restraints weight = 11933.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.194077 restraints weight = 8204.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.194413 restraints weight = 7922.818| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16224 Z= 0.135 Angle : 0.711 16.962 21947 Z= 0.346 Chirality : 0.045 0.219 2509 Planarity : 0.005 0.110 2788 Dihedral : 5.207 56.653 2173 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 3.91 % Allowed : 23.57 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 (0.19), residues: 1968 helix: 0.64 (0.19), residues: 771 sheet: -1.99 (0.31), residues: 266 loop : -1.93 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.017 0.001 TYR A1747 PHE 0.024 0.001 PHE A1908 TRP 0.037 0.002 TRP C 233 HIS 0.006 0.001 HIS A1972 Details of bonding type rmsd covalent geometry : bond 0.00297 (16223) covalent geometry : angle 0.71136 (21947) hydrogen bonds : bond 0.03754 ( 670) hydrogen bonds : angle 5.05543 ( 1908) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3096 (mmm) cc_final: 0.1681 (mmm) REVERT: C 23 MET cc_start: 0.6150 (ptm) cc_final: 0.5873 (ptm) REVERT: C 60 TRP cc_start: 0.8284 (t60) cc_final: 0.8017 (t-100) REVERT: C 61 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7805 (mtp85) REVERT: C 134 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7373 (mt) REVERT: C 166 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: C 223 MET cc_start: 0.7868 (tpp) cc_final: 0.7346 (mpp) REVERT: B 28 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7783 (mmmt) REVERT: B 51 ASN cc_start: 0.7984 (t0) cc_final: 0.7662 (t0) REVERT: B 122 PHE cc_start: 0.7913 (t80) cc_final: 0.6973 (t80) REVERT: B 126 MET cc_start: 0.7411 (mtm) cc_final: 0.6805 (mtm) REVERT: B 132 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.6931 (ttp-110) REVERT: B 217 LYS cc_start: 0.6840 (pttm) cc_final: 0.6588 (pttm) REVERT: B 223 MET cc_start: 0.8483 (ttt) cc_final: 0.8282 (ttt) REVERT: A 986 SER cc_start: 0.7049 (OUTLIER) cc_final: 0.6772 (m) REVERT: A 1014 GLU cc_start: 0.7022 (mp0) cc_final: 0.6187 (mt-10) REVERT: A 1042 LEU cc_start: 0.6694 (pt) cc_final: 0.6442 (pt) REVERT: A 1068 ASN cc_start: 0.8063 (t0) cc_final: 0.7470 (t0) REVERT: A 1130 GLU cc_start: 0.6856 (tp30) cc_final: 0.6584 (tp30) REVERT: A 1148 PHE cc_start: 0.6657 (t80) cc_final: 0.5857 (m-80) REVERT: A 1180 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5889 (tp) REVERT: A 1244 TRP cc_start: 0.5969 (m-10) cc_final: 0.5412 (m-90) REVERT: A 1256 LYS cc_start: 0.7480 (mmmm) cc_final: 0.7168 (mtmt) REVERT: A 1268 GLU cc_start: 0.7717 (pm20) cc_final: 0.7301 (pm20) REVERT: A 1269 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.5810 (t160) REVERT: A 1320 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7241 (mmm-85) REVERT: A 1334 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5699 (tpt170) REVERT: A 1371 ILE cc_start: 0.7211 (pt) cc_final: 0.6926 (mp) REVERT: A 1407 HIS cc_start: 0.7464 (m-70) cc_final: 0.7054 (m-70) REVERT: A 1425 GLN cc_start: 0.7638 (tp40) cc_final: 0.7419 (mm-40) REVERT: A 1432 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7477 (mmtt) REVERT: A 1439 LYS cc_start: 0.7474 (tppt) cc_final: 0.7260 (tppt) REVERT: A 1581 VAL cc_start: 0.7686 (p) cc_final: 0.7315 (t) REVERT: A 1599 GLU cc_start: 0.7360 (pt0) cc_final: 0.7054 (pt0) REVERT: A 1699 TYR cc_start: 0.6696 (m-80) cc_final: 0.6185 (m-80) REVERT: A 1728 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7432 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7530 (mtm-85) REVERT: A 1733 TYR cc_start: 0.7282 (m-80) cc_final: 0.6878 (m-80) REVERT: A 1811 TRP cc_start: 0.7629 (m100) cc_final: 0.7334 (m100) REVERT: A 1826 LEU cc_start: 0.7260 (mt) cc_final: 0.6378 (mt) REVERT: A 1838 ASP cc_start: 0.7558 (p0) cc_final: 0.7222 (p0) REVERT: A 1947 MET cc_start: 0.3904 (OUTLIER) cc_final: 0.3461 (mtm) REVERT: A 1952 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7552 (mmtt) REVERT: A 1973 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7686 (tpp-160) REVERT: A 1974 ILE cc_start: 0.8337 (mt) cc_final: 0.8089 (mt) REVERT: A 2064 TYR cc_start: 0.8170 (t80) cc_final: 0.7777 (t80) REVERT: A 2108 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5803 (tp30) REVERT: A 2137 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.5069 (tt) REVERT: A 2264 LEU cc_start: 0.6373 (mp) cc_final: 0.4721 (pp) REVERT: A 2289 LYS cc_start: 0.7666 (mptt) cc_final: 0.7349 (mptt) REVERT: A 2300 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 2371 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.7197 (Cg_exo) REVERT: A 2417 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6488 (mm) REVERT: A 2420 GLN cc_start: 0.5687 (tt0) cc_final: 0.5292 (tt0) REVERT: A 2436 LEU cc_start: 0.7310 (mm) cc_final: 0.7048 (mm) REVERT: A 2459 MET cc_start: 0.6431 (pmm) cc_final: 0.5365 (pmm) REVERT: A 2498 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7760 (pp) outliers start: 69 outliers final: 51 residues processed: 341 average time/residue: 0.1224 time to fit residues: 61.1590 Evaluate side-chains 367 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1379 GLN Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.218019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178609 restraints weight = 31325.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.184460 restraints weight = 18834.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.188604 restraints weight = 12901.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.191418 restraints weight = 9687.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.193442 restraints weight = 7784.097| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16224 Z= 0.162 Angle : 0.729 17.080 21947 Z= 0.357 Chirality : 0.046 0.241 2509 Planarity : 0.005 0.107 2788 Dihedral : 5.333 55.620 2173 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.38 % Rotamer: Outliers : 3.80 % Allowed : 23.80 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1968 helix: 0.62 (0.19), residues: 762 sheet: -2.12 (0.31), residues: 267 loop : -1.91 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1386 TYR 0.022 0.002 TYR A1332 PHE 0.022 0.002 PHE A1908 TRP 0.038 0.002 TRP C 233 HIS 0.005 0.001 HIS A 932 Details of bonding type rmsd covalent geometry : bond 0.00357 (16223) covalent geometry : angle 0.72920 (21947) hydrogen bonds : bond 0.03906 ( 670) hydrogen bonds : angle 5.17765 ( 1908) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 296 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3051 (mmm) cc_final: 0.1544 (mmm) REVERT: C 23 MET cc_start: 0.6130 (ptm) cc_final: 0.5864 (ptm) REVERT: C 60 TRP cc_start: 0.8311 (t60) cc_final: 0.8077 (t-100) REVERT: C 61 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7860 (mtp85) REVERT: C 134 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7365 (mt) REVERT: C 166 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: C 223 MET cc_start: 0.7793 (tpp) cc_final: 0.7301 (mpp) REVERT: B 28 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7810 (mmmt) REVERT: B 51 ASN cc_start: 0.8115 (t0) cc_final: 0.7825 (t0) REVERT: B 126 MET cc_start: 0.7456 (mtm) cc_final: 0.6778 (mtm) REVERT: B 132 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6595 (ttp-110) REVERT: B 217 LYS cc_start: 0.6937 (pttm) cc_final: 0.6664 (pttm) REVERT: B 223 MET cc_start: 0.8390 (ttt) cc_final: 0.8182 (ttt) REVERT: A 986 SER cc_start: 0.7132 (p) cc_final: 0.6874 (m) REVERT: A 1014 GLU cc_start: 0.7096 (mp0) cc_final: 0.6204 (mt-10) REVERT: A 1171 LEU cc_start: 0.2781 (OUTLIER) cc_final: 0.2213 (tp) REVERT: A 1180 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5931 (tp) REVERT: A 1244 TRP cc_start: 0.5937 (m-10) cc_final: 0.5337 (m-90) REVERT: A 1256 LYS cc_start: 0.7486 (mmmm) cc_final: 0.7174 (mtmt) REVERT: A 1268 GLU cc_start: 0.7692 (pm20) cc_final: 0.7255 (pm20) REVERT: A 1269 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.5896 (t160) REVERT: A 1334 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5719 (tpt170) REVERT: A 1338 MET cc_start: 0.6226 (mtm) cc_final: 0.5997 (mtm) REVERT: A 1371 ILE cc_start: 0.7426 (pt) cc_final: 0.7127 (mp) REVERT: A 1432 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7534 (mmtt) REVERT: A 1599 GLU cc_start: 0.7401 (pt0) cc_final: 0.7136 (pt0) REVERT: A 1699 TYR cc_start: 0.6709 (m-80) cc_final: 0.6214 (m-80) REVERT: A 1728 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7401 (ptt-90) REVERT: A 1731 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7503 (mtm-85) REVERT: A 1733 TYR cc_start: 0.7377 (m-80) cc_final: 0.6937 (m-80) REVERT: A 1811 TRP cc_start: 0.7662 (m100) cc_final: 0.7283 (m100) REVERT: A 1947 MET cc_start: 0.3978 (OUTLIER) cc_final: 0.3602 (mtm) REVERT: A 1952 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7496 (mmtt) REVERT: A 1956 ASP cc_start: 0.6840 (p0) cc_final: 0.6338 (t70) REVERT: A 1973 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7834 (tpp-160) REVERT: A 1974 ILE cc_start: 0.8525 (mt) cc_final: 0.8200 (mt) REVERT: A 2064 TYR cc_start: 0.8040 (t80) cc_final: 0.7696 (t80) REVERT: A 2108 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6021 (tp30) REVERT: A 2264 LEU cc_start: 0.6688 (mp) cc_final: 0.4998 (pp) REVERT: A 2289 LYS cc_start: 0.7862 (mptt) cc_final: 0.7527 (mptt) REVERT: A 2300 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 2367 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7394 (mmtt) REVERT: A 2371 PRO cc_start: 0.7558 (Cg_endo) cc_final: 0.7248 (Cg_exo) REVERT: A 2420 GLN cc_start: 0.5933 (tt0) cc_final: 0.5638 (tt0) REVERT: A 2436 LEU cc_start: 0.7346 (mm) cc_final: 0.7049 (mm) REVERT: A 2459 MET cc_start: 0.6320 (pmm) cc_final: 0.5685 (pmm) REVERT: A 2472 VAL cc_start: 0.7769 (t) cc_final: 0.7398 (t) REVERT: A 2498 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7913 (pp) outliers start: 67 outliers final: 48 residues processed: 339 average time/residue: 0.1194 time to fit residues: 59.7172 Evaluate side-chains 349 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 49 TYR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1246 ARG Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1334 ARG Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1349 THR Chi-restraints excluded: chain A residue 1379 GLN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1434 TRP Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1656 PHE Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1758 HIS Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2343 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2496 TRP Chi-restraints excluded: chain A residue 2498 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 145 optimal weight: 0.4980 chunk 187 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 51 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.218756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180061 restraints weight = 31171.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.185789 restraints weight = 18630.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189887 restraints weight = 12777.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.192720 restraints weight = 9590.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.194691 restraints weight = 7692.559| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16224 Z= 0.139 Angle : 0.723 17.085 21947 Z= 0.352 Chirality : 0.046 0.246 2509 Planarity : 0.005 0.105 2788 Dihedral : 5.264 56.413 2173 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.11 % Favored : 92.78 % Rotamer: Outliers : 3.34 % Allowed : 24.36 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -1.33 (0.19), residues: 1968 helix: 0.70 (0.19), residues: 755 sheet: -1.93 (0.32), residues: 260 loop : -1.91 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.016 0.001 TYR A1332 PHE 0.022 0.002 PHE A1908 TRP 0.042 0.002 TRP A2496 HIS 0.006 0.001 HIS A1972 Details of bonding type rmsd covalent geometry : bond 0.00307 (16223) covalent geometry : angle 0.72295 (21947) hydrogen bonds : bond 0.03810 ( 670) hydrogen bonds : angle 5.10472 ( 1908) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.85 seconds wall clock time: 49 minutes 4.28 seconds (2944.28 seconds total)