Starting phenix.real_space_refine on Sun May 18 11:57:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096.map" model { file = "/net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yad_39096/05_2025/8yad_39096_neut.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 10108 2.51 5 N 3280 2.21 5 O 3258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16653 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 7286 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 1174} Link IDs: {'PTRANS': 46, 'TRANS': 1349} Chain breaks: 8 Unresolved chain link angles: 42 Unresolved non-hydrogen bonds: 4159 Unresolved non-hydrogen angles: 5308 Unresolved non-hydrogen dihedrals: 3459 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 77, 'HIS:plan': 47, 'TYR:plan': 41, 'ASN:plan1': 50, 'TRP:plan': 14, 'ASP:plan': 62, 'PHE:plan': 46, 'GLU:plan': 107, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 2231 Chain: "C" Number of atoms: 9367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1811, 9367 Classifications: {'peptide': 1811} Incomplete info: {'truncation_to_alanine': 1494} Link IDs: {'PTRANS': 74, 'TRANS': 1736} Chain breaks: 20 Unresolved chain link angles: 60 Unresolved non-hydrogen bonds: 5251 Unresolved non-hydrogen angles: 6725 Unresolved non-hydrogen dihedrals: 4351 Unresolved non-hydrogen chiralities: 502 Planarities with less than four sites: {'GLN:plan1': 104, 'ASP:plan': 77, 'TYR:plan': 47, 'ASN:plan1': 47, 'TRP:plan': 23, 'HIS:plan': 57, 'PHE:plan': 49, 'GLU:plan': 128, 'ARG:plan': 88} Unresolved non-hydrogen planarities: 2855 Time building chain proxies: 18.41, per 1000 atoms: 1.11 Number of scatterers: 16653 At special positions: 0 Unit cell: (115.6, 244.8, 340, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 3258 8.00 N 3280 7.00 C 10108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 3.0 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6184 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 0 sheets defined 73.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'B' and resid 932 through 947 removed outlier: 3.965A pdb=" N ASN B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 956 removed outlier: 4.574A pdb=" N LEU B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 966 Processing helix chain 'B' and resid 989 through 999 Processing helix chain 'B' and resid 1002 through 1012 Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.987A pdb=" N GLU B1023 " --> pdb=" O PRO B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1031 Processing helix chain 'B' and resid 1031 through 1046 Processing helix chain 'B' and resid 1049 through 1065 Processing helix chain 'B' and resid 1071 through 1078 removed outlier: 3.629A pdb=" N MET B1075 " --> pdb=" O SER B1071 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B1078 " --> pdb=" O SER B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1089 removed outlier: 3.563A pdb=" N ALA B1084 " --> pdb=" O HIS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1101 Processing helix chain 'B' and resid 1106 through 1110 removed outlier: 3.679A pdb=" N LYS B1110 " --> pdb=" O CYS B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1119 Processing helix chain 'B' and resid 1123 through 1131 Processing helix chain 'B' and resid 1145 through 1152 removed outlier: 3.713A pdb=" N SER B1152 " --> pdb=" O HIS B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1161 removed outlier: 3.589A pdb=" N ARG B1160 " --> pdb=" O ASP B1157 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B1161 " --> pdb=" O PRO B1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1157 through 1161' Processing helix chain 'B' and resid 1184 through 1191 Processing helix chain 'B' and resid 1199 through 1206 Processing helix chain 'B' and resid 1207 through 1220 Processing helix chain 'B' and resid 1225 through 1243 Processing helix chain 'B' and resid 1247 through 1262 removed outlier: 3.827A pdb=" N GLY B1251 " --> pdb=" O ILE B1247 " (cutoff:3.500A) Processing helix chain 'B' and resid 1266 through 1278 Processing helix chain 'B' and resid 1279 through 1284 Processing helix chain 'B' and resid 1289 through 1306 Processing helix chain 'B' and resid 1308 through 1330 Processing helix chain 'B' and resid 1336 through 1353 removed outlier: 5.138A pdb=" N LEU B1345 " --> pdb=" O SER B1341 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL B1346 " --> pdb=" O GLN B1342 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B1347 " --> pdb=" O TRP B1343 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B1350 " --> pdb=" O VAL B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1367 removed outlier: 4.107A pdb=" N GLU B1364 " --> pdb=" O SER B1360 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1375 removed outlier: 3.622A pdb=" N PHE B1374 " --> pdb=" O ASP B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1380 Processing helix chain 'B' and resid 1384 through 1392 removed outlier: 3.774A pdb=" N VAL B1388 " --> pdb=" O HIS B1384 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B1389 " --> pdb=" O PRO B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1405 removed outlier: 3.642A pdb=" N LEU B1405 " --> pdb=" O ASP B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1440 through 1445 removed outlier: 3.571A pdb=" N LEU B1445 " --> pdb=" O LEU B1441 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1449 removed outlier: 3.750A pdb=" N SER B1449 " --> pdb=" O LEU B1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1446 through 1449' Processing helix chain 'B' and resid 1456 through 1465 removed outlier: 3.724A pdb=" N LYS B1464 " --> pdb=" O VAL B1460 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B1465 " --> pdb=" O GLU B1461 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1475 Processing helix chain 'B' and resid 1484 through 1492 removed outlier: 3.750A pdb=" N VAL B1488 " --> pdb=" O SER B1484 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1502 removed outlier: 3.535A pdb=" N ALA B1502 " --> pdb=" O VAL B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1503 through 1506 Processing helix chain 'B' and resid 1509 through 1513 removed outlier: 4.024A pdb=" N HIS B1513 " --> pdb=" O THR B1510 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1529 removed outlier: 3.854A pdb=" N VAL B1522 " --> pdb=" O GLU B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1535 through 1543 removed outlier: 5.215A pdb=" N GLN B1541 " --> pdb=" O ILE B1537 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B1542 " --> pdb=" O ARG B1538 " (cutoff:3.500A) Processing helix chain 'B' and resid 1548 through 1559 removed outlier: 4.644A pdb=" N TYR B1556 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B1557 " --> pdb=" O MET B1553 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B1558 " --> pdb=" O GLU B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1564 through 1583 removed outlier: 3.999A pdb=" N ALA B1568 " --> pdb=" O ASN B1564 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B1573 " --> pdb=" O GLU B1569 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B1574 " --> pdb=" O ALA B1570 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B1583 " --> pdb=" O LEU B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1596 through 1612 removed outlier: 4.525A pdb=" N CYS B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B1604 " --> pdb=" O ASP B1600 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1605 " --> pdb=" O GLN B1601 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B1607 " --> pdb=" O CYS B1603 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1627 removed outlier: 3.863A pdb=" N GLY B1620 " --> pdb=" O GLN B1616 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B1621 " --> pdb=" O TYR B1617 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B1622 " --> pdb=" O GLU B1618 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B1627 " --> pdb=" O LEU B1623 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1649 Processing helix chain 'B' and resid 1658 through 1663 Processing helix chain 'B' and resid 1667 through 1684 removed outlier: 5.127A pdb=" N SER B1675 " --> pdb=" O HIS B1671 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B1676 " --> pdb=" O GLU B1672 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B1683 " --> pdb=" O ARG B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1685 through 1697 removed outlier: 4.188A pdb=" N ALA B1689 " --> pdb=" O GLN B1685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B1690 " --> pdb=" O PHE B1686 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B1691 " --> pdb=" O ALA B1687 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1696 " --> pdb=" O VAL B1692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1700 through 1719 removed outlier: 4.313A pdb=" N VAL B1704 " --> pdb=" O VAL B1700 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B1705 " --> pdb=" O ASP B1701 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1742 removed outlier: 3.902A pdb=" N HIS B1735 " --> pdb=" O TRP B1731 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B1740 " --> pdb=" O GLU B1736 " (cutoff:3.500A) Processing helix chain 'B' and resid 1744 through 1759 removed outlier: 3.864A pdb=" N GLN B1755 " --> pdb=" O PHE B1751 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1784 removed outlier: 3.731A pdb=" N GLY B1780 " --> pdb=" O LEU B1776 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B1782 " --> pdb=" O LEU B1778 " (cutoff:3.500A) Processing helix chain 'B' and resid 1790 through 1812 removed outlier: 3.575A pdb=" N GLU B1796 " --> pdb=" O ASP B1792 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B1797 " --> pdb=" O LYS B1793 " (cutoff:3.500A) Processing helix chain 'B' and resid 1834 through 1842 Processing helix chain 'B' and resid 1847 through 1856 removed outlier: 6.710A pdb=" N SER B1852 " --> pdb=" O LEU B1849 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B1853 " --> pdb=" O ASN B1850 " (cutoff:3.500A) Processing helix chain 'B' and resid 1873 through 1889 removed outlier: 3.588A pdb=" N ARG B1884 " --> pdb=" O PHE B1880 " (cutoff:3.500A) Processing helix chain 'B' and resid 1890 through 1902 removed outlier: 3.550A pdb=" N SER B1895 " --> pdb=" O VAL B1891 " (cutoff:3.500A) Processing helix chain 'B' and resid 1905 through 1918 removed outlier: 3.738A pdb=" N ALA B1916 " --> pdb=" O LEU B1912 " (cutoff:3.500A) Processing helix chain 'B' and resid 1973 through 1980 removed outlier: 4.086A pdb=" N LEU B1977 " --> pdb=" O VAL B1973 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU B1980 " --> pdb=" O ASN B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1984 Processing helix chain 'B' and resid 1987 through 2005 removed outlier: 4.018A pdb=" N CYS B1991 " --> pdb=" O GLY B1987 " (cutoff:3.500A) Processing helix chain 'B' and resid 2007 through 2014 removed outlier: 3.838A pdb=" N GLN B2014 " --> pdb=" O ASP B2010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2015 through 2025 Processing helix chain 'B' and resid 2030 through 2043 removed outlier: 4.024A pdb=" N ARG B2034 " --> pdb=" O ASP B2030 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2065 Processing helix chain 'B' and resid 2078 through 2088 removed outlier: 4.167A pdb=" N THR B2082 " --> pdb=" O GLU B2078 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B2086 " --> pdb=" O THR B2082 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B2087 " --> pdb=" O PHE B2083 " (cutoff:3.500A) Processing helix chain 'B' and resid 2092 through 2104 removed outlier: 4.132A pdb=" N VAL B2096 " --> pdb=" O ASP B2092 " (cutoff:3.500A) Processing helix chain 'B' and resid 2105 through 2107 No H-bonds generated for 'chain 'B' and resid 2105 through 2107' Processing helix chain 'B' and resid 2112 through 2130 removed outlier: 3.603A pdb=" N GLU B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B2122 " --> pdb=" O LEU B2118 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS B2123 " --> pdb=" O LEU B2119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B2124 " --> pdb=" O ILE B2120 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU B2128 " --> pdb=" O HIS B2124 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B2129 " --> pdb=" O CYS B2125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2149 removed outlier: 3.554A pdb=" N HIS B2149 " --> pdb=" O LEU B2145 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2154 Processing helix chain 'B' and resid 2155 through 2165 Processing helix chain 'B' and resid 2166 through 2167 No H-bonds generated for 'chain 'B' and resid 2166 through 2167' Processing helix chain 'B' and resid 2168 through 2171 Processing helix chain 'B' and resid 2172 through 2182 removed outlier: 4.620A pdb=" N ASP B2177 " --> pdb=" O THR B2173 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B2178 " --> pdb=" O TYR B2174 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS B2180 " --> pdb=" O PHE B2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 2186 through 2190 Processing helix chain 'B' and resid 2197 through 2209 Processing helix chain 'B' and resid 2214 through 2221 Processing helix chain 'B' and resid 2228 through 2248 removed outlier: 3.724A pdb=" N ILE B2246 " --> pdb=" O GLN B2242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B2247 " --> pdb=" O LEU B2243 " (cutoff:3.500A) Processing helix chain 'B' and resid 2250 through 2256 removed outlier: 4.229A pdb=" N LYS B2256 " --> pdb=" O GLU B2252 " (cutoff:3.500A) Processing helix chain 'B' and resid 2257 through 2282 Processing helix chain 'B' and resid 2284 through 2307 Processing helix chain 'B' and resid 2317 through 2328 removed outlier: 4.215A pdb=" N MET B2322 " --> pdb=" O ARG B2318 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP B2323 " --> pdb=" O HIS B2319 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B2328 " --> pdb=" O CYS B2324 " (cutoff:3.500A) Processing helix chain 'B' and resid 2330 through 2342 removed outlier: 5.848A pdb=" N ILE B2336 " --> pdb=" O TYR B2332 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B2337 " --> pdb=" O GLN B2333 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B2338 " --> pdb=" O ALA B2334 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2355 removed outlier: 4.174A pdb=" N GLN B2353 " --> pdb=" O GLU B2349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B2354 " --> pdb=" O ILE B2350 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B2355 " --> pdb=" O LEU B2351 " (cutoff:3.500A) Processing helix chain 'B' and resid 2360 through 2371 Processing helix chain 'B' and resid 2374 through 2387 removed outlier: 4.267A pdb=" N SER B2382 " --> pdb=" O PHE B2378 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS B2383 " --> pdb=" O GLU B2379 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B2384 " --> pdb=" O GLU B2380 " (cutoff:3.500A) Processing helix chain 'B' and resid 2391 through 2399 removed outlier: 4.159A pdb=" N GLU B2396 " --> pdb=" O ASP B2392 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2402 No H-bonds generated for 'chain 'B' and resid 2400 through 2402' Processing helix chain 'B' and resid 2408 through 2419 removed outlier: 3.594A pdb=" N TYR B2416 " --> pdb=" O TYR B2412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2420 through 2428 Processing helix chain 'B' and resid 2430 through 2435 Processing helix chain 'B' and resid 2436 through 2441 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.716A pdb=" N SER C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.251A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 205 removed outlier: 3.987A pdb=" N GLN C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 233 through 248 removed outlier: 4.129A pdb=" N HIS C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 268 through 286 Processing helix chain 'C' and resid 302 through 312 removed outlier: 4.371A pdb=" N ALA C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 333 through 349 removed outlier: 3.514A pdb=" N GLN C 337 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 365 through 375 removed outlier: 4.517A pdb=" N THR C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 399 through 423 Processing helix chain 'C' and resid 428 through 438 Processing helix chain 'C' and resid 443 through 451 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 488 through 517 removed outlier: 3.629A pdb=" N LYS C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR C 506 " --> pdb=" O CYS C 502 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 508 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS C 516 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.746A pdb=" N SER C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 583 Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 683 through 701 removed outlier: 4.417A pdb=" N LEU C 689 " --> pdb=" O ILE C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 735 removed outlier: 3.789A pdb=" N GLU C 735 " --> pdb=" O LYS C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 750 Processing helix chain 'C' and resid 827 through 831 removed outlier: 3.692A pdb=" N PHE C 830 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 831 " --> pdb=" O MET C 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 827 through 831' Processing helix chain 'C' and resid 832 through 843 removed outlier: 3.925A pdb=" N ARG C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.896A pdb=" N ALA C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 892 removed outlier: 3.783A pdb=" N GLN C 874 " --> pdb=" O MET C 870 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 875 " --> pdb=" O GLU C 871 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 934 removed outlier: 3.683A pdb=" N LEU C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 952 removed outlier: 3.969A pdb=" N ILE C 949 " --> pdb=" O GLU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 965 Processing helix chain 'C' and resid 968 through 973 removed outlier: 3.762A pdb=" N ALA C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 982 removed outlier: 3.863A pdb=" N GLN C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS C 982 " --> pdb=" O ALA C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1007 removed outlier: 4.032A pdb=" N ALA C 995 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1042 Processing helix chain 'C' and resid 1075 through 1099 removed outlier: 3.777A pdb=" N SER C1093 " --> pdb=" O GLN C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1115 Processing helix chain 'C' and resid 1118 through 1124 removed outlier: 3.644A pdb=" N ALA C1124 " --> pdb=" O PRO C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1141 removed outlier: 3.631A pdb=" N GLN C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C1133 " --> pdb=" O ILE C1129 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY C1139 " --> pdb=" O GLN C1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1169 removed outlier: 3.654A pdb=" N LEU C1162 " --> pdb=" O TYR C1158 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C1163 " --> pdb=" O CYS C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1190 removed outlier: 3.707A pdb=" N GLN C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN C1190 " --> pdb=" O LEU C1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1186 through 1190' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.692A pdb=" N LEU C1195 " --> pdb=" O SER C1191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C1196 " --> pdb=" O SER C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1214 Processing helix chain 'C' and resid 1215 through 1218 Processing helix chain 'C' and resid 1224 through 1232 removed outlier: 4.056A pdb=" N SER C1229 " --> pdb=" O GLN C1225 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C1230 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS C1231 " --> pdb=" O ILE C1227 " (cutoff:3.500A) Processing helix chain 'C' and resid 1245 through 1262 removed outlier: 4.155A pdb=" N THR C1251 " --> pdb=" O SER C1247 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C1254 " --> pdb=" O LEU C1250 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1259 " --> pdb=" O THR C1255 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS C1260 " --> pdb=" O LEU C1256 " (cutoff:3.500A) Processing helix chain 'C' and resid 1304 through 1311 Processing helix chain 'C' and resid 1313 through 1321 removed outlier: 4.328A pdb=" N ALA C1319 " --> pdb=" O LEU C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1350 through 1362 removed outlier: 3.528A pdb=" N ARG C1358 " --> pdb=" O ARG C1354 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1379 removed outlier: 3.511A pdb=" N ARG C1378 " --> pdb=" O TRP C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1408 through 1415 removed outlier: 3.979A pdb=" N VAL C1412 " --> pdb=" O ILE C1408 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1421 Processing helix chain 'C' and resid 1442 through 1454 removed outlier: 4.570A pdb=" N ILE C1446 " --> pdb=" O ASP C1442 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C1450 " --> pdb=" O ILE C1446 " (cutoff:3.500A) Processing helix chain 'C' and resid 1455 through 1458 removed outlier: 4.387A pdb=" N ASP C1458 " --> pdb=" O VAL C1455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1455 through 1458' Processing helix chain 'C' and resid 1460 through 1465 removed outlier: 3.511A pdb=" N GLN C1463 " --> pdb=" O GLU C1460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C1464 " --> pdb=" O GLY C1461 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C1465 " --> pdb=" O TRP C1462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1460 through 1465' Processing helix chain 'C' and resid 1470 through 1481 Processing helix chain 'C' and resid 1489 through 1500 removed outlier: 3.895A pdb=" N TYR C1496 " --> pdb=" O GLU C1492 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS C1497 " --> pdb=" O ILE C1493 " (cutoff:3.500A) Processing helix chain 'C' and resid 1504 through 1525 removed outlier: 3.700A pdb=" N CYS C1509 " --> pdb=" O GLU C1505 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU C1510 " --> pdb=" O GLY C1506 " (cutoff:3.500A) Processing helix chain 'C' and resid 1535 through 1545 Processing helix chain 'C' and resid 1548 through 1556 Processing helix chain 'C' and resid 1559 through 1569 removed outlier: 3.652A pdb=" N CYS C1563 " --> pdb=" O GLU C1559 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C1565 " --> pdb=" O GLU C1561 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1591 removed outlier: 4.479A pdb=" N SER C1579 " --> pdb=" O GLU C1575 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C1583 " --> pdb=" O SER C1579 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS C1584 " --> pdb=" O LEU C1580 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C1585 " --> pdb=" O HIS C1581 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C1591 " --> pdb=" O HIS C1587 " (cutoff:3.500A) Processing helix chain 'C' and resid 1593 through 1603 Processing helix chain 'C' and resid 1606 through 1618 removed outlier: 3.596A pdb=" N LEU C1611 " --> pdb=" O PRO C1607 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C1618 " --> pdb=" O THR C1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 1623 through 1637 removed outlier: 4.624A pdb=" N ASN C1632 " --> pdb=" O HIS C1628 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS C1637 " --> pdb=" O TYR C1633 " (cutoff:3.500A) Processing helix chain 'C' and resid 1645 through 1655 removed outlier: 3.627A pdb=" N LEU C1653 " --> pdb=" O GLU C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1655 through 1661 Processing helix chain 'C' and resid 1667 through 1672 removed outlier: 3.872A pdb=" N TYR C1671 " --> pdb=" O HIS C1667 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C1672 " --> pdb=" O ARG C1668 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1667 through 1672' Processing helix chain 'C' and resid 1677 through 1688 removed outlier: 3.523A pdb=" N GLU C1683 " --> pdb=" O LEU C1679 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C1688 " --> pdb=" O GLN C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1705 removed outlier: 3.756A pdb=" N ALA C1694 " --> pdb=" O LYS C1690 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C1695 " --> pdb=" O VAL C1691 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL C1696 " --> pdb=" O ASP C1692 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C1697 " --> pdb=" O TRP C1693 " (cutoff:3.500A) Processing helix chain 'C' and resid 1713 through 1729 Processing helix chain 'C' and resid 1916 through 1924 Processing helix chain 'C' and resid 1933 through 1942 removed outlier: 3.941A pdb=" N CYS C1937 " --> pdb=" O SER C1933 " (cutoff:3.500A) Processing helix chain 'C' and resid 1946 through 1963 removed outlier: 4.064A pdb=" N LYS C1963 " --> pdb=" O CYS C1959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1964 through 1967 Processing helix chain 'C' and resid 1971 through 1992 removed outlier: 4.118A pdb=" N LYS C1992 " --> pdb=" O MET C1988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1995 through 2017 Processing helix chain 'C' and resid 2025 through 2030 Processing helix chain 'C' and resid 2032 through 2045 removed outlier: 3.939A pdb=" N THR C2036 " --> pdb=" O PRO C2032 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C2043 " --> pdb=" O ARG C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2047 through 2059 Processing helix chain 'C' and resid 2062 through 2075 Processing helix chain 'C' and resid 2078 through 2088 removed outlier: 3.781A pdb=" N ARG C2088 " --> pdb=" O GLU C2084 " (cutoff:3.500A) Processing helix chain 'C' and resid 2103 through 2115 removed outlier: 4.037A pdb=" N GLU C2111 " --> pdb=" O GLN C2107 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Processing helix chain 'C' and resid 2143 through 2145 No H-bonds generated for 'chain 'C' and resid 2143 through 2145' Processing helix chain 'C' and resid 2152 through 2157 Processing helix chain 'C' and resid 2157 through 2171 Processing helix chain 'C' and resid 2172 through 2183 removed outlier: 4.452A pdb=" N SER C2178 " --> pdb=" O LEU C2174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS C2183 " --> pdb=" O PHE C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2186 through 2196 Processing helix chain 'C' and resid 2201 through 2214 removed outlier: 4.180A pdb=" N ILE C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) Proline residue: C2210 - end of helix Processing helix chain 'C' and resid 2217 through 2228 removed outlier: 3.784A pdb=" N ASN C2222 " --> pdb=" O HIS C2218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C2228 " --> pdb=" O LEU C2224 " (cutoff:3.500A) Processing helix chain 'C' and resid 2236 through 2247 removed outlier: 3.921A pdb=" N ALA C2241 " --> pdb=" O TYR C2237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2261 Processing helix chain 'C' and resid 2264 through 2276 removed outlier: 4.538A pdb=" N CYS C2271 " --> pdb=" O ALA C2267 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C2272 " --> pdb=" O ALA C2268 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C2273 " --> pdb=" O MET C2269 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C2276 " --> pdb=" O ILE C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2284 through 2289 removed outlier: 4.096A pdb=" N LYS C2288 " --> pdb=" O GLU C2284 " (cutoff:3.500A) Processing helix chain 'C' and resid 2290 through 2309 Processing helix chain 'C' and resid 2324 through 2336 removed outlier: 4.437A pdb=" N ASN C2332 " --> pdb=" O SER C2328 " (cutoff:3.500A) Processing helix chain 'C' and resid 2337 through 2350 removed outlier: 4.437A pdb=" N CYS C2347 " --> pdb=" O PHE C2343 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C2350 " --> pdb=" O ARG C2346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2366 through 2381 removed outlier: 4.244A pdb=" N VAL C2373 " --> pdb=" O MET C2369 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA C2374 " --> pdb=" O LYS C2370 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS C2375 " --> pdb=" O MET C2371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C2376 " --> pdb=" O ASP C2372 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C2381 " --> pdb=" O VAL C2377 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2399 removed outlier: 5.734A pdb=" N GLY C2389 " --> pdb=" O GLU C2385 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE C2390 " --> pdb=" O ASP C2386 " (cutoff:3.500A) Processing helix chain 'C' and resid 2401 through 2416 removed outlier: 3.619A pdb=" N THR C2405 " --> pdb=" O ASP C2401 " (cutoff:3.500A) Processing helix chain 'C' and resid 2420 through 2430 removed outlier: 4.224A pdb=" N GLN C2424 " --> pdb=" O SER C2420 " (cutoff:3.500A) Processing helix chain 'C' and resid 2436 through 2440 removed outlier: 4.074A pdb=" N GLY C2440 " --> pdb=" O LYS C2437 " (cutoff:3.500A) Processing helix chain 'C' and resid 2441 through 2448 1377 hydrogen bonds defined for protein. 4074 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: 6.97 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4560 1.33 - 1.45: 2401 1.45 - 1.57: 9724 1.57 - 1.69: 1 1.69 - 1.81: 8 Bond restraints: 16694 Sorted by residual: bond pdb=" CA CYS C1453 " pdb=" C CYS C1453 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.34e-02 5.57e+03 3.74e+01 bond pdb=" C TRP C1485 " pdb=" N PRO C1486 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.20e-02 6.94e+03 9.44e+00 bond pdb=" CB PRO C1932 " pdb=" CG PRO C1932 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.10e+00 bond pdb=" CA ALA C1395 " pdb=" C ALA C1395 " ideal model delta sigma weight residual 1.523 1.482 0.040 1.41e-02 5.03e+03 8.17e+00 bond pdb=" CA LYS B1534 " pdb=" C LYS B1534 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.72e-02 3.38e+03 6.54e+00 ... (remaining 16689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 22937 2.47 - 4.93: 226 4.93 - 7.40: 33 7.40 - 9.87: 4 9.87 - 12.34: 2 Bond angle restraints: 23202 Sorted by residual: angle pdb=" CA PRO C1932 " pdb=" N PRO C1932 " pdb=" CD PRO C1932 " ideal model delta sigma weight residual 112.00 99.66 12.34 1.40e+00 5.10e-01 7.76e+01 angle pdb=" N VAL C 214 " pdb=" CA VAL C 214 " pdb=" C VAL C 214 " ideal model delta sigma weight residual 113.00 106.40 6.60 1.30e+00 5.92e-01 2.57e+01 angle pdb=" N ILE B1469 " pdb=" CA ILE B1469 " pdb=" C ILE B1469 " ideal model delta sigma weight residual 112.43 107.87 4.56 9.20e-01 1.18e+00 2.45e+01 angle pdb=" N ALA C1368 " pdb=" CA ALA C1368 " pdb=" C ALA C1368 " ideal model delta sigma weight residual 113.18 106.72 6.46 1.33e+00 5.65e-01 2.36e+01 angle pdb=" C GLU C 285 " pdb=" N LYS C 286 " pdb=" CA LYS C 286 " ideal model delta sigma weight residual 121.80 109.97 11.83 2.44e+00 1.68e-01 2.35e+01 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 9598 16.03 - 32.06: 172 32.06 - 48.10: 28 48.10 - 64.13: 6 64.13 - 80.16: 2 Dihedral angle restraints: 9806 sinusoidal: 436 harmonic: 9370 Sorted by residual: dihedral pdb=" CA LEU B1372 " pdb=" C LEU B1372 " pdb=" N GLN B1373 " pdb=" CA GLN B1373 " ideal model delta harmonic sigma weight residual 180.00 146.19 33.81 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA ARG C1438 " pdb=" C ARG C1438 " pdb=" N ASP C1439 " pdb=" CA ASP C1439 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE C1061 " pdb=" C ILE C1061 " pdb=" N THR C1062 " pdb=" CA THR C1062 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2232 0.040 - 0.080: 764 0.080 - 0.120: 149 0.120 - 0.160: 18 0.160 - 0.200: 10 Chirality restraints: 3173 Sorted by residual: chirality pdb=" CA PRO C 253 " pdb=" N PRO C 253 " pdb=" C PRO C 253 " pdb=" CB PRO C 253 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA PRO B1548 " pdb=" N PRO B1548 " pdb=" C PRO B1548 " pdb=" CB PRO B1548 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA TRP B1455 " pdb=" N TRP B1455 " pdb=" C TRP B1455 " pdb=" CB TRP B1455 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 3170 not shown) Planarity restraints: 3269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1931 " -0.084 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO C1932 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO C1932 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C1932 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1524 " -0.038 2.00e-02 2.50e+03 2.84e-02 2.02e+01 pdb=" CG TRP B1524 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B1524 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B1524 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B1524 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B1524 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1524 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1524 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1524 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1524 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C1206 " 0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO C1207 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C1207 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C1207 " 0.053 5.00e-02 4.00e+02 ... (remaining 3266 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4218 2.77 - 3.30: 17853 3.30 - 3.83: 26591 3.83 - 4.37: 25657 4.37 - 4.90: 40423 Nonbonded interactions: 114742 Sorted by model distance: nonbonded pdb=" O GLY C 213 " pdb=" N ILE C 218 " model vdw 2.237 3.120 nonbonded pdb=" O ASP B 987 " pdb=" N GLN B 991 " model vdw 2.244 3.120 nonbonded pdb=" O HIS B1928 " pdb=" N HIS B1932 " model vdw 2.249 3.120 nonbonded pdb=" O CYS C2073 " pdb=" N GLY C2077 " model vdw 2.262 3.120 nonbonded pdb=" O LEU B1009 " pdb=" N LYS B1013 " model vdw 2.269 3.120 ... (remaining 114737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 53.350 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 16694 Z= 0.280 Angle : 0.691 12.336 23202 Z= 0.431 Chirality : 0.041 0.200 3173 Planarity : 0.005 0.119 3269 Dihedral : 8.460 80.162 3622 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.53 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3147 helix: -0.03 (0.12), residues: 1991 sheet: None (None), residues: 0 loop : -2.37 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP B1524 HIS 0.014 0.002 HIS C1405 PHE 0.035 0.002 PHE C1185 TYR 0.037 0.002 TYR C1158 ARG 0.011 0.002 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.17436 ( 1377) hydrogen bonds : angle 6.51056 ( 4074) covalent geometry : bond 0.00477 (16694) covalent geometry : angle 0.69115 (23202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.868 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1499 time to fit residues: 21.3734 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.116372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065492 restraints weight = 149198.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.063685 restraints weight = 176004.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062634 restraints weight = 224896.843| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16694 Z= 0.279 Angle : 0.627 16.760 23202 Z= 0.362 Chirality : 0.039 0.209 3173 Planarity : 0.004 0.067 3269 Dihedral : 5.242 33.497 3196 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.85 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3147 helix: 0.23 (0.11), residues: 2090 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B1524 HIS 0.011 0.004 HIS C1260 PHE 0.045 0.002 PHE C1417 TYR 0.012 0.001 TYR B1556 ARG 0.005 0.001 ARG C1252 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 1377) hydrogen bonds : angle 5.18503 ( 4074) covalent geometry : bond 0.00496 (16694) covalent geometry : angle 0.62674 (23202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1543 time to fit residues: 22.0530 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 225 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 151 optimal weight: 30.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.107630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089729 restraints weight = 92292.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089729 restraints weight = 98241.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089729 restraints weight = 98241.687| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4632 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16694 Z= 0.115 Angle : 0.446 8.291 23202 Z= 0.256 Chirality : 0.036 0.148 3173 Planarity : 0.003 0.048 3269 Dihedral : 4.413 31.527 3196 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.90 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 3147 helix: 0.96 (0.11), residues: 2148 sheet: None (None), residues: 0 loop : -2.07 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1524 HIS 0.004 0.001 HIS C1260 PHE 0.013 0.001 PHE C1417 TYR 0.013 0.001 TYR B1565 ARG 0.003 0.001 ARG B1404 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 1377) hydrogen bonds : angle 4.44777 ( 4074) covalent geometry : bond 0.00203 (16694) covalent geometry : angle 0.44576 (23202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.806 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1519 time to fit residues: 21.6765 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 219 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 38 optimal weight: 9.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.096067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.083475 restraints weight = 120436.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.083475 restraints weight = 125318.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.083475 restraints weight = 125318.005| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16694 Z= 0.138 Angle : 0.462 11.884 23202 Z= 0.259 Chirality : 0.036 0.149 3173 Planarity : 0.003 0.084 3269 Dihedral : 4.069 32.440 3196 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.94 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 3147 helix: 1.46 (0.12), residues: 2191 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1524 HIS 0.006 0.002 HIS B1377 PHE 0.021 0.001 PHE C1417 TYR 0.018 0.001 TYR B1565 ARG 0.004 0.001 ARG B1538 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 1377) hydrogen bonds : angle 4.08780 ( 4074) covalent geometry : bond 0.00251 (16694) covalent geometry : angle 0.46184 (23202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.957 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1503 time to fit residues: 21.4701 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 10 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 283 optimal weight: 30.0000 chunk 64 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.084529 restraints weight = 118620.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.084529 restraints weight = 122978.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.084529 restraints weight = 122978.482| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3971 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 16694 Z= 0.260 Angle : 0.596 16.071 23202 Z= 0.335 Chirality : 0.039 0.192 3173 Planarity : 0.004 0.090 3269 Dihedral : 4.730 28.639 3196 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.26 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3147 helix: 1.05 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.08 (0.22), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C1374 HIS 0.009 0.003 HIS B1377 PHE 0.034 0.002 PHE C1369 TYR 0.022 0.002 TYR B1394 ARG 0.004 0.001 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1377) hydrogen bonds : angle 4.67768 ( 4074) covalent geometry : bond 0.00464 (16694) covalent geometry : angle 0.59593 (23202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1511 time to fit residues: 21.3755 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 210 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 159 optimal weight: 0.5980 chunk 249 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 137 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.094989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082802 restraints weight = 122759.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082802 restraints weight = 128770.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082802 restraints weight = 128773.178| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4323 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16694 Z= 0.104 Angle : 0.426 8.136 23202 Z= 0.241 Chirality : 0.036 0.148 3173 Planarity : 0.003 0.055 3269 Dihedral : 4.091 32.958 3196 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.59 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 3147 helix: 1.64 (0.12), residues: 2200 sheet: None (None), residues: 0 loop : -1.88 (0.22), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1374 HIS 0.003 0.001 HIS C1260 PHE 0.008 0.001 PHE C1417 TYR 0.013 0.001 TYR B1565 ARG 0.003 0.001 ARG C1474 Details of bonding type rmsd hydrogen bonds : bond 0.02710 ( 1377) hydrogen bonds : angle 4.07878 ( 4074) covalent geometry : bond 0.00182 (16694) covalent geometry : angle 0.42628 (23202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.934 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1505 time to fit residues: 21.5499 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 3.9990 chunk 216 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 230 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 244 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 266 optimal weight: 30.0000 overall best weight: 1.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.089643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083881 restraints weight = 152545.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082554 restraints weight = 201153.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082554 restraints weight = 230970.349| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4103 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16694 Z= 0.099 Angle : 0.405 7.908 23202 Z= 0.229 Chirality : 0.035 0.146 3173 Planarity : 0.003 0.071 3269 Dihedral : 3.705 27.235 3196 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 3147 helix: 1.98 (0.12), residues: 2223 sheet: None (None), residues: 0 loop : -1.79 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1524 HIS 0.003 0.001 HIS B1456 PHE 0.012 0.001 PHE C1417 TYR 0.012 0.001 TYR B1565 ARG 0.003 0.000 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.02380 ( 1377) hydrogen bonds : angle 3.76493 ( 4074) covalent geometry : bond 0.00178 (16694) covalent geometry : angle 0.40451 (23202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.801 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1480 time to fit residues: 21.0264 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 14 optimal weight: 50.0000 chunk 218 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 118 optimal weight: 40.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.095231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.082836 restraints weight = 119983.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.082836 restraints weight = 124291.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.082836 restraints weight = 124291.684| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4330 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16694 Z= 0.154 Angle : 0.450 10.469 23202 Z= 0.256 Chirality : 0.037 0.235 3173 Planarity : 0.003 0.050 3269 Dihedral : 3.943 32.527 3196 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.36 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 3147 helix: 1.98 (0.12), residues: 2215 sheet: None (None), residues: 0 loop : -1.76 (0.23), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1524 HIS 0.004 0.001 HIS B1456 PHE 0.020 0.001 PHE C1417 TYR 0.014 0.001 TYR B1383 ARG 0.002 0.000 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 1377) hydrogen bonds : angle 3.90139 ( 4074) covalent geometry : bond 0.00278 (16694) covalent geometry : angle 0.45035 (23202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.959 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1521 time to fit residues: 21.6003 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 114 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 165 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 60 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.082669 restraints weight = 120710.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.082669 restraints weight = 125315.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.082669 restraints weight = 125315.916| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4307 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16694 Z= 0.149 Angle : 0.446 8.100 23202 Z= 0.252 Chirality : 0.036 0.145 3173 Planarity : 0.003 0.068 3269 Dihedral : 3.888 29.397 3196 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.80 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 3147 helix: 2.00 (0.12), residues: 2221 sheet: None (None), residues: 0 loop : -1.74 (0.23), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1524 HIS 0.007 0.002 HIS B1377 PHE 0.017 0.001 PHE C1417 TYR 0.013 0.001 TYR B1565 ARG 0.005 0.001 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.02683 ( 1377) hydrogen bonds : angle 3.88587 ( 4074) covalent geometry : bond 0.00269 (16694) covalent geometry : angle 0.44635 (23202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.884 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1557 time to fit residues: 22.0821 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 39 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 chunk 171 optimal weight: 50.0000 chunk 45 optimal weight: 0.0570 chunk 137 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 129 optimal weight: 40.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.098519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084585 restraints weight = 121068.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084584 restraints weight = 124585.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084583 restraints weight = 124601.429| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4598 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 16694 Z= 0.358 Angle : 0.715 15.027 23202 Z= 0.405 Chirality : 0.041 0.227 3173 Planarity : 0.005 0.063 3269 Dihedral : 5.246 35.804 3196 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.15 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 3147 helix: 0.86 (0.11), residues: 2218 sheet: None (None), residues: 0 loop : -2.02 (0.22), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1524 HIS 0.013 0.004 HIS C1405 PHE 0.037 0.002 PHE C1369 TYR 0.020 0.002 TYR B1394 ARG 0.008 0.002 ARG C1474 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 1377) hydrogen bonds : angle 5.10400 ( 4074) covalent geometry : bond 0.00646 (16694) covalent geometry : angle 0.71487 (23202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.884 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1497 time to fit residues: 21.2457 Evaluate side-chains 66 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 291 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 317 optimal weight: 50.0000 chunk 217 optimal weight: 0.0070 chunk 289 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.094013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.082664 restraints weight = 119657.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.082664 restraints weight = 126287.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.082664 restraints weight = 126287.189| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3933 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16694 Z= 0.215 Angle : 0.522 10.398 23202 Z= 0.297 Chirality : 0.037 0.175 3173 Planarity : 0.003 0.058 3269 Dihedral : 4.591 31.556 3196 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.88 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 3147 helix: 1.24 (0.11), residues: 2243 sheet: None (None), residues: 0 loop : -2.27 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1524 HIS 0.008 0.002 HIS B1456 PHE 0.019 0.001 PHE C1417 TYR 0.019 0.001 TYR B1565 ARG 0.002 0.001 ARG C1428 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1377) hydrogen bonds : angle 4.60623 ( 4074) covalent geometry : bond 0.00387 (16694) covalent geometry : angle 0.52211 (23202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6971.61 seconds wall clock time: 125 minutes 11.18 seconds (7511.18 seconds total)