Starting phenix.real_space_refine on Fri Aug 7 07:07:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.cif Found real_map, /net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.map" model { file = "/net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11gp_75681/08_2026/11gp_75681.cif" } resolution = 3.43 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= 0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11972 2.51 5 N 3309 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19068 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2453, 19068 Classifications: {'peptide': 2453} Link IDs: {'PTRANS': 84, 'TRANS': 2368} Chain breaks: 3 Time building chain proxies: 3.94, per 1000 atoms: 0.21 Number of scatterers: 19068 At special positions: 0 Unit cell: (100.58, 140.17, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3695 8.00 N 3309 7.00 C 11972 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: 1.73 Conformation dependent library (CDL) restraints added in 795.7 milliseconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4602 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 16 sheets defined 65.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'A' and resid 1050 through 1059 Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1079 through 1110 removed outlier: 3.969A pdb=" N GLU A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1113 No H-bonds generated for 'chain 'A' and resid 1111 through 1113' Processing helix chain 'A' and resid 1114 through 1120 Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1129 through 1134 removed outlier: 3.573A pdb=" N ASN A1133 " --> pdb=" O LYS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1161 removed outlier: 4.146A pdb=" N THR A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1167 Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1182 through 1186 removed outlier: 3.623A pdb=" N LEU A1186 " --> pdb=" O GLN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1196 removed outlier: 4.106A pdb=" N GLN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 Processing helix chain 'A' and resid 1224 through 1229 Processing helix chain 'A' and resid 1229 through 1246 Processing helix chain 'A' and resid 1257 through 1259 No H-bonds generated for 'chain 'A' and resid 1257 through 1259' Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1286 through 1293 removed outlier: 3.657A pdb=" N GLU A1290 " --> pdb=" O THR A1286 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1333 Processing helix chain 'A' and resid 1340 through 1351 removed outlier: 3.529A pdb=" N GLN A1345 " --> pdb=" O THR A1341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1346 " --> pdb=" O PRO A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1370 through 1402 removed outlier: 4.086A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER A1383 " --> pdb=" O GLY A1379 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1396 " --> pdb=" O PHE A1392 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A1401 " --> pdb=" O GLN A1397 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1402 " --> pdb=" O VAL A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1439 removed outlier: 3.825A pdb=" N ALA A1439 " --> pdb=" O LEU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1468 Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 4.016A pdb=" N MET A1475 " --> pdb=" O VAL A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1490 Processing helix chain 'A' and resid 1492 through 1506 Processing helix chain 'A' and resid 1511 through 1521 Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1525 through 1539 Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1575 through 1583 Processing helix chain 'A' and resid 1595 through 1601 Processing helix chain 'A' and resid 1607 through 1627 removed outlier: 3.516A pdb=" N SER A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.618A pdb=" N GLN A1634 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1646 " --> pdb=" O SER A1642 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A1647 " --> pdb=" O LEU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1675 Processing helix chain 'A' and resid 1678 through 1706 removed outlier: 3.567A pdb=" N VAL A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1706 " --> pdb=" O LEU A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1719 Processing helix chain 'A' and resid 1720 through 1722 No H-bonds generated for 'chain 'A' and resid 1720 through 1722' Processing helix chain 'A' and resid 1724 through 1744 Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.511A pdb=" N TYR A1772 " --> pdb=" O PRO A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1803 removed outlier: 3.513A pdb=" N HIS A1788 " --> pdb=" O GLU A1784 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1789 " --> pdb=" O ASN A1785 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A1792 " --> pdb=" O HIS A1788 " (cutoff:3.500A) Proline residue: A1793 - end of helix removed outlier: 3.667A pdb=" N ASN A1796 " --> pdb=" O GLU A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1841 removed outlier: 3.783A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A1841 " --> pdb=" O ALA A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1862 Processing helix chain 'A' and resid 1863 through 1867 Processing helix chain 'A' and resid 1896 through 1899 removed outlier: 3.963A pdb=" N ARG A1899 " --> pdb=" O LEU A1896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1896 through 1899' Processing helix chain 'A' and resid 1912 through 1914 No H-bonds generated for 'chain 'A' and resid 1912 through 1914' Processing helix chain 'A' and resid 1915 through 1925 removed outlier: 3.632A pdb=" N PHE A1919 " --> pdb=" O ALA A1915 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A1920 " --> pdb=" O GLY A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1934 Processing helix chain 'A' and resid 1956 through 1972 Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.599A pdb=" N ASN A1979 " --> pdb=" O ASN A1975 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 Processing helix chain 'A' and resid 1997 through 2006 Processing helix chain 'A' and resid 2010 through 2015 removed outlier: 4.110A pdb=" N GLU A2015 " --> pdb=" O TYR A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.721A pdb=" N ILE A2029 " --> pdb=" O ALA A2025 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A2031 " --> pdb=" O SER A2027 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A2048 " --> pdb=" O HIS A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2144 through 2148 Processing helix chain 'A' and resid 2151 through 2167 Processing helix chain 'A' and resid 2176 through 2187 Processing helix chain 'A' and resid 2198 through 2203 Processing helix chain 'A' and resid 2222 through 2244 removed outlier: 3.611A pdb=" N GLU A2238 " --> pdb=" O SER A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2267 Processing helix chain 'A' and resid 2275 through 2294 Processing helix chain 'A' and resid 2299 through 2317 removed outlier: 3.666A pdb=" N ALA A2305 " --> pdb=" O ALA A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2318 through 2326 removed outlier: 3.846A pdb=" N LYS A2326 " --> pdb=" O ALA A2322 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2347 removed outlier: 3.565A pdb=" N TRP A2347 " --> pdb=" O LYS A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2384 removed outlier: 4.227A pdb=" N GLY A2384 " --> pdb=" O VAL A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2406 removed outlier: 3.834A pdb=" N SER A2399 " --> pdb=" O ASN A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2412 Processing helix chain 'A' and resid 2429 through 2442 removed outlier: 3.677A pdb=" N SER A2433 " --> pdb=" O ASN A2429 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A2436 " --> pdb=" O MET A2432 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A2439 " --> pdb=" O THR A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2470 removed outlier: 4.116A pdb=" N MET A2458 " --> pdb=" O SER A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2471 through 2473 No H-bonds generated for 'chain 'A' and resid 2471 through 2473' Processing helix chain 'A' and resid 2474 through 2488 removed outlier: 3.826A pdb=" N HIS A2487 " --> pdb=" O HIS A2483 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2493 Processing helix chain 'A' and resid 2501 through 2517 removed outlier: 4.204A pdb=" N ARG A2505 " --> pdb=" O ASN A2501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A2515 " --> pdb=" O LYS A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2542 removed outlier: 4.131A pdb=" N THR A2534 " --> pdb=" O SER A2530 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A2541 " --> pdb=" O GLY A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2550 removed outlier: 3.526A pdb=" N ARG A2546 " --> pdb=" O ASN A2542 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2559 Processing helix chain 'A' and resid 2568 through 2585 removed outlier: 3.534A pdb=" N THR A2574 " --> pdb=" O THR A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2616 removed outlier: 3.861A pdb=" N SER A2596 " --> pdb=" O ASN A2592 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A2598 " --> pdb=" O GLN A2594 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A2599 " --> pdb=" O ASP A2595 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A2610 " --> pdb=" O ALA A2606 " (cutoff:3.500A) Processing helix chain 'A' and resid 2617 through 2619 No H-bonds generated for 'chain 'A' and resid 2617 through 2619' Processing helix chain 'A' and resid 2624 through 2642 removed outlier: 4.316A pdb=" N GLU A2642 " --> pdb=" O GLU A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2657 through 2659 No H-bonds generated for 'chain 'A' and resid 2657 through 2659' Processing helix chain 'A' and resid 2660 through 2665 Processing helix chain 'A' and resid 2665 through 2675 Processing helix chain 'A' and resid 2680 through 2684 Processing helix chain 'A' and resid 2685 through 2694 Processing helix chain 'A' and resid 2695 through 2708 removed outlier: 3.561A pdb=" N LEU A2702 " --> pdb=" O PRO A2698 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASP A2705 " --> pdb=" O ASP A2701 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2736 removed outlier: 3.677A pdb=" N ILE A2727 " --> pdb=" O VAL A2723 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A2728 " --> pdb=" O LYS A2724 " (cutoff:3.500A) Processing helix chain 'A' and resid 2736 through 2745 removed outlier: 4.148A pdb=" N THR A2740 " --> pdb=" O GLU A2736 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A2741 " --> pdb=" O HIS A2737 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A2745 " --> pdb=" O VAL A2741 " (cutoff:3.500A) Processing helix chain 'A' and resid 2751 through 2763 Processing helix chain 'A' and resid 2766 through 2773 Processing helix chain 'A' and resid 2778 through 2783 Processing helix chain 'A' and resid 2787 through 2805 removed outlier: 3.541A pdb=" N ASN A2802 " --> pdb=" O LYS A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2825 Processing helix chain 'A' and resid 2836 through 2842 removed outlier: 3.894A pdb=" N LEU A2842 " --> pdb=" O ILE A2838 " (cutoff:3.500A) Processing helix chain 'A' and resid 2856 through 2868 Processing helix chain 'A' and resid 2873 through 2884 removed outlier: 3.892A pdb=" N GLU A2879 " --> pdb=" O ASP A2875 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A2882 " --> pdb=" O SER A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2907 Processing helix chain 'A' and resid 2909 through 2914 Processing helix chain 'A' and resid 2936 through 2943 removed outlier: 3.862A pdb=" N LYS A2941 " --> pdb=" O LYS A2937 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A2942 " --> pdb=" O GLU A2938 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A2943 " --> pdb=" O PHE A2939 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3022 removed outlier: 3.507A pdb=" N LYS A3019 " --> pdb=" O GLU A3015 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3057 removed outlier: 3.587A pdb=" N HIS A3055 " --> pdb=" O MET A3052 " (cutoff:3.500A) Processing helix chain 'A' and resid 3063 through 3099 removed outlier: 3.763A pdb=" N GLY A3067 " --> pdb=" O ALA A3063 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A3083 " --> pdb=" O ALA A3079 " (cutoff:3.500A) Processing helix chain 'A' and resid 3101 through 3106 Processing helix chain 'A' and resid 3117 through 3124 Processing helix chain 'A' and resid 3125 through 3127 No H-bonds generated for 'chain 'A' and resid 3125 through 3127' Processing helix chain 'A' and resid 3128 through 3140 removed outlier: 3.657A pdb=" N LEU A3138 " --> pdb=" O LYS A3134 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3155 removed outlier: 3.769A pdb=" N ASP A3153 " --> pdb=" O ASP A3149 " (cutoff:3.500A) Processing helix chain 'A' and resid 3156 through 3158 No H-bonds generated for 'chain 'A' and resid 3156 through 3158' Processing helix chain 'A' and resid 3173 through 3188 removed outlier: 4.805A pdb=" N THR A3179 " --> pdb=" O SER A3175 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A3180 " --> pdb=" O THR A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3197 Processing helix chain 'A' and resid 3202 through 3207 removed outlier: 3.605A pdb=" N LEU A3206 " --> pdb=" O THR A3202 " (cutoff:3.500A) Processing helix chain 'A' and resid 3210 through 3237 removed outlier: 3.631A pdb=" N ILE A3214 " --> pdb=" O ALA A3210 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A3221 " --> pdb=" O LYS A3217 " (cutoff:3.500A) Proline residue: A3222 - end of helix Processing helix chain 'A' and resid 3239 through 3271 removed outlier: 3.877A pdb=" N VAL A3245 " --> pdb=" O LYS A3241 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A3247 " --> pdb=" O ILE A3243 " (cutoff:3.500A) Proline residue: A3248 - end of helix Processing helix chain 'A' and resid 3272 through 3274 No H-bonds generated for 'chain 'A' and resid 3272 through 3274' Processing helix chain 'A' and resid 3277 through 3297 Processing helix chain 'A' and resid 3300 through 3306 removed outlier: 3.511A pdb=" N ILE A3304 " --> pdb=" O ILE A3300 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3329 removed outlier: 4.301A pdb=" N ALA A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A3329 " --> pdb=" O ALA A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3340 removed outlier: 3.515A pdb=" N LEU A3340 " --> pdb=" O LEU A3336 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3382 removed outlier: 3.576A pdb=" N GLN A3361 " --> pdb=" O THR A3357 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3400 removed outlier: 3.575A pdb=" N GLY A3395 " --> pdb=" O SER A3391 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A3396 " --> pdb=" O GLU A3392 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3407 Processing helix chain 'A' and resid 3417 through 3441 removed outlier: 4.009A pdb=" N TRP A3422 " --> pdb=" O MET A3418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A3439 " --> pdb=" O MET A3435 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3448 Processing helix chain 'A' and resid 3467 through 3474 Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3493 through 3500 Processing sheet with id=AA1, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA2, first strand: chain 'A' and resid 1136 through 1138 Processing sheet with id=AA3, first strand: chain 'A' and resid 1249 through 1255 Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1302 removed outlier: 4.227A pdb=" N PHE A1301 " --> pdb=" O HIS A1411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AA6, first strand: chain 'A' and resid 1414 through 1416 Processing sheet with id=AA7, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AA8, first strand: chain 'A' and resid 1587 through 1589 removed outlier: 3.617A pdb=" N PHE A1588 " --> pdb=" O SER A2053 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1745 through 1750 Processing sheet with id=AB1, first strand: chain 'A' and resid 1870 through 1871 Processing sheet with id=AB2, first strand: chain 'A' and resid 1881 through 1885 removed outlier: 3.681A pdb=" N SER A1882 " --> pdb=" O ALA A1908 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1891 through 1894 Processing sheet with id=AB4, first strand: chain 'A' and resid 2126 through 2127 removed outlier: 3.615A pdb=" N ILE A2172 " --> pdb=" O LEU A2136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A2171 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A2218 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A2173 " --> pdb=" O LEU A2218 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR A2209 " --> pdb=" O LEU A2370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2930 through 2935 removed outlier: 3.647A pdb=" N ASN A2930 " --> pdb=" O SER A2969 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A2934 " --> pdb=" O GLY A2965 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS A2964 " --> pdb=" O THR A2952 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR A2952 " --> pdb=" O LYS A2964 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A2966 " --> pdb=" O ILE A2950 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3007 through 3008 removed outlier: 6.909A pdb=" N ILE A3034 " --> pdb=" O VAL A3042 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR A3044 " --> pdb=" O MET A3032 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET A3032 " --> pdb=" O TYR A3044 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3108 through 3110 1057 hydrogen bonds defined for protein. 3006 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6374 1.34 - 1.45: 1983 1.45 - 1.57: 10829 1.57 - 1.69: 0 1.69 - 1.80: 184 Bond restraints: 19370 Sorted by residual: bond pdb=" C LYS A2049 " pdb=" N VAL A2050 " ideal model delta sigma weight residual 1.330 1.303 0.028 1.42e-02 4.96e+03 3.78e+00 bond pdb=" N VAL A3460 " pdb=" CA VAL A3460 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.25e-02 6.40e+03 3.70e+00 bond pdb=" C ASN A1429 " pdb=" N PRO A1430 " ideal model delta sigma weight residual 1.336 1.315 0.021 1.08e-02 8.57e+03 3.68e+00 bond pdb=" C ASP A1469 " pdb=" N ILE A1470 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.40e-02 5.10e+03 3.62e+00 bond pdb=" CD2 TRP A3069 " pdb=" CE2 TRP A3069 " ideal model delta sigma weight residual 1.409 1.383 0.026 1.70e-02 3.46e+03 2.34e+00 ... (remaining 19365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 25176 1.52 - 3.05: 844 3.05 - 4.57: 120 4.57 - 6.10: 34 6.10 - 7.62: 4 Bond angle restraints: 26178 Sorted by residual: angle pdb=" N ILE A3312 " pdb=" CA ILE A3312 " pdb=" C ILE A3312 " ideal model delta sigma weight residual 112.43 107.64 4.79 9.20e-01 1.18e+00 2.71e+01 angle pdb=" N VAL A2060 " pdb=" CA VAL A2060 " pdb=" C VAL A2060 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" N VAL A3450 " pdb=" CA VAL A3450 " pdb=" C VAL A3450 " ideal model delta sigma weight residual 113.71 110.11 3.60 9.50e-01 1.11e+00 1.44e+01 angle pdb=" N VAL A2663 " pdb=" CA VAL A2663 " pdb=" C VAL A2663 " ideal model delta sigma weight residual 112.12 109.20 2.92 8.40e-01 1.42e+00 1.21e+01 angle pdb=" N VAL A1017 " pdb=" CA VAL A1017 " pdb=" C VAL A1017 " ideal model delta sigma weight residual 110.42 113.66 -3.24 9.60e-01 1.09e+00 1.14e+01 ... (remaining 26173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10463 17.66 - 35.32: 1153 35.32 - 52.98: 216 52.98 - 70.64: 44 70.64 - 88.30: 20 Dihedral angle restraints: 11896 sinusoidal: 4773 harmonic: 7123 Sorted by residual: dihedral pdb=" CA LEU A2831 " pdb=" C LEU A2831 " pdb=" N LEU A2832 " pdb=" CA LEU A2832 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU A1886 " pdb=" C GLU A1886 " pdb=" N VAL A1887 " pdb=" CA VAL A1887 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A2833 " pdb=" C ARG A2833 " pdb=" N ASN A2834 " pdb=" CA ASN A2834 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 11893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2050 0.039 - 0.078: 727 0.078 - 0.117: 184 0.117 - 0.157: 22 0.157 - 0.196: 2 Chirality restraints: 2985 Sorted by residual: chirality pdb=" CG LEU A1207 " pdb=" CB LEU A1207 " pdb=" CD1 LEU A1207 " pdb=" CD2 LEU A1207 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB ILE A3317 " pdb=" CA ILE A3317 " pdb=" CG1 ILE A3317 " pdb=" CG2 ILE A3317 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA PRO A2976 " pdb=" N PRO A2976 " pdb=" C PRO A2976 " pdb=" CB PRO A2976 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2982 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A2921 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A2922 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A2922 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2922 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2076 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A2077 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A3069 " -0.006 2.00e-02 2.50e+03 1.10e-02 3.04e+00 pdb=" CG TRP A3069 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A3069 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A3069 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A3069 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A3069 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A3069 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3069 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3069 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A3069 " -0.022 2.00e-02 2.50e+03 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 244 2.62 - 3.19: 18373 3.19 - 3.76: 28715 3.76 - 4.33: 38587 4.33 - 4.90: 62993 Nonbonded interactions: 148912 Sorted by model distance: nonbonded pdb=" OE2 GLU A2797 " pdb=" OH TYR A2864 " model vdw 2.051 3.040 nonbonded pdb=" OD1 ASN A1316 " pdb=" OH TYR A1907 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR A1086 " pdb=" O PHE A1284 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR A2243 " pdb=" OE2 GLU A2260 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR A2765 " pdb=" OG SER A2865 " model vdw 2.138 3.040 ... (remaining 148907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.006 0.049 19370 Z= 0.283 Angle : 0.674 7.621 26178 Z= 0.390 Chirality : 0.042 0.196 2985 Planarity : 0.004 0.060 3411 Dihedral : 15.341 88.297 7294 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 1.56 % Allowed : 11.09 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2445 helix: 1.11 (0.14), residues: 1391 sheet: -1.28 (0.54), residues: 78 loop : -1.56 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2397 TYR 0.016 0.002 TYR A1414 PHE 0.013 0.002 PHE A1078 TRP 0.022 0.002 TRP A3069 HIS 0.008 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.28 (19370) covalent geometry : angle 0.67448 / 0.39 (26178) hydrogen bonds : bond 0.19288 / 12.62 ( 1057) hydrogen bonds : angle 6.67244 / 4.67 ( 3006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1198 MET cc_start: 0.8391 (mtm) cc_final: 0.7760 (ttm) REVERT: A 1256 MET cc_start: 0.9269 (mmm) cc_final: 0.8606 (mtp) REVERT: A 1478 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7959 (tp30) REVERT: A 1786 MET cc_start: 0.8636 (tpp) cc_final: 0.8284 (tpp) REVERT: A 1827 MET cc_start: 0.8489 (mmm) cc_final: 0.8166 (mmp) REVERT: A 1847 LYS cc_start: 0.9533 (mttt) cc_final: 0.9305 (tptp) REVERT: A 1988 MET cc_start: 0.8515 (mmm) cc_final: 0.8290 (mmm) REVERT: A 2405 PHE cc_start: 0.8630 (m-80) cc_final: 0.8396 (m-10) REVERT: A 2592 ASN cc_start: 0.8972 (m-40) cc_final: 0.8604 (t0) REVERT: A 2602 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 2833 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7396 (mtt-85) REVERT: A 2869 MET cc_start: 0.7270 (ttm) cc_final: 0.6891 (ttp) REVERT: A 2873 ASP cc_start: 0.8498 (t0) cc_final: 0.8227 (t70) REVERT: A 2920 TYR cc_start: 0.8664 (t80) cc_final: 0.8433 (t80) REVERT: A 3150 MET cc_start: 0.8744 (mmm) cc_final: 0.8131 (mmt) REVERT: A 3328 LYS cc_start: 0.9439 (ptpt) cc_final: 0.9089 (ptpp) REVERT: A 3435 MET cc_start: 0.9242 (tpp) cc_final: 0.8489 (tpp) REVERT: A 3455 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6455 (m) REVERT: A 3456 MET cc_start: 0.8073 (mmt) cc_final: 0.7508 (mmm) outliers start: 32 outliers final: 19 residues processed: 265 average time/residue: 0.1620 time to fit residues: 64.2992 Evaluate side-chains 171 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1884 ASN Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2225 THR Chi-restraints excluded: chain A residue 2409 VAL Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2637 ILE Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2833 ARG Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3131 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3455 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 GLN A1193 GLN A1313 GLN A1814 GLN ** A2394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3080 GLN A3330 HIS A3497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.078995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060714 restraints weight = 60444.336| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.69 r_work: 0.2917 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19370 Z= 0.240 Angle : 0.637 7.216 26178 Z= 0.340 Chirality : 0.043 0.161 2985 Planarity : 0.004 0.044 3411 Dihedral : 5.544 52.817 2663 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 14.50 % Favored : 82.87 % 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: 0.25 (0.17), residues: 2445 helix: 1.37 (0.14), residues: 1415 sheet: -1.35 (0.54), residues: 80 loop : -1.58 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2986 TYR 0.024 0.002 TYR A2170 PHE 0.016 0.002 PHE A1078 TRP 0.016 0.002 TRP A2314 HIS 0.008 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (19370) covalent geometry : angle 0.63680 / 0.34 (26178) hydrogen bonds : bond 0.05319 / 3.50 ( 1057) hydrogen bonds : angle 4.79473 / 3.36 ( 3006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8911 (m-80) REVERT: A 1198 MET cc_start: 0.8244 (mtm) cc_final: 0.7810 (mtp) REVERT: A 1256 MET cc_start: 0.9213 (mmm) cc_final: 0.8980 (mmp) REVERT: A 1416 MET cc_start: 0.8600 (mmm) cc_final: 0.8153 (mmm) REVERT: A 1480 MET cc_start: 0.9103 (tmm) cc_final: 0.8857 (tmm) REVERT: A 1786 MET cc_start: 0.8951 (tpp) cc_final: 0.8642 (tpp) REVERT: A 1818 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8818 (tp40) REVERT: A 1827 MET cc_start: 0.8535 (mmm) cc_final: 0.8234 (mmp) REVERT: A 1900 MET cc_start: 0.8833 (mpp) cc_final: 0.8185 (mpp) REVERT: A 1988 MET cc_start: 0.8737 (mmm) cc_final: 0.8536 (mmm) REVERT: A 2396 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: A 2400 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 2602 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 2690 MET cc_start: 0.9087 (mtp) cc_final: 0.8737 (mtp) REVERT: A 2774 MET cc_start: 0.8157 (ttm) cc_final: 0.7768 (tmm) REVERT: A 2776 MET cc_start: 0.8515 (ptm) cc_final: 0.8188 (pmm) REVERT: A 2833 ARG cc_start: 0.7471 (mpt-90) cc_final: 0.7195 (mtt90) REVERT: A 3150 MET cc_start: 0.8732 (mmm) cc_final: 0.7954 (mmm) REVERT: A 3333 MET cc_start: 0.9093 (mmm) cc_final: 0.8757 (mpp) REVERT: A 3339 LYS cc_start: 0.8308 (pttt) cc_final: 0.8087 (pttt) outliers start: 54 outliers final: 33 residues processed: 206 average time/residue: 0.1438 time to fit residues: 46.3628 Evaluate side-chains 179 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1429 ASN Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2225 THR Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2396 GLU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2549 ILE Chi-restraints excluded: chain A residue 2663 VAL Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2894 TYR Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3131 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3234 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 92 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062222 restraints weight = 60551.609| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.71 r_work: 0.2943 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19370 Z= 0.142 Angle : 0.537 7.304 26178 Z= 0.285 Chirality : 0.040 0.137 2985 Planarity : 0.004 0.045 3411 Dihedral : 5.060 54.307 2651 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.04 % Allowed : 15.67 % Favored : 82.29 % 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: 0.52 (0.17), residues: 2445 helix: 1.61 (0.14), residues: 1421 sheet: -1.20 (0.55), residues: 80 loop : -1.54 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2986 TYR 0.018 0.001 TYR A2170 PHE 0.016 0.001 PHE A1078 TRP 0.011 0.001 TRP A1159 HIS 0.006 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19370) covalent geometry : angle 0.53663 / 0.28 (26178) hydrogen bonds : bond 0.04296 / 2.81 ( 1057) hydrogen bonds : angle 4.28346 / 3.00 ( 3006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1198 MET cc_start: 0.8268 (mtm) cc_final: 0.7834 (mtp) REVERT: A 1256 MET cc_start: 0.9087 (mmm) cc_final: 0.8516 (mtp) REVERT: A 1480 MET cc_start: 0.9066 (tmm) cc_final: 0.8799 (tmm) REVERT: A 1602 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 1696 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 1786 MET cc_start: 0.8920 (tpp) cc_final: 0.8434 (tpp) REVERT: A 1818 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8946 (mm-40) REVERT: A 1827 MET cc_start: 0.8524 (mmm) cc_final: 0.8239 (mmp) REVERT: A 1900 MET cc_start: 0.8910 (mpp) cc_final: 0.8693 (mpp) REVERT: A 1988 MET cc_start: 0.8673 (mmm) cc_final: 0.8447 (mmm) REVERT: A 2359 MET cc_start: 0.9228 (mtm) cc_final: 0.8995 (mtp) REVERT: A 2400 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 2602 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 2690 MET cc_start: 0.9085 (mtp) cc_final: 0.8732 (mtp) REVERT: A 2774 MET cc_start: 0.8107 (ttm) cc_final: 0.7815 (tmm) REVERT: A 2776 MET cc_start: 0.8557 (ptm) cc_final: 0.8262 (pmm) REVERT: A 2833 ARG cc_start: 0.7475 (mpt-90) cc_final: 0.7219 (mtt90) REVERT: A 3150 MET cc_start: 0.8731 (mmm) cc_final: 0.7974 (mmm) REVERT: A 3319 ARG cc_start: 0.8698 (ttm170) cc_final: 0.8495 (ttm170) REVERT: A 3333 MET cc_start: 0.9095 (mmm) cc_final: 0.8803 (mpp) outliers start: 42 outliers final: 23 residues processed: 193 average time/residue: 0.1558 time to fit residues: 46.9098 Evaluate side-chains 173 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1429 ASN Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2225 THR Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3131 THR Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3234 ILE Chi-restraints excluded: chain A residue 3309 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 1 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 211 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3089 GLN A3133 HIS A3169 ASN A3500 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062119 restraints weight = 58343.745| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.48 r_work: 0.2958 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19370 Z= 0.147 Angle : 0.529 10.010 26178 Z= 0.278 Chirality : 0.040 0.139 2985 Planarity : 0.003 0.041 3411 Dihedral : 4.844 57.828 2647 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.34 % Allowed : 16.93 % Favored : 80.73 % 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: 0.64 (0.17), residues: 2445 helix: 1.69 (0.14), residues: 1441 sheet: -1.00 (0.57), residues: 75 loop : -1.55 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2986 TYR 0.016 0.001 TYR A2240 PHE 0.013 0.001 PHE A1078 TRP 0.010 0.001 TRP A1159 HIS 0.006 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19370) covalent geometry : angle 0.52939 / 0.28 (26178) hydrogen bonds : bond 0.04036 / 2.65 ( 1057) hydrogen bonds : angle 4.12791 / 2.89 ( 3006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1013 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: A 1147 GLN cc_start: 0.9022 (pm20) cc_final: 0.8750 (pm20) REVERT: A 1198 MET cc_start: 0.8200 (mtm) cc_final: 0.7556 (ttp) REVERT: A 1199 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8748 (t) REVERT: A 1256 MET cc_start: 0.9064 (mmm) cc_final: 0.8494 (mtp) REVERT: A 1424 MET cc_start: 0.8784 (ttm) cc_final: 0.8546 (ttp) REVERT: A 1480 MET cc_start: 0.9091 (tmm) cc_final: 0.8811 (tmm) REVERT: A 1786 MET cc_start: 0.8908 (tpp) cc_final: 0.8480 (tpp) REVERT: A 1818 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8837 (tp40) REVERT: A 1827 MET cc_start: 0.8489 (mmm) cc_final: 0.8207 (mmp) REVERT: A 1988 MET cc_start: 0.8666 (mmm) cc_final: 0.8427 (mmm) REVERT: A 2396 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: A 2400 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 2485 MET cc_start: 0.8670 (tpp) cc_final: 0.8250 (mmm) REVERT: A 2602 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 2690 MET cc_start: 0.9068 (mtp) cc_final: 0.8722 (mtp) REVERT: A 2774 MET cc_start: 0.8080 (ttm) cc_final: 0.7844 (tmm) REVERT: A 2833 ARG cc_start: 0.7456 (mpt-90) cc_final: 0.6782 (mtt-85) REVERT: A 2983 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7631 (mm-40) REVERT: A 3150 MET cc_start: 0.8737 (mmm) cc_final: 0.7874 (mmm) outliers start: 48 outliers final: 30 residues processed: 193 average time/residue: 0.1464 time to fit residues: 44.5344 Evaluate side-chains 176 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1429 ASN Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2396 GLU Chi-restraints excluded: chain A residue 2398 LEU Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2983 GLN Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061437 restraints weight = 58930.279| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.64 r_work: 0.2964 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19370 Z= 0.116 Angle : 0.504 9.145 26178 Z= 0.263 Chirality : 0.039 0.155 2985 Planarity : 0.003 0.046 3411 Dihedral : 4.677 59.684 2645 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 18.05 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2445 helix: 1.82 (0.14), residues: 1446 sheet: -0.90 (0.58), residues: 75 loop : -1.45 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2397 TYR 0.013 0.001 TYR A1030 PHE 0.018 0.001 PHE A1850 TRP 0.009 0.001 TRP A1159 HIS 0.005 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (19370) covalent geometry : angle 0.50400 / 0.26 (26178) hydrogen bonds : bond 0.03680 / 2.40 ( 1057) hydrogen bonds : angle 3.95898 / 2.77 ( 3006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1078 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5956 (m-80) REVERT: A 1147 GLN cc_start: 0.9005 (pm20) cc_final: 0.8736 (pm20) REVERT: A 1198 MET cc_start: 0.8192 (mtm) cc_final: 0.7608 (ttp) REVERT: A 1256 MET cc_start: 0.9087 (mmm) cc_final: 0.8482 (mtp) REVERT: A 1424 MET cc_start: 0.8814 (ttm) cc_final: 0.8578 (ttp) REVERT: A 1480 MET cc_start: 0.9021 (tmm) cc_final: 0.8789 (tmm) REVERT: A 1602 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 1786 MET cc_start: 0.8926 (tpp) cc_final: 0.8515 (tpp) REVERT: A 1818 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8856 (tp40) REVERT: A 1827 MET cc_start: 0.8477 (mmm) cc_final: 0.8200 (mmp) REVERT: A 1988 MET cc_start: 0.8614 (mmm) cc_final: 0.8365 (mmm) REVERT: A 2396 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: A 2400 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 2485 MET cc_start: 0.8618 (tpp) cc_final: 0.8202 (mmm) REVERT: A 2602 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 2690 MET cc_start: 0.9044 (mtp) cc_final: 0.8678 (mtp) REVERT: A 2774 MET cc_start: 0.8131 (ttm) cc_final: 0.7866 (ttp) REVERT: A 2833 ARG cc_start: 0.7027 (mpt-90) cc_final: 0.6707 (mpt-90) REVERT: A 3150 MET cc_start: 0.8721 (mmm) cc_final: 0.7920 (mmm) REVERT: A 3331 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 3435 MET cc_start: 0.9415 (tpp) cc_final: 0.9175 (tpp) outliers start: 47 outliers final: 34 residues processed: 193 average time/residue: 0.1438 time to fit residues: 44.4748 Evaluate side-chains 182 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1235 MET Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2396 GLU Chi-restraints excluded: chain A residue 2398 LEU Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2896 VAL Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3234 ILE Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 114 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 87 optimal weight: 0.0670 chunk 109 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 187 optimal weight: 0.1980 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1133 ASN ** A2426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061667 restraints weight = 58699.498| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.61 r_work: 0.2966 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19370 Z= 0.122 Angle : 0.505 8.383 26178 Z= 0.264 Chirality : 0.039 0.148 2985 Planarity : 0.003 0.043 3411 Dihedral : 4.589 58.139 2645 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.77 % Allowed : 18.25 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.94 (0.17), residues: 2445 helix: 1.92 (0.14), residues: 1448 sheet: -0.80 (0.58), residues: 75 loop : -1.43 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2986 TYR 0.027 0.001 TYR A1030 PHE 0.014 0.001 PHE A2297 TRP 0.009 0.001 TRP A1159 HIS 0.006 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19370) covalent geometry : angle 0.50544 / 0.26 (26178) hydrogen bonds : bond 0.03592 / 2.34 ( 1057) hydrogen bonds : angle 3.91183 / 2.73 ( 3006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1078 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: A 1198 MET cc_start: 0.8219 (mtm) cc_final: 0.7632 (ttp) REVERT: A 1256 MET cc_start: 0.9075 (mmm) cc_final: 0.8477 (mtp) REVERT: A 1424 MET cc_start: 0.8815 (ttm) cc_final: 0.8552 (ttp) REVERT: A 1480 MET cc_start: 0.9031 (tmm) cc_final: 0.8791 (tmm) REVERT: A 1786 MET cc_start: 0.8951 (tpp) cc_final: 0.8553 (tpp) REVERT: A 1818 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8867 (tp40) REVERT: A 1827 MET cc_start: 0.8453 (mmm) cc_final: 0.8174 (mmp) REVERT: A 1850 PHE cc_start: 0.8169 (t80) cc_final: 0.7862 (t80) REVERT: A 1988 MET cc_start: 0.8591 (mmm) cc_final: 0.8283 (mmm) REVERT: A 2143 ASN cc_start: 0.8841 (m110) cc_final: 0.8574 (p0) REVERT: A 2396 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 2400 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 2485 MET cc_start: 0.8638 (tpp) cc_final: 0.8230 (mmm) REVERT: A 2602 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 2690 MET cc_start: 0.9017 (mtp) cc_final: 0.8637 (mtp) REVERT: A 2773 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 2836 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7167 (m-70) REVERT: A 3150 MET cc_start: 0.8716 (mmm) cc_final: 0.7896 (mmm) REVERT: A 3233 MET cc_start: 0.8864 (tpp) cc_final: 0.8390 (tpp) REVERT: A 3331 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 3343 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8018 (mmtm) outliers start: 57 outliers final: 36 residues processed: 192 average time/residue: 0.1463 time to fit residues: 43.7950 Evaluate side-chains 181 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1235 MET Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2243 TYR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2396 GLU Chi-restraints excluded: chain A residue 2398 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2773 THR Chi-restraints excluded: chain A residue 2836 HIS Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3431 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.0040 chunk 214 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1785 ASN ** A2394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.080270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061718 restraints weight = 58897.493| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.54 r_work: 0.2968 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19370 Z= 0.127 Angle : 0.519 9.522 26178 Z= 0.269 Chirality : 0.039 0.148 2985 Planarity : 0.004 0.069 3411 Dihedral : 4.569 56.193 2645 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.77 % Allowed : 18.35 % Favored : 78.88 % 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: 0.98 (0.17), residues: 2445 helix: 1.96 (0.14), residues: 1449 sheet: -0.75 (0.58), residues: 75 loop : -1.45 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2833 TYR 0.016 0.001 TYR A1030 PHE 0.011 0.001 PHE A1078 TRP 0.009 0.001 TRP A1159 HIS 0.006 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19370) covalent geometry : angle 0.51926 / 0.27 (26178) hydrogen bonds : bond 0.03552 / 2.32 ( 1057) hydrogen bonds : angle 3.89324 / 2.72 ( 3006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1102 SER cc_start: 0.9485 (OUTLIER) cc_final: 0.9211 (p) REVERT: A 1198 MET cc_start: 0.8205 (mtm) cc_final: 0.7443 (ttp) REVERT: A 1256 MET cc_start: 0.9070 (mmm) cc_final: 0.8481 (mtp) REVERT: A 1424 MET cc_start: 0.8777 (ttm) cc_final: 0.8565 (ttp) REVERT: A 1602 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 1786 MET cc_start: 0.8958 (tpp) cc_final: 0.8583 (tpp) REVERT: A 1818 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8858 (tp40) REVERT: A 1827 MET cc_start: 0.8443 (mmm) cc_final: 0.8173 (mmp) REVERT: A 1850 PHE cc_start: 0.8312 (t80) cc_final: 0.8093 (t80) REVERT: A 1988 MET cc_start: 0.8596 (mmm) cc_final: 0.8324 (mmm) REVERT: A 2400 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8503 (tm-30) REVERT: A 2485 MET cc_start: 0.8600 (tpp) cc_final: 0.8231 (mmm) REVERT: A 2602 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 2690 MET cc_start: 0.9001 (mtp) cc_final: 0.8647 (mtp) REVERT: A 2773 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 2776 MET cc_start: 0.7853 (pmm) cc_final: 0.7609 (pmm) REVERT: A 2833 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6849 (mtt90) REVERT: A 2836 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7077 (m-70) REVERT: A 3150 MET cc_start: 0.8695 (mmm) cc_final: 0.7911 (mmm) REVERT: A 3233 MET cc_start: 0.8861 (tpp) cc_final: 0.8425 (tpp) REVERT: A 3343 LYS cc_start: 0.8303 (mmtp) cc_final: 0.8095 (mmtt) outliers start: 57 outliers final: 38 residues processed: 198 average time/residue: 0.1405 time to fit residues: 43.8075 Evaluate side-chains 183 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1785 ASN Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2243 TYR Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2398 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2773 THR Chi-restraints excluded: chain A residue 2836 HIS Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2931 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3431 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 129 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1381 ASN A1785 ASN A2228 HIS A2394 ASN ** A2426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2451 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062537 restraints weight = 58581.988| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.54 r_work: 0.2992 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19370 Z= 0.106 Angle : 0.515 9.514 26178 Z= 0.265 Chirality : 0.039 0.160 2985 Planarity : 0.004 0.056 3411 Dihedral : 4.473 54.500 2645 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 2.14 % Allowed : 18.98 % Favored : 78.88 % 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: 1.02 (0.17), residues: 2445 helix: 1.99 (0.14), residues: 1449 sheet: -0.64 (0.58), residues: 75 loop : -1.43 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2833 TYR 0.013 0.001 TYR A2240 PHE 0.015 0.001 PHE A2297 TRP 0.008 0.001 TRP A1159 HIS 0.005 0.001 HIS A3444 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19370) covalent geometry : angle 0.51475 / 0.26 (26178) hydrogen bonds : bond 0.03394 / 2.22 ( 1057) hydrogen bonds : angle 3.82498 / 2.67 ( 3006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1102 SER cc_start: 0.9491 (OUTLIER) cc_final: 0.9239 (p) REVERT: A 1198 MET cc_start: 0.8074 (mtm) cc_final: 0.7572 (ttp) REVERT: A 1256 MET cc_start: 0.9053 (mmm) cc_final: 0.8475 (mtp) REVERT: A 1424 MET cc_start: 0.8735 (ttm) cc_final: 0.8526 (ttp) REVERT: A 1602 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 1786 MET cc_start: 0.8963 (tpp) cc_final: 0.8619 (tpp) REVERT: A 1818 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8858 (tp40) REVERT: A 1827 MET cc_start: 0.8423 (mmm) cc_final: 0.8162 (mmp) REVERT: A 1850 PHE cc_start: 0.8445 (t80) cc_final: 0.8128 (t80) REVERT: A 1988 MET cc_start: 0.8552 (mmm) cc_final: 0.8280 (mmm) REVERT: A 2143 ASN cc_start: 0.8809 (m110) cc_final: 0.8601 (p0) REVERT: A 2400 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 2485 MET cc_start: 0.8561 (tpp) cc_final: 0.8192 (mmm) REVERT: A 2602 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 2690 MET cc_start: 0.8978 (mtp) cc_final: 0.8614 (mtp) REVERT: A 2774 MET cc_start: 0.7617 (tmm) cc_final: 0.7241 (tmm) REVERT: A 2776 MET cc_start: 0.7693 (pmm) cc_final: 0.7281 (pmm) REVERT: A 2836 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6967 (m-70) REVERT: A 3150 MET cc_start: 0.8684 (mmm) cc_final: 0.8101 (mmt) REVERT: A 3233 MET cc_start: 0.8843 (tpp) cc_final: 0.8400 (tpp) REVERT: A 3331 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 3343 LYS cc_start: 0.8259 (mmtp) cc_final: 0.8013 (mmtm) outliers start: 44 outliers final: 35 residues processed: 187 average time/residue: 0.1395 time to fit residues: 41.1801 Evaluate side-chains 179 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2243 TYR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2398 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2836 HIS Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2931 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3151 LEU Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3467 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 83 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 217 optimal weight: 0.0040 chunk 124 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 163 optimal weight: 0.0060 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1785 ASN ** A2426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061294 restraints weight = 58919.961| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.75 r_work: 0.2988 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19370 Z= 0.102 Angle : 0.510 9.078 26178 Z= 0.261 Chirality : 0.038 0.189 2985 Planarity : 0.003 0.055 3411 Dihedral : 4.309 54.761 2643 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.89 % Favored : 95.99 % Rotamer: Outliers : 2.04 % Allowed : 19.08 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2445 helix: 2.11 (0.14), residues: 1445 sheet: -0.56 (0.59), residues: 75 loop : -1.40 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2833 TYR 0.013 0.001 TYR A2240 PHE 0.010 0.001 PHE A3309 TRP 0.008 0.001 TRP A2755 HIS 0.006 0.001 HIS A3444 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (19370) covalent geometry : angle 0.50960 / 0.26 (26178) hydrogen bonds : bond 0.03217 / 2.10 ( 1057) hydrogen bonds : angle 3.75048 / 2.62 ( 3006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1102 SER cc_start: 0.9541 (m) cc_final: 0.9297 (p) REVERT: A 1198 MET cc_start: 0.8127 (mtm) cc_final: 0.7798 (ttp) REVERT: A 1256 MET cc_start: 0.9093 (mmm) cc_final: 0.8463 (mtp) REVERT: A 1424 MET cc_start: 0.8848 (ttm) cc_final: 0.8585 (ttp) REVERT: A 1602 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 1786 MET cc_start: 0.8975 (tpp) cc_final: 0.8655 (tpp) REVERT: A 1818 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8830 (tp40) REVERT: A 1827 MET cc_start: 0.8467 (mmm) cc_final: 0.8199 (mmp) REVERT: A 1850 PHE cc_start: 0.8486 (t80) cc_final: 0.8268 (t80) REVERT: A 1988 MET cc_start: 0.8573 (mmm) cc_final: 0.8269 (mmm) REVERT: A 2143 ASN cc_start: 0.8858 (m110) cc_final: 0.8618 (p0) REVERT: A 2400 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 2485 MET cc_start: 0.8552 (tpp) cc_final: 0.8197 (mmm) REVERT: A 2602 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8590 (tm-30) REVERT: A 2690 MET cc_start: 0.9033 (mtp) cc_final: 0.8650 (mtp) REVERT: A 2776 MET cc_start: 0.7793 (pmm) cc_final: 0.7436 (pmm) REVERT: A 2836 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7027 (m-70) REVERT: A 3150 MET cc_start: 0.8712 (mmm) cc_final: 0.8116 (mmt) REVERT: A 3233 MET cc_start: 0.8832 (tpp) cc_final: 0.8377 (tpp) REVERT: A 3331 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 3339 LYS cc_start: 0.8172 (pttt) cc_final: 0.7909 (tttt) REVERT: A 3343 LYS cc_start: 0.8304 (mmtp) cc_final: 0.8058 (mmtm) outliers start: 42 outliers final: 33 residues processed: 192 average time/residue: 0.1309 time to fit residues: 40.1705 Evaluate side-chains 176 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1785 ASN Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2243 TYR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2836 HIS Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2931 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 40 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1785 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063969 restraints weight = 59000.966| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.67 r_work: 0.2991 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19370 Z= 0.113 Angle : 0.526 9.388 26178 Z= 0.267 Chirality : 0.039 0.182 2985 Planarity : 0.004 0.077 3411 Dihedral : 4.321 54.515 2643 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.85 % Allowed : 19.71 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2445 helix: 2.10 (0.14), residues: 1446 sheet: -0.56 (0.58), residues: 75 loop : -1.38 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A2833 TYR 0.013 0.001 TYR A2240 PHE 0.017 0.001 PHE A2297 TRP 0.008 0.001 TRP A3301 HIS 0.007 0.001 HIS A3444 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19370) covalent geometry : angle 0.52634 / 0.27 (26178) hydrogen bonds : bond 0.03288 / 2.15 ( 1057) hydrogen bonds : angle 3.78418 / 2.64 ( 3006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1102 SER cc_start: 0.9555 (m) cc_final: 0.9314 (p) REVERT: A 1198 MET cc_start: 0.8062 (mtm) cc_final: 0.7760 (ttp) REVERT: A 1256 MET cc_start: 0.9088 (mmm) cc_final: 0.8485 (mtp) REVERT: A 1424 MET cc_start: 0.8778 (ttm) cc_final: 0.8550 (ttp) REVERT: A 1602 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 1786 MET cc_start: 0.8924 (tpp) cc_final: 0.8579 (tpp) REVERT: A 1818 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8841 (tp40) REVERT: A 1827 MET cc_start: 0.8460 (mmm) cc_final: 0.8204 (mmp) REVERT: A 1850 PHE cc_start: 0.8485 (t80) cc_final: 0.8259 (t80) REVERT: A 1988 MET cc_start: 0.8597 (mmm) cc_final: 0.8301 (mmm) REVERT: A 2143 ASN cc_start: 0.8824 (m110) cc_final: 0.8597 (p0) REVERT: A 2400 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 2485 MET cc_start: 0.8535 (tpp) cc_final: 0.8214 (mmm) REVERT: A 2602 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8625 (tm-30) REVERT: A 2690 MET cc_start: 0.9003 (mtp) cc_final: 0.8634 (mtp) REVERT: A 2776 MET cc_start: 0.7714 (pmm) cc_final: 0.7402 (pmm) REVERT: A 2836 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7004 (m-70) REVERT: A 3127 MET cc_start: 0.7902 (mtm) cc_final: 0.7693 (mtt) REVERT: A 3150 MET cc_start: 0.8657 (mmm) cc_final: 0.8041 (mmt) REVERT: A 3233 MET cc_start: 0.8747 (tpp) cc_final: 0.8365 (tpp) REVERT: A 3339 LYS cc_start: 0.8170 (pttt) cc_final: 0.7887 (tttt) outliers start: 38 outliers final: 32 residues processed: 181 average time/residue: 0.1390 time to fit residues: 39.9193 Evaluate side-chains 173 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1194 PHE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1513 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2243 TYR Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2490 VAL Chi-restraints excluded: chain A residue 2836 HIS Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2931 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3009 THR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3165 VAL Chi-restraints excluded: chain A residue 3172 TRP Chi-restraints excluded: chain A residue 3196 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3309 PHE Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 17 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 98 optimal weight: 0.0370 chunk 196 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1785 ASN A2426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063714 restraints weight = 58838.225| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.56 r_work: 0.3010 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19370 Z= 0.103 Angle : 0.533 12.500 26178 Z= 0.268 Chirality : 0.038 0.168 2985 Planarity : 0.004 0.072 3411 Dihedral : 4.127 54.291 2641 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 1.85 % Allowed : 19.76 % Favored : 78.39 % 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: 1.21 (0.17), residues: 2445 helix: 2.15 (0.14), residues: 1447 sheet: -0.58 (0.58), residues: 75 loop : -1.36 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A2833 TYR 0.012 0.001 TYR A2240 PHE 0.011 0.001 PHE A3309 TRP 0.009 0.001 TRP A2755 HIS 0.006 0.001 HIS A3444 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (19370) covalent geometry : angle 0.53319 / 0.27 (26178) hydrogen bonds : bond 0.03177 / 2.08 ( 1057) hydrogen bonds : angle 3.78121 / 2.64 ( 3006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.10 seconds wall clock time: 66 minutes 59.82 seconds (4019.82 seconds total)