Starting phenix.real_space_refine on Sun Sep 13 03:08:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wge_21663/09_2026/6wge_21663.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 92 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 12574 2.51 5 N 3470 2.21 5 O 3950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20194 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3099 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 4008 Classifications: {'peptide': 490} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1395 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 2 Chain: "E" Number of atoms: 9865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1226, 9865 Classifications: {'peptide': 1226} Link IDs: {'PTRANS': 35, 'TRANS': 1190} Chain breaks: 11 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 903 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 860 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.13, per 1000 atoms: 0.20 Number of scatterers: 20194 At special positions: 0 Unit cell: (147.4, 142.04, 172.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 92 15.00 Mg 2 11.99 O 3950 8.00 N 3470 7.00 C 12574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 756.6 milliseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4376 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 10 sheets defined 68.1% alpha, 6.0% beta 35 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.639A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.625A pdb=" N ARG A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.716A pdb=" N SER A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.755A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.593A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1089 removed outlier: 3.914A pdb=" N GLN A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A1058 " --> pdb=" O LYS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 Processing helix chain 'A' and resid 1129 through 1148 removed outlier: 3.679A pdb=" N VAL A1135 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A1148 " --> pdb=" O ILE A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1179 removed outlier: 4.337A pdb=" N THR A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.700A pdb=" N TYR A1194 " --> pdb=" O LYS A1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 removed outlier: 3.898A pdb=" N PHE B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.614A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 236 removed outlier: 4.342A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 947 removed outlier: 4.172A pdb=" N GLY B 947 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 979 Processing helix chain 'B' and resid 985 through 1048 Processing helix chain 'B' and resid 1116 through 1135 Processing helix chain 'B' and resid 1144 through 1148 removed outlier: 3.769A pdb=" N GLN B1147 " --> pdb=" O GLN B1144 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA B1148 " --> pdb=" O ILE B1145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1144 through 1148' Processing helix chain 'B' and resid 1150 through 1165 Processing helix chain 'B' and resid 1176 through 1182 removed outlier: 3.799A pdb=" N LEU B1179 " --> pdb=" O ARG B1176 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER B1182 " --> pdb=" O LEU B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1211 removed outlier: 3.793A pdb=" N GLU B1211 " --> pdb=" O LYS B1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 23 Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.906A pdb=" N PHE C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 removed outlier: 4.198A pdb=" N SER C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 86 removed outlier: 3.566A pdb=" N LYS C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 572 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 589 through 606 removed outlier: 3.772A pdb=" N GLN C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1216 removed outlier: 3.537A pdb=" N MET E1216 " --> pdb=" O ASN E1212 " (cutoff:3.500A) Processing helix chain 'E' and resid 1234 through 1247 removed outlier: 3.551A pdb=" N LEU E1238 " --> pdb=" O GLY E1234 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS E1247 " --> pdb=" O SER E1243 " (cutoff:3.500A) Processing helix chain 'E' and resid 1248 through 1253 removed outlier: 3.892A pdb=" N GLY E1252 " --> pdb=" O ILE E1248 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E1253 " --> pdb=" O LYS E1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1248 through 1253' Processing helix chain 'E' and resid 1257 through 1273 Processing helix chain 'E' and resid 1294 through 1319 removed outlier: 3.761A pdb=" N MET E1318 " --> pdb=" O THR E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1329 through 1353 removed outlier: 3.962A pdb=" N ILE E1333 " --> pdb=" O ILE E1329 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR E1349 " --> pdb=" O GLN E1345 " (cutoff:3.500A) Proline residue: E1350 - end of helix Processing helix chain 'E' and resid 1381 through 1404 removed outlier: 3.546A pdb=" N GLN E1404 " --> pdb=" O LEU E1400 " (cutoff:3.500A) Processing helix chain 'E' and resid 1407 through 1420 removed outlier: 3.846A pdb=" N GLN E1413 " --> pdb=" O THR E1409 " (cutoff:3.500A) Processing helix chain 'E' and resid 1421 through 1424 removed outlier: 3.712A pdb=" N VAL E1424 " --> pdb=" O PRO E1421 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1421 through 1424' Processing helix chain 'E' and resid 1427 through 1445 removed outlier: 3.597A pdb=" N TYR E1445 " --> pdb=" O VAL E1441 " (cutoff:3.500A) Processing helix chain 'E' and resid 1448 through 1458 Processing helix chain 'E' and resid 1489 through 1501 removed outlier: 3.516A pdb=" N VAL E1501 " --> pdb=" O LEU E1497 " (cutoff:3.500A) Processing helix chain 'E' and resid 1525 through 1551 removed outlier: 4.505A pdb=" N SER E1551 " --> pdb=" O LYS E1547 " (cutoff:3.500A) Processing helix chain 'E' and resid 1558 through 1572 Processing helix chain 'E' and resid 1580 through 1597 Processing helix chain 'E' and resid 1603 through 1628 Processing helix chain 'E' and resid 1647 through 1666 removed outlier: 3.590A pdb=" N GLU E1664 " --> pdb=" O ASP E1660 " (cutoff:3.500A) Processing helix chain 'E' and resid 1668 through 1690 removed outlier: 3.976A pdb=" N SER E1672 " --> pdb=" O SER E1668 " (cutoff:3.500A) Processing helix chain 'E' and resid 1709 through 1728 Processing helix chain 'E' and resid 1749 through 1764 Processing helix chain 'E' and resid 1766 through 1768 No H-bonds generated for 'chain 'E' and resid 1766 through 1768' Processing helix chain 'E' and resid 1769 through 1781 removed outlier: 3.545A pdb=" N LEU E1781 " --> pdb=" O ILE E1777 " (cutoff:3.500A) Processing helix chain 'E' and resid 1785 through 1803 removed outlier: 3.535A pdb=" N ARG E1789 " --> pdb=" O ALA E1785 " (cutoff:3.500A) Processing helix chain 'E' and resid 1809 through 1821 Processing helix chain 'E' and resid 1824 through 1842 Processing helix chain 'E' and resid 1849 through 1855 Processing helix chain 'E' and resid 1856 through 1858 No H-bonds generated for 'chain 'E' and resid 1856 through 1858' Processing helix chain 'E' and resid 1862 through 1879 Processing helix chain 'E' and resid 1884 through 1895 Processing helix chain 'E' and resid 1896 through 1898 No H-bonds generated for 'chain 'E' and resid 1896 through 1898' Processing helix chain 'E' and resid 1900 through 1914 Processing helix chain 'E' and resid 1922 through 1941 removed outlier: 3.965A pdb=" N MET E1926 " --> pdb=" O ASP E1922 " (cutoff:3.500A) Processing helix chain 'E' and resid 1945 through 1958 Processing helix chain 'E' and resid 1965 through 1986 removed outlier: 3.835A pdb=" N ALA E1970 " --> pdb=" O PRO E1966 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E1986 " --> pdb=" O ILE E1982 " (cutoff:3.500A) Processing helix chain 'E' and resid 1999 through 2016 removed outlier: 3.518A pdb=" N ARG E2016 " --> pdb=" O PHE E2012 " (cutoff:3.500A) Processing helix chain 'E' and resid 2017 through 2021 Processing helix chain 'E' and resid 2023 through 2033 Proline residue: E2029 - end of helix removed outlier: 3.824A pdb=" N THR E2032 " --> pdb=" O GLN E2028 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E2033 " --> pdb=" O PRO E2029 " (cutoff:3.500A) Processing helix chain 'E' and resid 2037 through 2055 Processing helix chain 'E' and resid 2056 through 2058 No H-bonds generated for 'chain 'E' and resid 2056 through 2058' Processing helix chain 'E' and resid 2062 through 2078 Processing helix chain 'E' and resid 2081 through 2099 removed outlier: 4.043A pdb=" N CYS E2091 " --> pdb=" O HIS E2087 " (cutoff:3.500A) Processing helix chain 'E' and resid 2102 through 2126 removed outlier: 4.465A pdb=" N VAL E2106 " --> pdb=" O ASN E2102 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU E2126 " --> pdb=" O SER E2122 " (cutoff:3.500A) Processing helix chain 'E' and resid 2132 through 2154 Proline residue: E2138 - end of helix Processing helix chain 'E' and resid 2158 through 2163 removed outlier: 4.294A pdb=" N LYS E2162 " --> pdb=" O LEU E2158 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E2163 " --> pdb=" O GLU E2159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2158 through 2163' Processing helix chain 'E' and resid 2168 through 2182 removed outlier: 4.148A pdb=" N LYS E2182 " --> pdb=" O MET E2178 " (cutoff:3.500A) Processing helix chain 'E' and resid 2186 through 2203 removed outlier: 3.801A pdb=" N GLN E2202 " --> pdb=" O PHE E2198 " (cutoff:3.500A) Processing helix chain 'E' and resid 2204 through 2208 Processing helix chain 'E' and resid 2209 through 2220 Processing helix chain 'E' and resid 2227 through 2253 removed outlier: 3.602A pdb=" N ILE E2231 " --> pdb=" O VAL E2227 " (cutoff:3.500A) Processing helix chain 'E' and resid 2258 through 2262 Processing helix chain 'E' and resid 2273 through 2289 removed outlier: 4.300A pdb=" N MET E2279 " --> pdb=" O SER E2275 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN E2280 " --> pdb=" O SER E2276 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E2281 " --> pdb=" O SER E2277 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E2282 " --> pdb=" O ILE E2278 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS E2284 " --> pdb=" O GLN E2280 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN E2285 " --> pdb=" O LEU E2281 " (cutoff:3.500A) Processing helix chain 'E' and resid 2295 through 2310 removed outlier: 3.750A pdb=" N ASN E2310 " --> pdb=" O ALA E2306 " (cutoff:3.500A) Processing helix chain 'E' and resid 2320 through 2326 Processing helix chain 'E' and resid 2331 through 2349 removed outlier: 3.712A pdb=" N ARG E2335 " --> pdb=" O GLU E2331 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS E2348 " --> pdb=" O GLU E2344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E2349 " --> pdb=" O ILE E2345 " (cutoff:3.500A) Processing helix chain 'E' and resid 2351 through 2356 removed outlier: 3.723A pdb=" N MET E2355 " --> pdb=" O GLY E2351 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E2356 " --> pdb=" O PHE E2352 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2351 through 2356' Processing helix chain 'E' and resid 2357 through 2372 removed outlier: 3.512A pdb=" N MET E2361 " --> pdb=" O ALA E2357 " (cutoff:3.500A) Processing helix chain 'E' and resid 2392 through 2400 removed outlier: 3.655A pdb=" N TYR E2396 " --> pdb=" O CYS E2392 " (cutoff:3.500A) Processing helix chain 'E' and resid 2402 through 2418 Processing helix chain 'E' and resid 2424 through 2438 removed outlier: 3.638A pdb=" N LEU E2429 " --> pdb=" O VAL E2425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2443 through 2471 removed outlier: 3.803A pdb=" N LEU E2447 " --> pdb=" O GLN E2443 " (cutoff:3.500A) Processing helix chain 'E' and resid 2534 through 2558 Processing helix chain 'E' and resid 2560 through 2567 Processing helix chain 'E' and resid 2588 through 2601 removed outlier: 3.623A pdb=" N ASP E2600 " --> pdb=" O PHE E2596 " (cutoff:3.500A) Processing helix chain 'E' and resid 2607 through 2626 removed outlier: 3.701A pdb=" N LYS E2611 " --> pdb=" O THR E2607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.978A pdb=" N GLN A 19 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 83 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A 7 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER A 81 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 9 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 79 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 86 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.978A pdb=" N GLN A 19 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 83 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A 7 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER A 81 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 9 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 79 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 80 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 106 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 105 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.638A pdb=" N THR A 28 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A1185 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1096 through 1100 Processing sheet with id=AA5, first strand: chain 'A' and resid 1199 through 1206 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.798A pdb=" N VAL B 78 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.865A pdb=" N VAL B 139 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1052 through 1057 Processing sheet with id=AA9, first strand: chain 'B' and resid 1188 through 1192 Processing sheet with id=AB1, first strand: chain 'C' and resid 579 through 580 1165 hydrogen bonds defined for protein. 3408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 2.43 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: 4746 1.33 - 1.45: 4470 1.45 - 1.58: 11132 1.58 - 1.70: 181 1.70 - 1.82: 179 Bond restraints: 20708 Sorted by residual: bond pdb=" N3B ANP B2000 " pdb=" PG ANP B2000 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N3B ANP A2000 " pdb=" PG ANP A2000 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" O3A ANP B2000 " pdb=" PB ANP B2000 " ideal model delta sigma weight residual 1.700 1.591 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" O3A ANP A2000 " pdb=" PB ANP A2000 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C3' DT G 15 " pdb=" O3' DT G 15 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.78e+01 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 27744 3.05 - 6.11: 441 6.11 - 9.16: 51 9.16 - 12.21: 7 12.21 - 15.27: 3 Bond angle restraints: 28246 Sorted by residual: angle pdb=" O4' DA F 39 " pdb=" C1' DA F 39 " pdb=" N9 DA F 39 " ideal model delta sigma weight residual 108.00 102.88 5.12 7.00e-01 2.04e+00 5.36e+01 angle pdb=" O5' DT G 25 " pdb=" C5' DT G 25 " pdb=" C4' DT G 25 " ideal model delta sigma weight residual 109.40 114.41 -5.01 8.00e-01 1.56e+00 3.93e+01 angle pdb=" PB ANP B2000 " pdb=" N3B ANP B2000 " pdb=" PG ANP B2000 " ideal model delta sigma weight residual 126.95 111.83 15.12 3.00e+00 1.11e-01 2.54e+01 angle pdb=" O4' DA F 38 " pdb=" C1' DA F 38 " pdb=" N9 DA F 38 " ideal model delta sigma weight residual 108.00 104.60 3.40 7.00e-01 2.04e+00 2.36e+01 angle pdb=" O4' DA F 8 " pdb=" C1' DA F 8 " pdb=" N9 DA F 8 " ideal model delta sigma weight residual 108.00 104.71 3.29 7.00e-01 2.04e+00 2.21e+01 ... (remaining 28241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11830 35.30 - 70.59: 706 70.59 - 105.89: 20 105.89 - 141.19: 0 141.19 - 176.49: 2 Dihedral angle restraints: 12558 sinusoidal: 5849 harmonic: 6709 Sorted by residual: dihedral pdb=" CA GLU B1111 " pdb=" C GLU B1111 " pdb=" N MET B1112 " pdb=" CA MET B1112 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL E2317 " pdb=" C VAL E2317 " pdb=" N GLN E2318 " pdb=" CA GLN E2318 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLY E2351 " pdb=" C GLY E2351 " pdb=" N PHE E2352 " pdb=" CA PHE E2352 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 12555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2674 0.076 - 0.152: 472 0.152 - 0.228: 39 0.228 - 0.304: 8 0.304 - 0.380: 2 Chirality restraints: 3195 Sorted by residual: chirality pdb=" C3' ANP A2000 " pdb=" C2' ANP A2000 " pdb=" C4' ANP A2000 " pdb=" O3' ANP A2000 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C3' ANP B2000 " pdb=" C2' ANP B2000 " pdb=" C4' ANP B2000 " pdb=" O3' ANP B2000 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE B1098 " pdb=" CA ILE B1098 " pdb=" CG1 ILE B1098 " pdb=" CG2 ILE B1098 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3192 not shown) Planarity restraints: 3284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E1986 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C GLU E1986 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU E1986 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E1987 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E2408 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ALA E2408 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA E2408 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE E2409 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1117 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A1118 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A1118 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1118 " -0.034 5.00e-02 4.00e+02 ... (remaining 3281 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 146 2.52 - 3.11: 15154 3.11 - 3.71: 31071 3.71 - 4.30: 40894 4.30 - 4.90: 65934 Nonbonded interactions: 153199 Sorted by model distance: nonbonded pdb=" NE2 GLN B 141 " pdb="MG MG B2001 " model vdw 1.921 2.250 nonbonded pdb=" O3G ANP B2000 " pdb="MG MG B2001 " model vdw 1.924 2.170 nonbonded pdb=" OE1 GLN B 141 " pdb="MG MG B2001 " model vdw 2.059 2.170 nonbonded pdb=" NE2 GLN A 137 " pdb="MG MG A2001 " model vdw 2.160 2.250 nonbonded pdb=" O ILE E1315 " pdb=" OG1 THR E1319 " model vdw 2.184 3.040 ... (remaining 153194 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.008 0.177 20708 Z= 0.431 Angle : 1.013 15.265 28246 Z= 0.617 Chirality : 0.058 0.380 3195 Planarity : 0.006 0.060 3284 Dihedral : 19.176 176.485 8182 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.35 % Favored : 91.61 % Rotamer: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.16), residues: 2240 helix: -0.67 (0.12), residues: 1382 sheet: -2.45 (0.39), residues: 157 loop : -3.01 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E2407 TYR 0.026 0.003 TYR C 67 PHE 0.032 0.003 PHE E2161 TRP 0.016 0.002 TRP C 18 HIS 0.020 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.43 (20708) covalent geometry : angle 1.01261 / 0.62 (28246) hydrogen bonds : bond 0.13258 / 8.97 ( 1232) hydrogen bonds : angle 5.42272 / 3.84 ( 3548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1108 LEU cc_start: 0.9202 (tp) cc_final: 0.8823 (tp) REVERT: B 62 LEU cc_start: 0.9557 (tt) cc_final: 0.9314 (tp) REVERT: B 946 LEU cc_start: 0.8502 (mt) cc_final: 0.8271 (mt) REVERT: C 33 PHE cc_start: 0.8525 (t80) cc_final: 0.8022 (t80) REVERT: C 44 ILE cc_start: 0.8040 (mm) cc_final: 0.7742 (mm) REVERT: C 80 GLU cc_start: 0.8781 (tp30) cc_final: 0.8490 (tp30) REVERT: C 163 PHE cc_start: 0.8165 (m-80) cc_final: 0.7942 (m-80) REVERT: C 563 MET cc_start: 0.7166 (tpp) cc_final: 0.6725 (tpp) REVERT: C 583 GLU cc_start: 0.8317 (tp30) cc_final: 0.8062 (tp30) REVERT: E 1193 MET cc_start: 0.6705 (mtp) cc_final: 0.5866 (mtm) REVERT: E 1254 MET cc_start: 0.7620 (ptp) cc_final: 0.7093 (tpp) REVERT: E 1312 LEU cc_start: 0.9340 (mm) cc_final: 0.9065 (mm) REVERT: E 1859 ASP cc_start: 0.7551 (t0) cc_final: 0.7346 (t0) REVERT: E 2025 MET cc_start: 0.8667 (mpp) cc_final: 0.8081 (mtt) REVERT: E 2207 MET cc_start: 0.8982 (mmt) cc_final: 0.8533 (mmt) REVERT: E 2624 LEU cc_start: 0.8581 (mt) cc_final: 0.7916 (mt) outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 0.1559 time to fit residues: 54.3207 Evaluate side-chains 152 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2424 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0970 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 187 HIS A1114 ASN A1166 ASN B 134 ASN B 958 GLN B 973 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 158 ASN C 587 ASN E1343 HIS E1539 GLN E1567 GLN E1813 GLN E2023 HIS E2086 GLN E2124 HIS E2153 HIS E2224 ASN E2236 ASN E2292 HIS E2294 GLN E2315 HIS E2372 ASN E2434 ASN E2551 GLN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071884 restraints weight = 54555.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072971 restraints weight = 37032.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073053 restraints weight = 26319.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073449 restraints weight = 25267.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073677 restraints weight = 23471.275| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20708 Z= 0.160 Angle : 0.646 11.566 28246 Z= 0.348 Chirality : 0.041 0.251 3195 Planarity : 0.004 0.040 3284 Dihedral : 19.516 174.233 3489 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.28 % Allowed : 13.25 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2240 helix: 1.09 (0.13), residues: 1397 sheet: -1.61 (0.41), residues: 154 loop : -2.57 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2407 TYR 0.018 0.001 TYR B 137 PHE 0.019 0.001 PHE E1596 TRP 0.009 0.001 TRP C 18 HIS 0.009 0.001 HIS E2394 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (20708) covalent geometry : angle 0.64553 / 0.35 (28246) hydrogen bonds : bond 0.07142 / 4.82 ( 1232) hydrogen bonds : angle 4.50341 / 3.20 ( 3548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7393 (tmm) cc_final: 0.7128 (tmm) REVERT: B 72 ARG cc_start: 0.6297 (mtp180) cc_final: 0.5981 (mtp180) REVERT: B 946 LEU cc_start: 0.8461 (mt) cc_final: 0.8109 (mt) REVERT: C 33 PHE cc_start: 0.8438 (t80) cc_final: 0.7793 (t80) REVERT: C 44 ILE cc_start: 0.8056 (mm) cc_final: 0.7758 (mm) REVERT: C 163 PHE cc_start: 0.8328 (m-80) cc_final: 0.8050 (m-80) REVERT: E 1193 MET cc_start: 0.6334 (mtp) cc_final: 0.5725 (mtm) REVERT: E 1251 MET cc_start: 0.8016 (mpp) cc_final: 0.7622 (mpp) REVERT: E 1254 MET cc_start: 0.7718 (ptp) cc_final: 0.7113 (tpp) REVERT: E 1312 LEU cc_start: 0.9357 (mm) cc_final: 0.9035 (mm) REVERT: E 1323 MET cc_start: 0.8203 (mtp) cc_final: 0.7971 (mtp) REVERT: E 1666 ASP cc_start: 0.7727 (t0) cc_final: 0.7526 (t0) REVERT: E 2025 MET cc_start: 0.8661 (mpp) cc_final: 0.8060 (mtt) REVERT: E 2207 MET cc_start: 0.8948 (mmt) cc_final: 0.8705 (mmt) REVERT: E 2334 MET cc_start: 0.8279 (tpp) cc_final: 0.7973 (mtp) REVERT: E 2361 MET cc_start: 0.8882 (mmm) cc_final: 0.8450 (tpp) REVERT: E 2624 LEU cc_start: 0.8310 (mt) cc_final: 0.8037 (mt) outliers start: 26 outliers final: 11 residues processed: 205 average time/residue: 0.1332 time to fit residues: 44.8653 Evaluate side-chains 164 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 940 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain E residue 1688 THR Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 2015 ILE Chi-restraints excluded: chain E residue 2621 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 218 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 ASN C 613 GLN E1343 HIS E1977 ASN E2202 GLN ** E2394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.071720 restraints weight = 55060.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072453 restraints weight = 39749.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073017 restraints weight = 29574.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073318 restraints weight = 26324.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073371 restraints weight = 24115.435| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20708 Z= 0.160 Angle : 0.609 8.617 28246 Z= 0.328 Chirality : 0.040 0.263 3195 Planarity : 0.003 0.041 3284 Dihedral : 19.466 178.440 3487 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.96 % Allowed : 16.64 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2240 helix: 1.63 (0.13), residues: 1389 sheet: -1.19 (0.41), residues: 154 loop : -2.37 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1110 TYR 0.024 0.001 TYR B 2 PHE 0.020 0.001 PHE E2290 TRP 0.007 0.001 TRP C 18 HIS 0.007 0.001 HIS E2394 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (20708) covalent geometry : angle 0.60895 / 0.33 (28246) hydrogen bonds : bond 0.06784 / 4.57 ( 1232) hydrogen bonds : angle 4.35707 / 3.09 ( 3548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7411 (tmm) cc_final: 0.7165 (tmm) REVERT: B 946 LEU cc_start: 0.8438 (mt) cc_final: 0.8162 (mt) REVERT: B 977 LYS cc_start: 0.8929 (mttt) cc_final: 0.8523 (mttt) REVERT: B 1108 GLU cc_start: 0.6728 (mp0) cc_final: 0.6423 (mt-10) REVERT: C 33 PHE cc_start: 0.8499 (t80) cc_final: 0.7795 (t80) REVERT: C 163 PHE cc_start: 0.8301 (m-80) cc_final: 0.8012 (m-80) REVERT: E 1193 MET cc_start: 0.6314 (mtp) cc_final: 0.5722 (mtm) REVERT: E 1251 MET cc_start: 0.8054 (mpp) cc_final: 0.7725 (mpp) REVERT: E 1254 MET cc_start: 0.7768 (ptp) cc_final: 0.7234 (tpp) REVERT: E 1264 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7528 (ptpt) REVERT: E 1312 LEU cc_start: 0.9339 (mm) cc_final: 0.9004 (mm) REVERT: E 1323 MET cc_start: 0.8412 (mtp) cc_final: 0.8191 (mtp) REVERT: E 1570 LEU cc_start: 0.8121 (mt) cc_final: 0.7814 (mt) REVERT: E 1858 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8017 (mt) REVERT: E 2334 MET cc_start: 0.8253 (tpp) cc_final: 0.8053 (mtp) REVERT: E 2339 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7857 (t70) REVERT: E 2361 MET cc_start: 0.8891 (mmm) cc_final: 0.8452 (tpp) outliers start: 40 outliers final: 21 residues processed: 189 average time/residue: 0.1239 time to fit residues: 39.2262 Evaluate side-chains 168 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 940 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2426 THR Chi-restraints excluded: chain E residue 2621 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN B 17 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 964 GLN B 992 ASN E1343 HIS E1977 ASN E2394 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068460 restraints weight = 55526.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069114 restraints weight = 42618.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069648 restraints weight = 30702.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.069961 restraints weight = 27395.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070129 restraints weight = 25221.365| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20708 Z= 0.274 Angle : 0.701 8.144 28246 Z= 0.374 Chirality : 0.044 0.297 3195 Planarity : 0.004 0.040 3284 Dihedral : 19.584 179.987 3487 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.70 % Allowed : 19.78 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2240 helix: 1.55 (0.13), residues: 1392 sheet: -1.12 (0.42), residues: 155 loop : -2.40 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.023 0.002 TYR B 2 PHE 0.022 0.002 PHE E2409 TRP 0.006 0.001 TRP E2107 HIS 0.010 0.002 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 (20708) covalent geometry : angle 0.70072 / 0.37 (28246) hydrogen bonds : bond 0.07453 / 4.98 ( 1232) hydrogen bonds : angle 4.64380 / 3.28 ( 3548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8423 (mt) cc_final: 0.8141 (mt) REVERT: B 977 LYS cc_start: 0.8928 (mttt) cc_final: 0.8504 (mttt) REVERT: B 1122 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9029 (mm) REVERT: C 33 PHE cc_start: 0.8460 (t80) cc_final: 0.7815 (t80) REVERT: C 44 ILE cc_start: 0.8214 (tp) cc_final: 0.7782 (tt) REVERT: C 163 PHE cc_start: 0.8481 (m-80) cc_final: 0.8266 (m-80) REVERT: E 1193 MET cc_start: 0.6334 (mtp) cc_final: 0.5645 (mtm) REVERT: E 1251 MET cc_start: 0.7981 (mpp) cc_final: 0.7640 (mpp) REVERT: E 1254 MET cc_start: 0.7571 (ptp) cc_final: 0.7111 (tpp) REVERT: E 1312 LEU cc_start: 0.9343 (mm) cc_final: 0.9049 (mm) REVERT: E 1402 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8474 (tm-30) REVERT: E 1858 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8121 (mt) REVERT: E 2339 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7834 (t70) outliers start: 55 outliers final: 39 residues processed: 189 average time/residue: 0.1224 time to fit residues: 39.0740 Evaluate side-chains 180 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1688 THR Chi-restraints excluded: chain E residue 1726 PHE Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1802 VAL Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1977 ASN Chi-restraints excluded: chain E residue 2015 ILE Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2426 THR Chi-restraints excluded: chain E residue 2546 LEU Chi-restraints excluded: chain E residue 2553 LEU Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 150 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN E1343 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071823 restraints weight = 54452.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072473 restraints weight = 41381.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073058 restraints weight = 30231.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073359 restraints weight = 26702.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073539 restraints weight = 24704.986| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20708 Z= 0.139 Angle : 0.584 11.814 28246 Z= 0.314 Chirality : 0.040 0.267 3195 Planarity : 0.003 0.042 3284 Dihedral : 19.355 179.398 3487 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.70 % Allowed : 20.47 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2240 helix: 1.99 (0.13), residues: 1391 sheet: -0.76 (0.43), residues: 152 loop : -2.28 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1110 TYR 0.023 0.001 TYR B 2 PHE 0.017 0.001 PHE E1596 TRP 0.009 0.001 TRP E2255 HIS 0.021 0.001 HIS E1343 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (20708) covalent geometry : angle 0.58373 / 0.31 (28246) hydrogen bonds : bond 0.06503 / 4.38 ( 1232) hydrogen bonds : angle 4.19394 / 2.97 ( 3548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8424 (mt) cc_final: 0.8149 (mt) REVERT: B 1108 GLU cc_start: 0.6826 (mp0) cc_final: 0.6506 (mt-10) REVERT: C 33 PHE cc_start: 0.8439 (t80) cc_final: 0.7731 (t80) REVERT: C 44 ILE cc_start: 0.8201 (tp) cc_final: 0.7809 (tt) REVERT: C 163 PHE cc_start: 0.8299 (m-80) cc_final: 0.8011 (m-80) REVERT: C 620 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8783 (mm) REVERT: E 1193 MET cc_start: 0.6185 (mtp) cc_final: 0.5555 (mtm) REVERT: E 1210 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6702 (mm) REVERT: E 1251 MET cc_start: 0.7928 (mpp) cc_final: 0.7625 (mpp) REVERT: E 1254 MET cc_start: 0.7678 (ptp) cc_final: 0.7235 (tpp) REVERT: E 1312 LEU cc_start: 0.9307 (mm) cc_final: 0.9003 (mm) REVERT: E 1858 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8037 (mt) REVERT: E 1864 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8303 (p) REVERT: E 2339 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7888 (t70) REVERT: E 2361 MET cc_start: 0.9019 (mmm) cc_final: 0.8555 (tpp) outliers start: 55 outliers final: 27 residues processed: 202 average time/residue: 0.1167 time to fit residues: 39.7694 Evaluate side-chains 182 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2201 ILE Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2426 THR Chi-restraints excluded: chain E residue 2621 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 193 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 234 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1343 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071176 restraints weight = 54408.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071765 restraints weight = 42157.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072346 restraints weight = 30615.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072650 restraints weight = 27177.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072813 restraints weight = 25245.390| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20708 Z= 0.163 Angle : 0.592 11.163 28246 Z= 0.317 Chirality : 0.040 0.280 3195 Planarity : 0.003 0.041 3284 Dihedral : 19.318 179.192 3487 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.65 % Allowed : 21.55 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2240 helix: 2.09 (0.13), residues: 1391 sheet: -0.61 (0.44), residues: 152 loop : -2.28 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.001 TYR B 2 PHE 0.017 0.001 PHE E1596 TRP 0.006 0.001 TRP E1680 HIS 0.009 0.001 HIS E1343 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (20708) covalent geometry : angle 0.59246 / 0.32 (28246) hydrogen bonds : bond 0.06438 / 4.33 ( 1232) hydrogen bonds : angle 4.19571 / 2.97 ( 3548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8405 (mt) cc_final: 0.8068 (mt) REVERT: B 1108 GLU cc_start: 0.6827 (mp0) cc_final: 0.6469 (mt-10) REVERT: C 33 PHE cc_start: 0.8443 (t80) cc_final: 0.7749 (t80) REVERT: C 44 ILE cc_start: 0.8153 (tp) cc_final: 0.7716 (tt) REVERT: C 163 PHE cc_start: 0.8372 (m-80) cc_final: 0.8134 (m-80) REVERT: C 620 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8737 (mm) REVERT: E 1193 MET cc_start: 0.6189 (mtp) cc_final: 0.5557 (mtm) REVERT: E 1210 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6843 (mm) REVERT: E 1251 MET cc_start: 0.7958 (mpp) cc_final: 0.7617 (mpp) REVERT: E 1254 MET cc_start: 0.7500 (ptp) cc_final: 0.7131 (tpp) REVERT: E 1312 LEU cc_start: 0.9308 (mm) cc_final: 0.8999 (mm) REVERT: E 1858 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8072 (mt) REVERT: E 1864 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (p) REVERT: E 2339 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7904 (t70) outliers start: 54 outliers final: 35 residues processed: 194 average time/residue: 0.1144 time to fit residues: 37.8611 Evaluate side-chains 185 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1486 TYR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 64 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 76 optimal weight: 0.0970 chunk 131 optimal weight: 10.0000 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.072659 restraints weight = 54654.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073195 restraints weight = 40961.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073833 restraints weight = 31104.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074121 restraints weight = 27342.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074243 restraints weight = 25056.435| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20708 Z= 0.133 Angle : 0.575 10.815 28246 Z= 0.306 Chirality : 0.039 0.273 3195 Planarity : 0.003 0.042 3284 Dihedral : 19.197 178.513 3487 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.50 % Allowed : 22.48 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2240 helix: 2.25 (0.13), residues: 1395 sheet: -0.47 (0.45), residues: 153 loop : -2.19 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1110 TYR 0.018 0.001 TYR B 2 PHE 0.034 0.001 PHE B 993 TRP 0.007 0.001 TRP E2255 HIS 0.009 0.001 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (20708) covalent geometry : angle 0.57549 / 0.31 (28246) hydrogen bonds : bond 0.06038 / 4.07 ( 1232) hydrogen bonds : angle 4.02916 / 2.85 ( 3548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8406 (mt) cc_final: 0.8056 (mt) REVERT: B 1108 GLU cc_start: 0.6850 (mp0) cc_final: 0.6524 (mt-10) REVERT: C 33 PHE cc_start: 0.8403 (t80) cc_final: 0.7685 (t80) REVERT: C 44 ILE cc_start: 0.8139 (tp) cc_final: 0.7708 (tt) REVERT: C 163 PHE cc_start: 0.8319 (m-80) cc_final: 0.8080 (m-80) REVERT: C 620 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8717 (mm) REVERT: E 1193 MET cc_start: 0.6319 (mtp) cc_final: 0.5691 (mtm) REVERT: E 1210 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6634 (mm) REVERT: E 1251 MET cc_start: 0.7978 (mpp) cc_final: 0.7633 (mpp) REVERT: E 1254 MET cc_start: 0.7507 (ptp) cc_final: 0.7175 (tpp) REVERT: E 1312 LEU cc_start: 0.9315 (mm) cc_final: 0.9008 (mm) REVERT: E 1570 LEU cc_start: 0.8123 (mt) cc_final: 0.7811 (mt) REVERT: E 1858 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8069 (mt) REVERT: E 1864 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8242 (p) REVERT: E 2339 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7749 (t70) outliers start: 51 outliers final: 39 residues processed: 203 average time/residue: 0.1233 time to fit residues: 42.5418 Evaluate side-chains 200 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1486 TYR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2426 THR Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 112 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1954 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072173 restraints weight = 54768.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072710 restraints weight = 40946.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073462 restraints weight = 31031.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073732 restraints weight = 26869.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073861 restraints weight = 24378.119| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20708 Z= 0.146 Angle : 0.581 10.313 28246 Z= 0.309 Chirality : 0.039 0.281 3195 Planarity : 0.003 0.040 3284 Dihedral : 19.165 177.842 3487 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.70 % Allowed : 22.78 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2240 helix: 2.32 (0.13), residues: 1396 sheet: -0.36 (0.45), residues: 153 loop : -2.20 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.016 0.001 TYR B 137 PHE 0.038 0.001 PHE E2110 TRP 0.006 0.001 TRP E1680 HIS 0.005 0.001 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (20708) covalent geometry : angle 0.58089 / 0.31 (28246) hydrogen bonds : bond 0.06017 / 4.04 ( 1232) hydrogen bonds : angle 4.01436 / 2.84 ( 3548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8408 (mt) cc_final: 0.8082 (mt) REVERT: B 1108 GLU cc_start: 0.6790 (mp0) cc_final: 0.6440 (mt-10) REVERT: C 33 PHE cc_start: 0.8403 (t80) cc_final: 0.7691 (t80) REVERT: C 163 PHE cc_start: 0.8322 (m-80) cc_final: 0.8070 (m-80) REVERT: C 620 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8705 (mm) REVERT: E 1193 MET cc_start: 0.6291 (mtp) cc_final: 0.5673 (mtm) REVERT: E 1210 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6632 (mm) REVERT: E 1251 MET cc_start: 0.7928 (mpp) cc_final: 0.7520 (mpp) REVERT: E 1254 MET cc_start: 0.7519 (ptp) cc_final: 0.7179 (tpp) REVERT: E 1301 MET cc_start: 0.6905 (mpp) cc_final: 0.6666 (mpp) REVERT: E 1312 LEU cc_start: 0.9313 (mm) cc_final: 0.9001 (mm) REVERT: E 1570 LEU cc_start: 0.8145 (mt) cc_final: 0.7829 (mt) REVERT: E 1858 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8119 (mt) REVERT: E 1864 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (p) REVERT: E 1954 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8735 (t0) REVERT: E 2339 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7821 (t70) outliers start: 55 outliers final: 39 residues processed: 195 average time/residue: 0.1223 time to fit residues: 40.5292 Evaluate side-chains 193 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1486 TYR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1954 ASN Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2426 THR Chi-restraints excluded: chain E residue 2553 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 196 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 198 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073376 restraints weight = 54189.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073988 restraints weight = 40036.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.074696 restraints weight = 30325.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074980 restraints weight = 26571.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075104 restraints weight = 23958.782| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20708 Z= 0.127 Angle : 0.573 11.915 28246 Z= 0.304 Chirality : 0.039 0.276 3195 Planarity : 0.003 0.042 3284 Dihedral : 19.094 177.188 3487 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.16 % Allowed : 23.37 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 2240 helix: 2.36 (0.13), residues: 1404 sheet: -0.19 (0.48), residues: 145 loop : -2.19 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1110 TYR 0.017 0.001 TYR B 2 PHE 0.030 0.001 PHE E2110 TRP 0.008 0.001 TRP E2255 HIS 0.011 0.001 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (20708) covalent geometry : angle 0.57348 / 0.30 (28246) hydrogen bonds : bond 0.05769 / 3.89 ( 1232) hydrogen bonds : angle 3.94719 / 2.78 ( 3548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7407 (pt0) cc_final: 0.7104 (pt0) REVERT: B 946 LEU cc_start: 0.8409 (mt) cc_final: 0.8078 (mt) REVERT: B 1108 GLU cc_start: 0.6734 (mp0) cc_final: 0.6385 (mt-10) REVERT: B 1114 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8362 (pp30) REVERT: C 33 PHE cc_start: 0.8437 (t80) cc_final: 0.7667 (t80) REVERT: C 85 ILE cc_start: 0.7340 (tp) cc_final: 0.7137 (tp) REVERT: C 163 PHE cc_start: 0.8187 (m-80) cc_final: 0.7958 (m-80) REVERT: C 620 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8721 (mm) REVERT: E 1193 MET cc_start: 0.6302 (mtp) cc_final: 0.5681 (mtm) REVERT: E 1210 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6610 (mm) REVERT: E 1251 MET cc_start: 0.7896 (mpp) cc_final: 0.7540 (mpp) REVERT: E 1254 MET cc_start: 0.7471 (ptp) cc_final: 0.7168 (tpp) REVERT: E 1312 LEU cc_start: 0.9311 (mm) cc_final: 0.8995 (mm) REVERT: E 1570 LEU cc_start: 0.8060 (mt) cc_final: 0.7759 (mt) REVERT: E 1864 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8202 (p) REVERT: E 2011 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9394 (mp) REVERT: E 2339 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7789 (t70) REVERT: E 2349 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8125 (m-80) outliers start: 44 outliers final: 31 residues processed: 196 average time/residue: 0.1197 time to fit residues: 39.9302 Evaluate side-chains 191 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1486 TYR Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 2011 LEU Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 50 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073771 restraints weight = 55416.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.074382 restraints weight = 40798.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075071 restraints weight = 31038.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075342 restraints weight = 27397.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075461 restraints weight = 24892.848| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20708 Z= 0.128 Angle : 0.581 13.250 28246 Z= 0.305 Chirality : 0.039 0.280 3195 Planarity : 0.003 0.040 3284 Dihedral : 19.039 176.474 3487 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.26 % Allowed : 23.47 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2240 helix: 2.45 (0.13), residues: 1403 sheet: -0.06 (0.48), residues: 144 loop : -2.16 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1303 TYR 0.016 0.001 TYR B 137 PHE 0.028 0.001 PHE E2110 TRP 0.007 0.001 TRP E1680 HIS 0.011 0.001 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (20708) covalent geometry : angle 0.58059 / 0.30 (28246) hydrogen bonds : bond 0.05581 / 3.76 ( 1232) hydrogen bonds : angle 3.88479 / 2.73 ( 3548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7380 (pt0) cc_final: 0.7074 (pt0) REVERT: B 946 LEU cc_start: 0.8380 (mt) cc_final: 0.8072 (mt) REVERT: B 1108 GLU cc_start: 0.6899 (mp0) cc_final: 0.6483 (mt-10) REVERT: B 1114 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8421 (pp30) REVERT: C 33 PHE cc_start: 0.8420 (t80) cc_final: 0.7657 (t80) REVERT: C 163 PHE cc_start: 0.8143 (m-80) cc_final: 0.7920 (m-80) REVERT: C 620 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (mm) REVERT: E 1193 MET cc_start: 0.6283 (mtp) cc_final: 0.5668 (mtm) REVERT: E 1210 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6575 (mm) REVERT: E 1251 MET cc_start: 0.7934 (mpp) cc_final: 0.7572 (mpp) REVERT: E 1254 MET cc_start: 0.7528 (ptp) cc_final: 0.6868 (tpt) REVERT: E 1312 LEU cc_start: 0.9314 (mm) cc_final: 0.8992 (mm) REVERT: E 1570 LEU cc_start: 0.8053 (mt) cc_final: 0.7769 (mt) REVERT: E 1864 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 2339 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7801 (t70) REVERT: E 2349 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7935 (m-80) outliers start: 46 outliers final: 35 residues processed: 201 average time/residue: 0.1180 time to fit residues: 40.0263 Evaluate side-chains 198 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1486 TYR Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN A1177 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.070815 restraints weight = 54945.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071287 restraints weight = 42008.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071892 restraints weight = 31962.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.072179 restraints weight = 28051.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.072308 restraints weight = 25629.255| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20708 Z= 0.226 Angle : 0.650 12.663 28246 Z= 0.342 Chirality : 0.042 0.298 3195 Planarity : 0.004 0.042 3284 Dihedral : 19.137 175.809 3487 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.45 % Allowed : 23.37 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2240 helix: 2.27 (0.13), residues: 1408 sheet: -0.16 (0.48), residues: 144 loop : -2.24 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.020 0.002 TYR B 2 PHE 0.025 0.002 PHE E2110 TRP 0.007 0.001 TRP C 23 HIS 0.012 0.001 HIS E2627 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (20708) covalent geometry : angle 0.65016 / 0.34 (28246) hydrogen bonds : bond 0.06297 / 4.20 ( 1232) hydrogen bonds : angle 4.15201 / 2.91 ( 3548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.18 seconds wall clock time: 47 minutes 53.52 seconds (2873.52 seconds total)