Starting phenix.real_space_refine on Fri Aug 7 07:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.cif Found real_map, /net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11fw_75669/08_2026/11fw_75669.map" } resolution = 3.35 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= 0.024 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 11963 2.51 5 N 3306 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 19054 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2451, 19054 Classifications: {'peptide': 2451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 84, 'TRANS': 2366} Chain breaks: 3 Time building chain proxies: 3.77, per 1000 atoms: 0.20 Number of scatterers: 19054 At special positions: 0 Unit cell: (102.72, 138.03, 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 3693 8.00 N 3306 7.00 C 11963 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: 1.67 Conformation dependent library (CDL) restraints added in 740.4 milliseconds 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 16 sheets defined 65.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 1008 through 1013 Processing helix chain 'A' and resid 1030 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: 3.726A pdb=" N GLU A1094 " --> pdb=" O MET A1090 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1096 " --> pdb=" O HIS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1119 Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.664A pdb=" N ASN A1133 " --> pdb=" O LYS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1163 removed outlier: 3.646A pdb=" N LEU A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A1162 " --> pdb=" O GLN A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 removed outlier: 3.924A pdb=" N THR A1167 " --> pdb=" O THR A1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1164 through 1167' Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1189 through 1196 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.936A pdb=" N SER A1206 " --> pdb=" O GLU A1202 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1322 through 1334 removed outlier: 3.640A pdb=" N ALA A1334 " --> pdb=" O LYS A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1360 removed outlier: 3.572A pdb=" N VAL A1344 " --> pdb=" O HIS A1340 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS A1352 " --> pdb=" O GLU A1348 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP A1353 " --> pdb=" O THR A1349 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.613A pdb=" N LEU A1368 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A1369 " --> pdb=" O LYS A1366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1365 through 1369' Processing helix chain 'A' and resid 1376 through 1402 removed outlier: 4.071A pdb=" N SER A1383 " --> pdb=" O GLY A1379 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A1401 " --> pdb=" O GLN A1397 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A1402 " --> pdb=" O VAL A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.532A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 removed outlier: 3.569A pdb=" N ARG A1437 " --> pdb=" O ALA A1433 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1433 through 1438' Processing helix chain 'A' and resid 1454 through 1468 Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 3.555A pdb=" N THR A1474 " --> pdb=" O LYS A1471 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A1475 " --> pdb=" O VAL A1472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1471 through 1475' Processing helix chain 'A' and resid 1476 through 1489 Processing helix chain 'A' and resid 1492 through 1505 Processing helix chain 'A' and resid 1511 through 1521 Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1525 through 1541 removed outlier: 3.519A pdb=" N LEU A1529 " --> pdb=" O SER A1525 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A1530 " --> pdb=" O PHE A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1569 Processing helix chain 'A' and resid 1575 through 1583 removed outlier: 3.511A pdb=" N ALA A1583 " --> pdb=" O ILE A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1601 Processing helix chain 'A' and resid 1607 through 1627 removed outlier: 3.873A pdb=" N TYR A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.567A pdb=" N GLN A1634 " --> pdb=" O ASN A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1675 Processing helix chain 'A' and resid 1678 through 1708 Processing helix chain 'A' and resid 1712 through 1719 Processing helix chain 'A' and resid 1724 through 1743 removed outlier: 3.695A pdb=" N THR A1743 " --> pdb=" O MET A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.713A pdb=" N TYR A1772 " --> pdb=" O PRO A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1789 removed outlier: 3.569A pdb=" N PHE A1789 " --> pdb=" O ASN A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1803 Processing helix chain 'A' and resid 1803 through 1841 removed outlier: 3.780A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.825A 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 1912 through 1914 No H-bonds generated for 'chain 'A' and resid 1912 through 1914' Processing helix chain 'A' and resid 1915 through 1924 Processing helix chain 'A' and resid 1925 through 1936 removed outlier: 3.516A pdb=" N SER A1934 " --> pdb=" O MET A1930 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A1935 " --> pdb=" O GLN A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1973 Processing helix chain 'A' and resid 1975 through 1990 removed outlier: 3.638A pdb=" N ASN A1979 " --> pdb=" O ASN A1975 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.585A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2009 removed outlier: 3.779A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2017 removed outlier: 3.621A pdb=" N ARG A2014 " --> pdb=" O TYR A2011 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A2015 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A2016 " --> pdb=" O GLN A2013 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A2017 " --> pdb=" O ARG A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.584A pdb=" N ASP A2048 " --> pdb=" O HIS A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2097 removed outlier: 3.502A pdb=" N GLN A2097 " --> pdb=" O GLU A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2142 removed outlier: 3.604A pdb=" N ARG A2142 " --> pdb=" O THR A2139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2139 through 2142' Processing helix chain 'A' and resid 2143 through 2148 removed outlier: 3.710A pdb=" N ILE A2147 " --> pdb=" O ASN A2143 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A2148 " --> pdb=" O LEU A2144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2143 through 2148' Processing helix chain 'A' and resid 2151 through 2167 removed outlier: 3.621A pdb=" N ALA A2167 " --> pdb=" O LYS A2163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2187 Processing helix chain 'A' and resid 2222 through 2244 removed outlier: 3.715A pdb=" N LEU A2226 " --> pdb=" O SER A2222 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A2227 " --> pdb=" O MET A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2267 removed outlier: 3.625A pdb=" N ARG A2267 " --> pdb=" O MET A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2275 through 2294 removed outlier: 3.860A pdb=" N ALA A2281 " --> pdb=" O GLU A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2323 removed outlier: 3.698A pdb=" N LYS A2304 " --> pdb=" O PRO A2300 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A2305 " --> pdb=" O ALA A2301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A2318 " --> pdb=" O TRP A2314 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A2320 " --> pdb=" O LEU A2316 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A2321 " --> pdb=" O ALA A2317 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A2323 " --> pdb=" O ARG A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2347 removed outlier: 3.573A pdb=" N GLN A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2384 removed outlier: 3.504A pdb=" N ASP A2383 " --> pdb=" O ALA A2379 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A2384 " --> pdb=" O VAL A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2408 removed outlier: 3.663A pdb=" N SER A2399 " --> pdb=" O ASN A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2409 through 2412 removed outlier: 3.607A pdb=" N TYR A2412 " --> pdb=" O VAL A2409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2409 through 2412' Processing helix chain 'A' and resid 2430 through 2444 removed outlier: 3.917A pdb=" N ARG A2439 " --> pdb=" O THR A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2470 removed outlier: 3.628A pdb=" N ALA A2462 " --> pdb=" O MET A2458 " (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: 3.562A pdb=" N GLN A2478 " --> pdb=" O MET A2474 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A2485 " --> pdb=" O TYR A2481 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A2486 " --> pdb=" O THR A2482 " (cutoff:3.500A) removed outlier: 4.198A 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: 3.978A pdb=" N ARG A2505 " --> pdb=" O ASN A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2540 removed outlier: 3.517A pdb=" N THR A2534 " --> pdb=" O SER A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2551 removed outlier: 3.610A pdb=" N SER A2547 " --> pdb=" O GLU A2543 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2559 Processing helix chain 'A' and resid 2568 through 2586 removed outlier: 3.849A pdb=" N THR A2574 " --> pdb=" O THR A2570 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A2576 " --> pdb=" O ALA A2572 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A2586 " --> pdb=" O ARG A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2618 removed outlier: 3.728A pdb=" N SER A2596 " --> pdb=" O ASN A2592 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A2599 " --> pdb=" O ASP A2595 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A2610 " --> pdb=" O ALA A2606 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A2611 " --> pdb=" O ALA A2607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A2618 " --> pdb=" O PHE A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2624 through 2642 removed outlier: 3.803A pdb=" N GLU A2642 " --> pdb=" O GLU A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2662 Processing helix chain 'A' and resid 2664 through 2675 Processing helix chain 'A' and resid 2680 through 2684 Processing helix chain 'A' and resid 2685 through 2693 Processing helix chain 'A' and resid 2695 through 2707 removed outlier: 3.612A pdb=" N PHE A2699 " --> pdb=" O VAL A2695 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A2702 " --> pdb=" O PRO A2698 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2737 removed outlier: 3.743A pdb=" N ILE A2727 " --> pdb=" O VAL A2723 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A2728 " --> pdb=" O LYS A2724 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A2737 " --> pdb=" O GLN A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2737 through 2744 Processing helix chain 'A' and resid 2751 through 2763 Processing helix chain 'A' and resid 2766 through 2773 removed outlier: 3.542A pdb=" N GLU A2772 " --> pdb=" O VAL A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2777 through 2783 Processing helix chain 'A' and resid 2787 through 2804 removed outlier: 4.077A pdb=" N ASN A2802 " --> pdb=" O LYS A2798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A2804 " --> pdb=" O ILE A2800 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2825 removed outlier: 3.843A pdb=" N ILE A2823 " --> pdb=" O ALA A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2836 through 2843 removed outlier: 3.536A pdb=" N ARG A2840 " --> pdb=" O HIS A2836 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A2841 " --> pdb=" O ALA A2837 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A2842 " --> pdb=" O ILE A2838 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A2843 " --> pdb=" O SER A2839 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2836 through 2843' Processing helix chain 'A' and resid 2855 through 2868 Processing helix chain 'A' and resid 2870 through 2884 removed outlier: 3.645A 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 2935 through 2943 removed outlier: 3.538A pdb=" N PHE A2939 " --> pdb=" O ASP A2935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3022 removed outlier: 3.509A pdb=" N ALA A3022 " --> pdb=" O THR A3018 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3057 Processing helix chain 'A' and resid 3063 through 3101 removed outlier: 3.553A pdb=" N GLY A3067 " --> pdb=" O ALA A3063 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A3100 " --> pdb=" O LYS A3096 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3102 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: 3.698A pdb=" N LEU A3138 " --> pdb=" O LYS A3134 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3155 Processing helix chain 'A' and resid 3173 through 3188 Processing helix chain 'A' and resid 3189 through 3197 removed outlier: 3.569A pdb=" N VAL A3195 " --> pdb=" O LYS A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3202 through 3207 Processing helix chain 'A' and resid 3209 through 3237 removed outlier: 3.860A pdb=" N ILE A3214 " --> pdb=" O ALA A3210 " (cutoff:3.500A) removed outlier: 4.384A 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 3245 removed outlier: 3.677A pdb=" N ILE A3243 " --> pdb=" O PRO A3239 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A3245 " --> pdb=" O LYS A3241 " (cutoff:3.500A) Processing helix chain 'A' and resid 3246 through 3270 removed outlier: 3.530A pdb=" N GLU A3270 " --> pdb=" O ASP A3266 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3275 Processing helix chain 'A' and resid 3277 through 3298 removed outlier: 3.883A pdb=" N MET A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3306 Processing helix chain 'A' and resid 3309 through 3316 removed outlier: 4.370A pdb=" N ALA A3315 " --> pdb=" O SER A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3329 removed outlier: 3.631A pdb=" N ALA A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A3327 " --> pdb=" O LEU A3323 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A3329 " --> pdb=" O ALA A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3338 removed outlier: 3.511A pdb=" N GLU A3334 " --> pdb=" O HIS A3330 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A3335 " --> pdb=" O GLU A3331 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3384 removed outlier: 3.564A pdb=" N GLN A3361 " --> pdb=" O THR A3357 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A3372 " --> pdb=" O GLU A3368 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A3373 " --> pdb=" O TYR A3369 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A3374 " --> pdb=" O SER A3370 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3400 removed outlier: 3.792A pdb=" N GLY A3395 " --> pdb=" O SER A3391 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A3396 " --> pdb=" O GLU A3392 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A3400 " --> pdb=" O GLN A3396 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3407 Processing helix chain 'A' and resid 3417 through 3441 removed outlier: 3.737A pdb=" N MET A3421 " --> pdb=" O SER A3417 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP A3422 " --> pdb=" O MET A3418 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3448 Processing helix chain 'A' and resid 3467 through 3475 removed outlier: 3.659A pdb=" N GLY A3475 " --> pdb=" O MET A3471 " (cutoff:3.500A) Processing helix chain 'A' and resid 3484 through 3488 removed outlier: 3.554A pdb=" N ARG A3488 " --> pdb=" O GLN A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3493 through 3499 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 1135 through 1138 Processing sheet with id=AA3, first strand: chain 'A' and resid 1198 through 1199 Processing sheet with id=AA4, first strand: chain 'A' and resid 1312 through 1313 removed outlier: 4.031A pdb=" N GLN A1313 " --> pdb=" O ASN A1316 " (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 1445 through 1447 Processing sheet with id=AA8, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AA9, first strand: chain 'A' and resid 1588 through 1589 Processing sheet with id=AB1, first strand: chain 'A' and resid 1745 through 1750 Processing sheet with id=AB2, first strand: chain 'A' and resid 1870 through 1871 Processing sheet with id=AB3, first strand: chain 'A' and resid 1891 through 1893 removed outlier: 6.845A pdb=" N VAL A1902 " --> pdb=" O LEU A1892 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2134 through 2137 removed outlier: 6.795A pdb=" N LYS A2171 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A2208 " --> pdb=" O TYR A2217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2930 through 2931 removed outlier: 3.852A pdb=" N ASN A2930 " --> pdb=" O SER A2969 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3007 through 3008 Processing sheet with id=AB7, first strand: chain 'A' and resid 3108 through 3110 1052 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 2.15 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: 6418 1.34 - 1.46: 3111 1.46 - 1.58: 9643 1.58 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 19356 Sorted by residual: bond pdb=" CA TYR A1675 " pdb=" C TYR A1675 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.41e-02 5.03e+03 2.82e+00 bond pdb=" CA LYS A2964 " pdb=" C LYS A2964 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" CB LYS A3339 " pdb=" CG LYS A3339 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CG1 ILE A2271 " pdb=" CD1 ILE A2271 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.34e+00 bond pdb=" CG LYS A3339 " pdb=" CD LYS A3339 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 ... (remaining 19351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 25776 2.09 - 4.18: 340 4.18 - 6.27: 42 6.27 - 8.36: 2 8.36 - 10.45: 1 Bond angle restraints: 26161 Sorted by residual: angle pdb=" CA LYS A2964 " pdb=" C LYS A2964 " pdb=" N GLY A2965 " ideal model delta sigma weight residual 118.27 128.72 -10.45 1.31e+00 5.83e-01 6.36e+01 angle pdb=" CA ASN A2394 " pdb=" C ASN A2394 " pdb=" O ASN A2394 " ideal model delta sigma weight residual 117.94 120.98 -3.04 5.80e-01 2.97e+00 2.76e+01 angle pdb=" CA LYS A2964 " pdb=" C LYS A2964 " pdb=" O LYS A2964 " ideal model delta sigma weight residual 119.35 113.83 5.52 1.17e+00 7.31e-01 2.23e+01 angle pdb=" O LYS A2964 " pdb=" C LYS A2964 " pdb=" N GLY A2965 " ideal model delta sigma weight residual 122.34 117.42 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" CA ASN A2394 " pdb=" C ASN A2394 " pdb=" N ASN A2395 " ideal model delta sigma weight residual 120.47 116.47 4.00 1.03e+00 9.43e-01 1.51e+01 ... (remaining 26156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10578 17.74 - 35.48: 1064 35.48 - 53.22: 199 53.22 - 70.96: 29 70.96 - 88.70: 16 Dihedral angle restraints: 11886 sinusoidal: 4769 harmonic: 7117 Sorted by residual: dihedral pdb=" CA HIS A1373 " pdb=" C HIS A1373 " pdb=" N ALA A1374 " pdb=" CA ALA A1374 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR A2392 " pdb=" C TYR A2392 " pdb=" N GLY A2393 " pdb=" CA GLY A2393 " ideal model delta harmonic sigma weight residual 180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG A1600 " pdb=" C ARG A1600 " pdb=" N SER A1601 " pdb=" CA SER A1601 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2125 0.040 - 0.081: 660 0.081 - 0.121: 178 0.121 - 0.161: 19 0.161 - 0.202: 1 Chirality restraints: 2983 Sorted by residual: chirality pdb=" CB ILE A2565 " pdb=" CA ILE A2565 " pdb=" CG1 ILE A2565 " pdb=" CG2 ILE A2565 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A1906 " pdb=" N ILE A1906 " pdb=" C ILE A1906 " pdb=" CB ILE A1906 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL A2050 " pdb=" N VAL A2050 " pdb=" C VAL A2050 " pdb=" CB VAL A2050 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2980 not shown) Planarity restraints: 3410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2620 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A2621 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A2621 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2621 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1549 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A1550 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1550 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1550 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A2862 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A2862 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A2862 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A2863 " -0.010 2.00e-02 2.50e+03 ... (remaining 3407 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 218 2.64 - 3.20: 18400 3.20 - 3.77: 28762 3.77 - 4.33: 38591 4.33 - 4.90: 62674 Nonbonded interactions: 148645 Sorted by model distance: nonbonded pdb=" OH TYR A2966 " pdb=" OE2 GLU A3029 " model vdw 2.070 3.040 nonbonded pdb=" OE2 GLU A2797 " pdb=" OH TYR A2864 " model vdw 2.102 3.040 nonbonded pdb=" OG1 THR A2773 " pdb=" OE1 GLU A2778 " model vdw 2.114 3.040 nonbonded pdb=" NH1 ARG A2986 " pdb=" OG1 THR A3491 " model vdw 2.129 3.120 nonbonded pdb=" O HIS A2292 " pdb=" OG SER A2303 " model vdw 2.151 3.040 ... (remaining 148640 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.060 19356 Z= 0.249 Angle : 0.644 10.448 26161 Z= 0.376 Chirality : 0.041 0.202 2983 Planarity : 0.004 0.055 3410 Dihedral : 14.552 88.698 7288 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.49 % Favored : 93.94 % Rotamer: Outliers : 0.29 % Allowed : 7.31 % Favored : 92.40 % 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 (0.15), residues: 2443 helix: -1.11 (0.10), residues: 1382 sheet: -2.22 (0.52), residues: 85 loop : 0.16 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3345 TYR 0.016 0.002 TYR A2339 PHE 0.022 0.002 PHE A3457 TRP 0.012 0.001 TRP A3422 HIS 0.008 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (19356) covalent geometry : angle 0.64434 / 0.38 (26161) hydrogen bonds : bond 0.18109 / 12.01 ( 1052) hydrogen bonds : angle 6.09919 / 4.36 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1233 THR cc_start: 0.8886 (p) cc_final: 0.8668 (t) REVERT: A 1368 LEU cc_start: 0.9262 (mt) cc_final: 0.8586 (tt) REVERT: A 1438 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8884 (mm-30) REVERT: A 1530 MET cc_start: 0.9003 (ttt) cc_final: 0.8660 (tpp) REVERT: A 1692 ASP cc_start: 0.8741 (m-30) cc_final: 0.8383 (m-30) REVERT: A 2012 ASP cc_start: 0.9177 (m-30) cc_final: 0.8581 (t0) REVERT: A 2589 LYS cc_start: 0.9430 (mttt) cc_final: 0.9218 (mppt) REVERT: A 2776 MET cc_start: 0.7869 (mmm) cc_final: 0.7559 (tpp) REVERT: A 2956 SER cc_start: 0.8878 (p) cc_final: 0.8651 (m) REVERT: A 3127 MET cc_start: 0.8606 (ttt) cc_final: 0.8178 (ptm) REVERT: A 3150 MET cc_start: 0.8542 (mmm) cc_final: 0.7793 (mmm) REVERT: A 3418 MET cc_start: 0.9116 (tpp) cc_final: 0.8698 (tpp) REVERT: A 3456 MET cc_start: 0.8751 (mmm) cc_final: 0.8288 (mmm) outliers start: 6 outliers final: 1 residues processed: 209 average time/residue: 0.1595 time to fit residues: 49.4559 Evaluate side-chains 149 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3262 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0670 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2325 GLN A2834 ASN ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3500 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057166 restraints weight = 55583.260| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.09 r_work: 0.2758 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19356 Z= 0.205 Angle : 0.605 8.854 26161 Z= 0.324 Chirality : 0.041 0.203 2983 Planarity : 0.004 0.048 3410 Dihedral : 4.736 54.668 2636 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 1.22 % Allowed : 10.42 % Favored : 88.36 % 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: 0.46 (0.17), residues: 2443 helix: 0.91 (0.13), residues: 1417 sheet: -1.53 (0.58), residues: 76 loop : -0.33 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2986 TYR 0.016 0.001 TYR A2339 PHE 0.014 0.001 PHE A1078 TRP 0.013 0.001 TRP A2208 HIS 0.007 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (19356) covalent geometry : angle 0.60482 / 0.32 (26161) hydrogen bonds : bond 0.05082 / 3.36 ( 1052) hydrogen bonds : angle 4.51361 / 3.21 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 LEU cc_start: 0.9052 (mt) cc_final: 0.8643 (tt) REVERT: A 1530 MET cc_start: 0.9017 (ttt) cc_final: 0.8784 (ttm) REVERT: A 1692 ASP cc_start: 0.8747 (m-30) cc_final: 0.8380 (m-30) REVERT: A 2012 ASP cc_start: 0.9215 (m-30) cc_final: 0.8662 (t0) REVERT: A 2400 GLN cc_start: 0.8542 (tp40) cc_final: 0.8217 (tm-30) REVERT: A 2408 LEU cc_start: 0.8062 (mt) cc_final: 0.7749 (mm) REVERT: A 2414 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.8344 (ptt-90) REVERT: A 2432 MET cc_start: 0.8514 (mmm) cc_final: 0.8272 (mmt) REVERT: A 2589 LYS cc_start: 0.9418 (mttt) cc_final: 0.9196 (mppt) REVERT: A 2924 GLU cc_start: 0.8294 (tt0) cc_final: 0.8030 (tp30) REVERT: A 2956 SER cc_start: 0.8726 (p) cc_final: 0.8511 (m) REVERT: A 3127 MET cc_start: 0.8720 (ttt) cc_final: 0.8311 (ptm) REVERT: A 3150 MET cc_start: 0.8352 (mmm) cc_final: 0.7655 (mmm) REVERT: A 3339 LYS cc_start: 0.7046 (tmtt) cc_final: 0.6492 (tptt) REVERT: A 3418 MET cc_start: 0.9191 (tpp) cc_final: 0.8794 (tpp) REVERT: A 3456 MET cc_start: 0.8734 (mmm) cc_final: 0.8068 (mmm) outliers start: 25 outliers final: 15 residues processed: 179 average time/residue: 0.1412 time to fit residues: 39.6140 Evaluate side-chains 161 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3262 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 14 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2429 ASN A2542 ASN A2979 GLN A3232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060124 restraints weight = 54909.001| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.99 r_work: 0.2834 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19356 Z= 0.109 Angle : 0.518 10.018 26161 Z= 0.272 Chirality : 0.039 0.427 2983 Planarity : 0.003 0.048 3410 Dihedral : 4.368 56.060 2636 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.61 % Allowed : 11.54 % Favored : 86.85 % 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: 1.07 (0.17), residues: 2443 helix: 1.63 (0.14), residues: 1415 sheet: -1.30 (0.58), residues: 74 loop : -0.49 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3282 TYR 0.012 0.001 TYR A2011 PHE 0.014 0.001 PHE A1078 TRP 0.010 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (19356) covalent geometry : angle 0.51772 / 0.27 (26161) hydrogen bonds : bond 0.03882 / 2.58 ( 1052) hydrogen bonds : angle 3.96365 / 2.82 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 LEU cc_start: 0.9035 (mt) cc_final: 0.8514 (tt) REVERT: A 1438 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8515 (mm-30) REVERT: A 1530 MET cc_start: 0.8924 (ttt) cc_final: 0.8642 (ttm) REVERT: A 1692 ASP cc_start: 0.8668 (m-30) cc_final: 0.8342 (m-30) REVERT: A 2012 ASP cc_start: 0.9187 (m-30) cc_final: 0.8589 (t0) REVERT: A 2400 GLN cc_start: 0.8404 (tp40) cc_final: 0.8105 (tm-30) REVERT: A 2414 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8270 (ptt-90) REVERT: A 2432 MET cc_start: 0.8323 (mmm) cc_final: 0.8088 (mmt) REVERT: A 2589 LYS cc_start: 0.9426 (mttt) cc_final: 0.9195 (mppt) REVERT: A 2924 GLU cc_start: 0.8273 (tt0) cc_final: 0.8041 (tp30) REVERT: A 2956 SER cc_start: 0.8715 (p) cc_final: 0.8395 (m) REVERT: A 2966 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: A 3127 MET cc_start: 0.8826 (ttt) cc_final: 0.8416 (ptm) REVERT: A 3150 MET cc_start: 0.8331 (mmm) cc_final: 0.8127 (mmm) REVERT: A 3418 MET cc_start: 0.9091 (tpp) cc_final: 0.8769 (tpp) REVERT: A 3456 MET cc_start: 0.8566 (mmm) cc_final: 0.7961 (mmm) outliers start: 33 outliers final: 15 residues processed: 196 average time/residue: 0.1452 time to fit residues: 44.6765 Evaluate side-chains 166 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2532 LEU 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 2706 ILE Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2966 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 145 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2195 GLN ** A2979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058221 restraints weight = 55455.829| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.97 r_work: 0.2786 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19356 Z= 0.166 Angle : 0.539 9.286 26161 Z= 0.281 Chirality : 0.039 0.322 2983 Planarity : 0.004 0.046 3410 Dihedral : 4.240 56.474 2634 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 12.66 % Favored : 85.48 % 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: 1.25 (0.17), residues: 2443 helix: 1.90 (0.14), residues: 1420 sheet: -1.40 (0.57), residues: 74 loop : -0.62 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3282 TYR 0.034 0.001 TYR A1144 PHE 0.015 0.001 PHE A3496 TRP 0.010 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (19356) covalent geometry : angle 0.53914 / 0.28 (26161) hydrogen bonds : bond 0.04019 / 2.66 ( 1052) hydrogen bonds : angle 3.95988 / 2.80 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 LEU cc_start: 0.9052 (mt) cc_final: 0.8509 (tt) REVERT: A 1438 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8816 (mm-30) REVERT: A 1530 MET cc_start: 0.8975 (ttt) cc_final: 0.8706 (ttm) REVERT: A 1698 MET cc_start: 0.8794 (mmm) cc_final: 0.8270 (mmm) REVERT: A 2012 ASP cc_start: 0.9189 (m-30) cc_final: 0.8645 (t0) REVERT: A 2400 GLN cc_start: 0.8598 (tp40) cc_final: 0.8177 (tm-30) REVERT: A 2414 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8201 (ptt-90) REVERT: A 2423 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8477 (ptp90) REVERT: A 2432 MET cc_start: 0.8367 (mmm) cc_final: 0.8072 (mmt) REVERT: A 2589 LYS cc_start: 0.9421 (mttt) cc_final: 0.9208 (mppt) REVERT: A 2776 MET cc_start: 0.8184 (tpp) cc_final: 0.7959 (tpp) REVERT: A 2924 GLU cc_start: 0.8426 (tt0) cc_final: 0.8146 (tp30) REVERT: A 2956 SER cc_start: 0.8846 (p) cc_final: 0.8589 (m) REVERT: A 2966 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: A 3127 MET cc_start: 0.8841 (ttt) cc_final: 0.8440 (ptm) REVERT: A 3150 MET cc_start: 0.8292 (mmm) cc_final: 0.7577 (mmm) REVERT: A 3309 PHE cc_start: 0.9288 (t80) cc_final: 0.9028 (t80) REVERT: A 3339 LYS cc_start: 0.6888 (tmtt) cc_final: 0.6501 (tptt) REVERT: A 3418 MET cc_start: 0.9172 (tpp) cc_final: 0.8870 (tpp) REVERT: A 3456 MET cc_start: 0.8546 (mmm) cc_final: 0.7925 (mmm) outliers start: 38 outliers final: 25 residues processed: 184 average time/residue: 0.1445 time to fit residues: 41.7536 Evaluate side-chains 173 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2271 ILE Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2514 THR Chi-restraints excluded: chain A residue 2532 LEU 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 2822 MET Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2942 LEU Chi-restraints excluded: chain A residue 2966 TYR Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3438 ILE Chi-restraints excluded: chain A residue 3468 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 224 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 90 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 chunk 243 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2979 GLN ** 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 = 0.3379 r_free = 0.3379 target = 0.079831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060143 restraints weight = 54686.624| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.13 r_work: 0.2837 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19356 Z= 0.102 Angle : 0.504 9.945 26161 Z= 0.260 Chirality : 0.038 0.441 2983 Planarity : 0.003 0.045 3410 Dihedral : 4.033 57.705 2634 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 1.51 % Allowed : 13.44 % Favored : 85.05 % 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: 1.48 (0.17), residues: 2443 helix: 2.17 (0.14), residues: 1419 sheet: -1.30 (0.57), residues: 74 loop : -0.68 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3282 TYR 0.041 0.001 TYR A1144 PHE 0.013 0.001 PHE A3496 TRP 0.009 0.001 TRP A1159 HIS 0.005 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (19356) covalent geometry : angle 0.50404 / 0.26 (26161) hydrogen bonds : bond 0.03306 / 2.19 ( 1052) hydrogen bonds : angle 3.68157 / 2.60 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 LEU cc_start: 0.9029 (mt) cc_final: 0.8473 (tt) REVERT: A 1438 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8583 (mm-30) REVERT: A 1530 MET cc_start: 0.8953 (ttt) cc_final: 0.8690 (ttm) REVERT: A 2012 ASP cc_start: 0.9136 (m-30) cc_final: 0.8534 (t0) REVERT: A 2400 GLN cc_start: 0.8502 (tp40) cc_final: 0.8146 (tm-30) REVERT: A 2414 ARG cc_start: 0.8661 (ptt-90) cc_final: 0.8344 (ptt-90) REVERT: A 2423 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8433 (ptp90) REVERT: A 2424 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7171 (ttt180) REVERT: A 2432 MET cc_start: 0.8265 (mmm) cc_final: 0.8012 (mmt) REVERT: A 2589 LYS cc_start: 0.9421 (mttt) cc_final: 0.9216 (mppt) REVERT: A 2776 MET cc_start: 0.8192 (tpp) cc_final: 0.7956 (tpp) REVERT: A 2924 GLU cc_start: 0.8400 (tt0) cc_final: 0.8107 (tp30) REVERT: A 2956 SER cc_start: 0.8815 (p) cc_final: 0.8454 (m) REVERT: A 3127 MET cc_start: 0.8819 (ttt) cc_final: 0.8495 (ptm) REVERT: A 3150 MET cc_start: 0.8393 (mmm) cc_final: 0.7638 (mmm) REVERT: A 3309 PHE cc_start: 0.9320 (t80) cc_final: 0.9058 (t80) REVERT: A 3339 LYS cc_start: 0.6963 (tmtt) cc_final: 0.6606 (tptt) REVERT: A 3418 MET cc_start: 0.9113 (tpp) cc_final: 0.8804 (tpp) REVERT: A 3456 MET cc_start: 0.8553 (mmm) cc_final: 0.7637 (mmm) outliers start: 31 outliers final: 17 residues processed: 181 average time/residue: 0.1518 time to fit residues: 43.4671 Evaluate side-chains 171 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2424 ARG Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2942 LEU Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3438 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 194 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2979 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.076285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.056786 restraints weight = 56060.839| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.00 r_work: 0.2744 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19356 Z= 0.294 Angle : 0.636 9.832 26161 Z= 0.332 Chirality : 0.042 0.417 2983 Planarity : 0.004 0.051 3410 Dihedral : 4.311 57.363 2634 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.05 % Allowed : 13.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.31 (0.17), residues: 2443 helix: 2.09 (0.14), residues: 1412 sheet: -1.49 (0.58), residues: 74 loop : -0.81 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3282 TYR 0.030 0.002 TYR A1144 PHE 0.016 0.002 PHE A2365 TRP 0.010 0.002 TRP A3422 HIS 0.006 0.001 HIS A1340 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 (19356) covalent geometry : angle 0.63607 / 0.33 (26161) hydrogen bonds : bond 0.04466 / 2.95 ( 1052) hydrogen bonds : angle 4.10500 / 2.88 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1091 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 1368 LEU cc_start: 0.9113 (mt) cc_final: 0.8623 (tt) REVERT: A 1438 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8844 (mm-30) REVERT: A 1530 MET cc_start: 0.8994 (ttt) cc_final: 0.8728 (ttm) REVERT: A 1692 ASP cc_start: 0.8721 (m-30) cc_final: 0.8334 (m-30) REVERT: A 1715 MET cc_start: 0.9216 (mmm) cc_final: 0.8952 (mmm) REVERT: A 2012 ASP cc_start: 0.9136 (m-30) cc_final: 0.8580 (t0) REVERT: A 2269 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9225 (mm) REVERT: A 2400 GLN cc_start: 0.8649 (tp40) cc_final: 0.8237 (tm-30) REVERT: A 2414 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8365 (ptt-90) REVERT: A 2423 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8475 (ptp90) REVERT: A 2424 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7223 (ttt180) REVERT: A 2432 MET cc_start: 0.8504 (mmm) cc_final: 0.8204 (mmt) REVERT: A 2776 MET cc_start: 0.8293 (tpp) cc_final: 0.8052 (tpp) REVERT: A 2924 GLU cc_start: 0.8497 (tt0) cc_final: 0.8147 (tp30) REVERT: A 2956 SER cc_start: 0.8912 (p) cc_final: 0.8670 (m) REVERT: A 3127 MET cc_start: 0.8845 (ttt) cc_final: 0.8534 (ptm) REVERT: A 3309 PHE cc_start: 0.9312 (t80) cc_final: 0.9047 (t80) REVERT: A 3339 LYS cc_start: 0.6990 (tmtt) cc_final: 0.6291 (tptt) REVERT: A 3343 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8217 (mmtp) REVERT: A 3418 MET cc_start: 0.9239 (tpp) cc_final: 0.8872 (tpp) REVERT: A 3456 MET cc_start: 0.8577 (mmm) cc_final: 0.7677 (mmm) outliers start: 42 outliers final: 29 residues processed: 177 average time/residue: 0.1506 time to fit residues: 42.2393 Evaluate side-chains 177 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2424 ARG 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 2577 MET Chi-restraints excluded: chain A residue 2670 THR Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2865 SER Chi-restraints excluded: chain A residue 2869 MET Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3240 VAL Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3438 ILE Chi-restraints excluded: chain A residue 3468 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 140 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 158 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2979 GLN ** 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 = 0.3359 r_free = 0.3359 target = 0.078675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058976 restraints weight = 54915.936| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.11 r_work: 0.2806 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19356 Z= 0.107 Angle : 0.518 11.374 26161 Z= 0.266 Chirality : 0.038 0.345 2983 Planarity : 0.003 0.045 3410 Dihedral : 4.104 58.647 2634 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.27 % Allowed : 14.66 % Favored : 84.07 % 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: 1.53 (0.18), residues: 2443 helix: 2.28 (0.14), residues: 1418 sheet: -1.39 (0.58), residues: 74 loop : -0.78 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3282 TYR 0.031 0.001 TYR A1144 PHE 0.010 0.001 PHE A3496 TRP 0.009 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (19356) covalent geometry : angle 0.51769 / 0.27 (26161) hydrogen bonds : bond 0.03530 / 2.33 ( 1052) hydrogen bonds : angle 3.71347 / 2.61 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1091 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 1368 LEU cc_start: 0.9051 (mt) cc_final: 0.8472 (tt) REVERT: A 1438 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8748 (mm-30) REVERT: A 1530 MET cc_start: 0.8968 (ttt) cc_final: 0.8676 (ttm) REVERT: A 2012 ASP cc_start: 0.9142 (m-30) cc_final: 0.8562 (t0) REVERT: A 2269 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9223 (mm) REVERT: A 2400 GLN cc_start: 0.8508 (tp40) cc_final: 0.8210 (tm-30) REVERT: A 2414 ARG cc_start: 0.8617 (ptt-90) cc_final: 0.8374 (ptt-90) REVERT: A 2423 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8385 (ptp90) REVERT: A 2424 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7199 (ttt180) REVERT: A 2432 MET cc_start: 0.8345 (mmm) cc_final: 0.8058 (mmt) REVERT: A 2776 MET cc_start: 0.8277 (tpp) cc_final: 0.8000 (tpp) REVERT: A 2924 GLU cc_start: 0.8443 (tt0) cc_final: 0.8179 (tp30) REVERT: A 2956 SER cc_start: 0.8875 (p) cc_final: 0.8606 (m) REVERT: A 3127 MET cc_start: 0.8870 (ttt) cc_final: 0.8530 (ptm) REVERT: A 3150 MET cc_start: 0.8223 (mmm) cc_final: 0.7422 (mmm) REVERT: A 3309 PHE cc_start: 0.9327 (t80) cc_final: 0.9054 (t80) REVERT: A 3339 LYS cc_start: 0.7011 (tmtt) cc_final: 0.6602 (tptt) REVERT: A 3418 MET cc_start: 0.9192 (tpp) cc_final: 0.8906 (tpp) REVERT: A 3456 MET cc_start: 0.8639 (mmm) cc_final: 0.7681 (mmm) outliers start: 26 outliers final: 20 residues processed: 175 average time/residue: 0.1478 time to fit residues: 40.7998 Evaluate side-chains 173 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2424 ARG Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2695 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3438 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 138 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 236 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059137 restraints weight = 55233.366| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.12 r_work: 0.2816 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19356 Z= 0.108 Angle : 0.496 10.882 26161 Z= 0.256 Chirality : 0.038 0.326 2983 Planarity : 0.003 0.044 3410 Dihedral : 3.986 59.089 2634 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.56 % Allowed : 14.52 % Favored : 83.93 % 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: 1.63 (0.18), residues: 2443 helix: 2.37 (0.14), residues: 1418 sheet: -1.35 (0.58), residues: 74 loop : -0.76 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3282 TYR 0.028 0.001 TYR A1144 PHE 0.010 0.001 PHE A2088 TRP 0.009 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (19356) covalent geometry : angle 0.49609 / 0.26 (26161) hydrogen bonds : bond 0.03316 / 2.19 ( 1052) hydrogen bonds : angle 3.61509 / 2.53 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1091 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 1368 LEU cc_start: 0.8999 (mt) cc_final: 0.8438 (tt) REVERT: A 1438 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8766 (mm-30) REVERT: A 1530 MET cc_start: 0.8955 (ttt) cc_final: 0.8644 (ttm) REVERT: A 1926 ASP cc_start: 0.8822 (m-30) cc_final: 0.8328 (t0) REVERT: A 2012 ASP cc_start: 0.9137 (m-30) cc_final: 0.8597 (t0) REVERT: A 2269 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9202 (mm) REVERT: A 2400 GLN cc_start: 0.8597 (tp40) cc_final: 0.8195 (tm-30) REVERT: A 2414 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8353 (ptp90) REVERT: A 2423 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8360 (ptp90) REVERT: A 2424 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7130 (ttt180) REVERT: A 2432 MET cc_start: 0.8366 (mmm) cc_final: 0.8093 (mmt) REVERT: A 2776 MET cc_start: 0.8272 (tpp) cc_final: 0.7956 (tpp) REVERT: A 2924 GLU cc_start: 0.8405 (tt0) cc_final: 0.8198 (tp30) REVERT: A 2956 SER cc_start: 0.8869 (p) cc_final: 0.8600 (m) REVERT: A 3127 MET cc_start: 0.8872 (ttt) cc_final: 0.8542 (ptm) REVERT: A 3150 MET cc_start: 0.8314 (mmm) cc_final: 0.7514 (mmm) REVERT: A 3309 PHE cc_start: 0.9332 (t80) cc_final: 0.9060 (t80) REVERT: A 3339 LYS cc_start: 0.6871 (tmtt) cc_final: 0.6512 (tptt) REVERT: A 3418 MET cc_start: 0.9166 (tpp) cc_final: 0.8877 (tpp) REVERT: A 3456 MET cc_start: 0.8594 (mmm) cc_final: 0.7676 (mmm) outliers start: 32 outliers final: 23 residues processed: 179 average time/residue: 0.1255 time to fit residues: 35.7315 Evaluate side-chains 175 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2424 ARG Chi-restraints excluded: chain A residue 2438 VAL 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 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3438 ILE Chi-restraints excluded: chain A residue 3460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 109 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057671 restraints weight = 55371.876| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.09 r_work: 0.2782 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19356 Z= 0.177 Angle : 0.551 10.351 26161 Z= 0.283 Chirality : 0.040 0.463 2983 Planarity : 0.004 0.043 3410 Dihedral : 4.087 59.005 2634 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 1.32 % Allowed : 15.20 % Favored : 83.49 % 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: 1.60 (0.18), residues: 2443 helix: 2.37 (0.14), residues: 1416 sheet: -1.35 (0.58), residues: 74 loop : -0.80 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3282 TYR 0.026 0.001 TYR A1144 PHE 0.012 0.001 PHE A2088 TRP 0.008 0.001 TRP A3422 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (19356) covalent geometry : angle 0.55052 / 0.28 (26161) hydrogen bonds : bond 0.03754 / 2.47 ( 1052) hydrogen bonds : angle 3.76490 / 2.63 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1091 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 1368 LEU cc_start: 0.9096 (mt) cc_final: 0.8490 (tt) REVERT: A 1438 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8726 (mm-30) REVERT: A 1530 MET cc_start: 0.8990 (ttt) cc_final: 0.8729 (ttm) REVERT: A 1926 ASP cc_start: 0.8856 (m-30) cc_final: 0.8377 (t0) REVERT: A 2012 ASP cc_start: 0.9137 (m-30) cc_final: 0.8577 (t0) REVERT: A 2269 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 2400 GLN cc_start: 0.8669 (tp40) cc_final: 0.8208 (tm-30) REVERT: A 2414 ARG cc_start: 0.8632 (ptt-90) cc_final: 0.8369 (ptp90) REVERT: A 2423 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8351 (ptp90) REVERT: A 2424 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7127 (ttt180) REVERT: A 2432 MET cc_start: 0.8449 (mmm) cc_final: 0.8161 (mmt) REVERT: A 2552 MET cc_start: 0.8826 (mtt) cc_final: 0.8552 (mtp) REVERT: A 2776 MET cc_start: 0.8250 (tpp) cc_final: 0.7924 (tpp) REVERT: A 2924 GLU cc_start: 0.8340 (tt0) cc_final: 0.8056 (tp30) REVERT: A 2956 SER cc_start: 0.8889 (p) cc_final: 0.8627 (m) REVERT: A 3127 MET cc_start: 0.8820 (ttt) cc_final: 0.8519 (ptm) REVERT: A 3150 MET cc_start: 0.8339 (mmm) cc_final: 0.7371 (mmm) REVERT: A 3309 PHE cc_start: 0.9323 (t80) cc_final: 0.9026 (t80) REVERT: A 3339 LYS cc_start: 0.6833 (tmtt) cc_final: 0.6263 (tptt) REVERT: A 3418 MET cc_start: 0.9232 (tpp) cc_final: 0.8957 (tpp) REVERT: A 3456 MET cc_start: 0.8614 (mmm) cc_final: 0.7701 (mmm) outliers start: 27 outliers final: 24 residues processed: 170 average time/residue: 0.1314 time to fit residues: 35.2273 Evaluate side-chains 175 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2423 ARG Chi-restraints excluded: chain A residue 2424 ARG Chi-restraints excluded: chain A residue 2438 VAL 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 2861 ILE Chi-restraints excluded: chain A residue 2865 SER Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3438 ILE Chi-restraints excluded: chain A residue 3460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058621 restraints weight = 55257.661| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.11 r_work: 0.2805 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19356 Z= 0.120 Angle : 0.520 10.384 26161 Z= 0.267 Chirality : 0.039 0.466 2983 Planarity : 0.003 0.044 3410 Dihedral : 4.027 59.344 2634 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.36 % Allowed : 15.29 % Favored : 83.34 % 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: 1.66 (0.18), residues: 2443 helix: 2.43 (0.14), residues: 1417 sheet: -1.34 (0.58), residues: 74 loop : -0.79 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3282 TYR 0.029 0.001 TYR A1144 PHE 0.011 0.001 PHE A2088 TRP 0.009 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19356) covalent geometry : angle 0.51995 / 0.27 (26161) hydrogen bonds : bond 0.03472 / 2.28 ( 1052) hydrogen bonds : angle 3.65097 / 2.56 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4886 Ramachandran restraints generated. 2443 Oldfield, 0 Emsley, 2443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1091 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 1368 LEU cc_start: 0.9067 (mt) cc_final: 0.8498 (tt) REVERT: A 1438 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 1530 MET cc_start: 0.8963 (ttt) cc_final: 0.8582 (ttm) REVERT: A 1926 ASP cc_start: 0.8775 (m-30) cc_final: 0.8344 (t0) REVERT: A 2012 ASP cc_start: 0.9151 (m-30) cc_final: 0.8574 (t0) REVERT: A 2269 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 2400 GLN cc_start: 0.8636 (tp40) cc_final: 0.8228 (tm-30) REVERT: A 2414 ARG cc_start: 0.8636 (ptt-90) cc_final: 0.8370 (ptp90) REVERT: A 2424 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7114 (ttt180) REVERT: A 2432 MET cc_start: 0.8346 (mmm) cc_final: 0.8060 (mmt) REVERT: A 2776 MET cc_start: 0.8237 (tpp) cc_final: 0.7908 (tpp) REVERT: A 2924 GLU cc_start: 0.8419 (tt0) cc_final: 0.8212 (tp30) REVERT: A 2956 SER cc_start: 0.8874 (p) cc_final: 0.8606 (m) REVERT: A 3127 MET cc_start: 0.8830 (ttt) cc_final: 0.8516 (ptm) REVERT: A 3150 MET cc_start: 0.8382 (mmm) cc_final: 0.7413 (mmm) REVERT: A 3309 PHE cc_start: 0.9333 (t80) cc_final: 0.9023 (t80) REVERT: A 3339 LYS cc_start: 0.6933 (tmtt) cc_final: 0.6483 (tptt) REVERT: A 3418 MET cc_start: 0.9212 (tpp) cc_final: 0.8930 (tpp) REVERT: A 3456 MET cc_start: 0.8629 (mmm) cc_final: 0.7724 (mmm) outliers start: 28 outliers final: 23 residues processed: 173 average time/residue: 0.1405 time to fit residues: 38.7654 Evaluate side-chains 174 residues out of total 2053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2424 ARG Chi-restraints excluded: chain A residue 2438 VAL 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 2861 ILE Chi-restraints excluded: chain A residue 2880 LEU Chi-restraints excluded: chain A residue 2932 ILE Chi-restraints excluded: chain A residue 2996 THR Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3146 VAL Chi-restraints excluded: chain A residue 3431 ILE Chi-restraints excluded: chain A residue 3438 ILE Chi-restraints excluded: chain A residue 3460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 chunk 138 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058524 restraints weight = 55372.651| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.11 r_work: 0.2802 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19356 Z= 0.132 Angle : 0.527 13.154 26161 Z= 0.269 Chirality : 0.039 0.468 2983 Planarity : 0.003 0.043 3410 Dihedral : 4.016 58.925 2634 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 1.32 % Allowed : 15.34 % Favored : 83.34 % 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: 1.68 (0.18), residues: 2443 helix: 2.44 (0.14), residues: 1417 sheet: -1.31 (0.58), residues: 74 loop : -0.79 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2423 TYR 0.028 0.001 TYR A1144 PHE 0.011 0.001 PHE A3496 TRP 0.008 0.001 TRP A1159 HIS 0.004 0.001 HIS A2836 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19356) covalent geometry : angle 0.52684 / 0.27 (26161) hydrogen bonds : bond 0.03472 / 2.28 ( 1052) hydrogen bonds : angle 3.66532 / 2.56 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.12 seconds wall clock time: 62 minutes 57.59 seconds (3777.59 seconds total)