Starting phenix.real_space_refine on Wed May 21 14:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.map" model { file = "/net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vlx_43347/05_2025/8vlx_43347.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 133 5.16 5 C 13592 2.51 5 N 3666 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21239 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2431, 19107 Classifications: {'peptide': 2431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 109, 'TRANS': 2321} Chain breaks: 17 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2102 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'A1ACS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.96, per 1000 atoms: 0.52 Number of scatterers: 21239 At special positions: 0 Unit cell: (113.71, 136.12, 145.25, 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 133 16.00 O 3848 8.00 N 3666 7.00 C 13592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 177 " distance=2.04 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 834 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.5 seconds 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5186 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.660A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.631A pdb=" N GLU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 203 removed outlier: 3.767A pdb=" N ASN A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.799A pdb=" N GLU A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.552A pdb=" N ALA A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 225 through 228 Processing helix chain 'A' and resid 229 through 245 Proline residue: A 238 - end of helix removed outlier: 3.721A pdb=" N LYS A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.554A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 260 - end of helix removed outlier: 3.860A pdb=" N SER A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.725A pdb=" N LYS A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 310 through 327 removed outlier: 3.673A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 377 through 392 removed outlier: 3.503A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 Processing helix chain 'A' and resid 415 through 423 removed outlier: 3.700A pdb=" N THR A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.913A pdb=" N HIS A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 753 removed outlier: 3.615A pdb=" N LEU A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 removed outlier: 3.729A pdb=" N SER A 759 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.515A pdb=" N ASP A 785 " --> pdb=" O ASN A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.756A pdb=" N CYS A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 826 removed outlier: 3.676A pdb=" N THR A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 832 No H-bonds generated for 'chain 'A' and resid 830 through 832' Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.818A pdb=" N LEU A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 843 " --> pdb=" O ARG A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.510A pdb=" N CYS A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 removed outlier: 3.626A pdb=" N LEU A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.570A pdb=" N ASN A 885 " --> pdb=" O THR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 901 Processing helix chain 'A' and resid 903 through 913 removed outlier: 3.535A pdb=" N LYS A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 975 through 989 removed outlier: 3.627A pdb=" N ASP A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1042 removed outlier: 3.634A pdb=" N ILE A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1063 Processing helix chain 'A' and resid 1069 through 1073 removed outlier: 3.831A pdb=" N HIS A1073 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1102 removed outlier: 4.332A pdb=" N LEU A1100 " --> pdb=" O MET A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1127 removed outlier: 3.891A pdb=" N SER A1127 " --> pdb=" O LEU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1132 removed outlier: 3.991A pdb=" N LEU A1132 " --> pdb=" O PRO A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1184 Processing helix chain 'A' and resid 1260 through 1279 removed outlier: 3.587A pdb=" N VAL A1279 " --> pdb=" O ALA A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1305 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1316 through 1329 removed outlier: 4.146A pdb=" N ILE A1320 " --> pdb=" O CYS A1316 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1326 " --> pdb=" O GLY A1322 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1380 through 1386 Processing helix chain 'A' and resid 1386 through 1402 removed outlier: 3.802A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A1402 " --> pdb=" O ALA A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 3.905A pdb=" N LYS A1458 " --> pdb=" O PRO A1454 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1459 " --> pdb=" O LEU A1455 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1485 Processing helix chain 'A' and resid 1488 through 1493 removed outlier: 3.956A pdb=" N LEU A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1510 removed outlier: 3.645A pdb=" N PHE A1506 " --> pdb=" O VAL A1502 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A1507 " --> pdb=" O LEU A1503 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1532 removed outlier: 3.894A pdb=" N ILE A1520 " --> pdb=" O GLU A1516 " (cutoff:3.500A) Proline residue: A1522 - end of helix Processing helix chain 'A' and resid 1543 through 1556 Processing helix chain 'A' and resid 1564 through 1577 Proline residue: A1571 - end of helix Processing helix chain 'A' and resid 1590 through 1605 removed outlier: 3.611A pdb=" N LEU A1605 " --> pdb=" O MET A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1626 removed outlier: 3.606A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1647 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1654 through 1668 Processing helix chain 'A' and resid 1669 through 1673 Processing helix chain 'A' and resid 1676 through 1684 Processing helix chain 'A' and resid 1692 through 1714 Processing helix chain 'A' and resid 1715 through 1726 Processing helix chain 'A' and resid 1729 through 1733 removed outlier: 4.325A pdb=" N ILE A1733 " --> pdb=" O PRO A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1744 Processing helix chain 'A' and resid 1762 through 1784 removed outlier: 3.517A pdb=" N LEU A1774 " --> pdb=" O PHE A1770 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1783 " --> pdb=" O LEU A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1817 removed outlier: 4.243A pdb=" N GLY A1817 " --> pdb=" O ILE A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1831 removed outlier: 3.601A pdb=" N ARG A1831 " --> pdb=" O THR A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1851 removed outlier: 3.554A pdb=" N SER A1851 " --> pdb=" O LEU A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1870 Processing helix chain 'A' and resid 1874 through 1882 removed outlier: 3.580A pdb=" N TRP A1878 " --> pdb=" O ASP A1874 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU A1880 " --> pdb=" O ARG A1876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1936 Processing helix chain 'A' and resid 1940 through 1957 removed outlier: 4.059A pdb=" N THR A1944 " --> pdb=" O SER A1940 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1951 " --> pdb=" O ILE A1947 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLN A1952 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A1953 " --> pdb=" O ASN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1972 Processing helix chain 'A' and resid 1973 through 1987 Processing helix chain 'A' and resid 1993 through 2004 Processing helix chain 'A' and resid 2008 through 2010 No H-bonds generated for 'chain 'A' and resid 2008 through 2010' Processing helix chain 'A' and resid 2011 through 2023 removed outlier: 3.559A pdb=" N VAL A2020 " --> pdb=" O LEU A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2048 Processing helix chain 'A' and resid 2050 through 2058 Processing helix chain 'A' and resid 2059 through 2073 removed outlier: 3.584A pdb=" N GLN A2067 " --> pdb=" O LEU A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2079 Processing helix chain 'A' and resid 2079 through 2093 removed outlier: 3.803A pdb=" N SER A2092 " --> pdb=" O ARG A2088 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2136 removed outlier: 3.775A pdb=" N HIS A2129 " --> pdb=" O ASP A2125 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A2130 " --> pdb=" O TRP A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2142 through 2152 removed outlier: 3.531A pdb=" N ARG A2152 " --> pdb=" O GLU A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2164 removed outlier: 4.119A pdb=" N ASN A2159 " --> pdb=" O ALA A2155 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A2160 " --> pdb=" O GLU A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2170 No H-bonds generated for 'chain 'A' and resid 2168 through 2170' Processing helix chain 'A' and resid 2171 through 2185 removed outlier: 3.709A pdb=" N GLU A2182 " --> pdb=" O LEU A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2209 removed outlier: 3.888A pdb=" N GLN A2209 " --> pdb=" O GLY A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2237 Processing helix chain 'A' and resid 2238 through 2257 removed outlier: 3.504A pdb=" N SER A2244 " --> pdb=" O ALA A2240 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Proline residue: A2246 - end of helix Processing helix chain 'A' and resid 2258 through 2262 Processing helix chain 'A' and resid 2263 through 2267 Processing helix chain 'A' and resid 2269 through 2271 No H-bonds generated for 'chain 'A' and resid 2269 through 2271' Processing helix chain 'A' and resid 2272 through 2294 Processing helix chain 'A' and resid 2298 through 2313 Processing helix chain 'A' and resid 2315 through 2323 removed outlier: 3.718A pdb=" N VAL A2321 " --> pdb=" O GLY A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2347 Processing helix chain 'A' and resid 2380 through 2397 removed outlier: 3.920A pdb=" N THR A2384 " --> pdb=" O PRO A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2405 through 2411 removed outlier: 4.130A pdb=" N GLY A2410 " --> pdb=" O ARG A2407 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2428 Processing helix chain 'A' and resid 2432 through 2438 removed outlier: 3.712A pdb=" N VAL A2438 " --> pdb=" O SER A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2445 Processing helix chain 'A' and resid 2463 through 2468 removed outlier: 3.844A pdb=" N LEU A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A2468 " --> pdb=" O VAL A2464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2463 through 2468' Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.531A pdb=" N GLU A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2487 through 2502 removed outlier: 3.578A pdb=" N LEU A2502 " --> pdb=" O LEU A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2523 through 2539 Processing helix chain 'A' and resid 2540 through 2542 No H-bonds generated for 'chain 'A' and resid 2540 through 2542' Processing helix chain 'A' and resid 2570 through 2590 removed outlier: 3.633A pdb=" N MET A2588 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A2590 " --> pdb=" O GLN A2586 " (cutoff:3.500A) Processing helix chain 'A' and resid 2620 through 2624 Processing helix chain 'A' and resid 2645 through 2654 removed outlier: 4.392A pdb=" N GLY A2652 " --> pdb=" O SER A2648 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A2653 " --> pdb=" O VAL A2649 " (cutoff:3.500A) Processing helix chain 'A' and resid 2694 through 2711 removed outlier: 3.960A pdb=" N CYS A2698 " --> pdb=" O ASP A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2720 through 2735 removed outlier: 3.918A pdb=" N SER A2725 " --> pdb=" O ALA A2721 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A2726 " --> pdb=" O ILE A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2736 through 2738 No H-bonds generated for 'chain 'A' and resid 2736 through 2738' Processing helix chain 'A' and resid 2740 through 2758 removed outlier: 3.522A pdb=" N PHE A2744 " --> pdb=" O GLU A2740 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A2753 " --> pdb=" O VAL A2749 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A2754 " --> pdb=" O THR A2750 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A2756 " --> pdb=" O THR A2752 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2781 Proline residue: A2771 - end of helix Processing helix chain 'A' and resid 2783 through 2799 removed outlier: 3.660A pdb=" N GLU A2788 " --> pdb=" O LYS A2784 " (cutoff:3.500A) Proline residue: A2789 - end of helix removed outlier: 3.554A pdb=" N LEU A2794 " --> pdb=" O VAL A2790 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A2795 " --> pdb=" O SER A2791 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A2799 " --> pdb=" O GLU A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2802 through 2817 removed outlier: 3.747A pdb=" N ARG A2806 " --> pdb=" O HIS A2802 " (cutoff:3.500A) Processing helix chain 'A' and resid 2823 through 2827 removed outlier: 3.517A pdb=" N LYS A2827 " --> pdb=" O ASP A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2828 through 2843 removed outlier: 3.823A pdb=" N VAL A2832 " --> pdb=" O GLN A2828 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A2841 " --> pdb=" O LEU A2837 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A2843 " --> pdb=" O SER A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2870 removed outlier: 3.864A pdb=" N VAL A2856 " --> pdb=" O SER A2852 " (cutoff:3.500A) Processing helix chain 'A' and resid 2875 through 2891 removed outlier: 4.031A pdb=" N MET A2889 " --> pdb=" O MET A2885 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A2890 " --> pdb=" O CYS A2886 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2915 Processing helix chain 'A' and resid 2919 through 2928 removed outlier: 3.620A pdb=" N LYS A2928 " --> pdb=" O GLU A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2938 through 2957 removed outlier: 3.636A pdb=" N GLY A2956 " --> pdb=" O CYS A2952 " (cutoff:3.500A) Processing helix chain 'A' and resid 2980 through 2994 removed outlier: 4.131A pdb=" N VAL A2987 " --> pdb=" O GLU A2983 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A2992 " --> pdb=" O LEU A2988 " (cutoff:3.500A) Processing helix chain 'A' and resid 2996 through 3015 Proline residue: A3008 - end of helix Processing helix chain 'A' and resid 3021 through 3029 Processing helix chain 'A' and resid 3035 through 3052 removed outlier: 3.946A pdb=" N THR A3041 " --> pdb=" O GLN A3037 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A3042 " --> pdb=" O PHE A3038 " (cutoff:3.500A) Processing helix chain 'A' and resid 3057 through 3072 removed outlier: 3.513A pdb=" N ASP A3061 " --> pdb=" O SER A3057 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A3066 " --> pdb=" O TRP A3062 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A3068 " --> pdb=" O MET A3064 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A3069 " --> pdb=" O LEU A3065 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A3072 " --> pdb=" O SER A3068 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3090 Processing helix chain 'A' and resid 3096 through 3098 No H-bonds generated for 'chain 'A' and resid 3096 through 3098' Processing helix chain 'A' and resid 3099 through 3106 removed outlier: 3.518A pdb=" N ARG A3106 " --> pdb=" O HIS A3102 " (cutoff:3.500A) Processing helix chain 'A' and resid 3111 through 3127 removed outlier: 3.656A pdb=" N PHE A3125 " --> pdb=" O VAL A3121 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3145 removed outlier: 3.643A pdb=" N ARG A3136 " --> pdb=" O GLU A3132 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A3137 " --> pdb=" O GLU A3133 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A3138 " --> pdb=" O LEU A3134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A3143 " --> pdb=" O PHE A3139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A3145 " --> pdb=" O SER A3141 " (cutoff:3.500A) Processing helix chain 'A' and resid 3151 through 3162 removed outlier: 4.078A pdb=" N ASN A3162 " --> pdb=" O THR A3158 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 Processing helix chain 'B' and resid 80 through 99 removed outlier: 3.775A pdb=" N TRP B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 133 through 153 removed outlier: 3.605A pdb=" N GLN B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 175 through 191 Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 214 through 233 Processing helix chain 'B' and resid 278 through 299 removed outlier: 3.819A pdb=" N VAL B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.773A pdb=" N TYR B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 367 through 383 1353 hydrogen bonds defined for protein. 3963 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: 7.85 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3441 1.31 - 1.44: 5467 1.44 - 1.57: 12546 1.57 - 1.70: 5 1.70 - 1.82: 193 Bond restraints: 21652 Sorted by residual: bond pdb=" C02 A1ACS B 401 " pdb=" N03 A1ACS B 401 " ideal model delta sigma weight residual 1.454 1.280 0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C10 A1ACS B 401 " pdb=" C14 A1ACS B 401 " ideal model delta sigma weight residual 1.539 1.366 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C12 A1ACS B 401 " pdb=" C13 A1ACS B 401 " ideal model delta sigma weight residual 1.539 1.383 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" C13 A1ACS B 401 " pdb=" C14 A1ACS B 401 " ideal model delta sigma weight residual 1.545 1.680 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C06 A1ACS B 401 " pdb=" C23 A1ACS B 401 " ideal model delta sigma weight residual 1.527 1.427 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 21647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 29071 2.47 - 4.94: 275 4.94 - 7.41: 42 7.41 - 9.88: 15 9.88 - 12.35: 3 Bond angle restraints: 29406 Sorted by residual: angle pdb=" CA ARG A2522 " pdb=" CB ARG A2522 " pdb=" CG ARG A2522 " ideal model delta sigma weight residual 114.10 122.50 -8.40 2.00e+00 2.50e-01 1.76e+01 angle pdb=" N ILE A1313 " pdb=" CA ILE A1313 " pdb=" C ILE A1313 " ideal model delta sigma weight residual 113.71 109.72 3.99 9.50e-01 1.11e+00 1.76e+01 angle pdb=" CB MET A2060 " pdb=" CG MET A2060 " pdb=" SD MET A2060 " ideal model delta sigma weight residual 112.70 125.05 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" N VAL A1511 " pdb=" CA VAL A1511 " pdb=" C VAL A1511 " ideal model delta sigma weight residual 112.43 108.65 3.78 9.20e-01 1.18e+00 1.68e+01 angle pdb=" C LEU A2566 " pdb=" N ASP A2567 " pdb=" CA ASP A2567 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 ... (remaining 29401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11179 17.93 - 35.87: 1454 35.87 - 53.80: 411 53.80 - 71.74: 102 71.74 - 89.67: 38 Dihedral angle restraints: 13184 sinusoidal: 5244 harmonic: 7940 Sorted by residual: dihedral pdb=" CB CYS A 799 " pdb=" SG CYS A 799 " pdb=" SG CYS A 834 " pdb=" CB CYS A 834 " ideal model delta sinusoidal sigma weight residual -86.00 -143.49 57.49 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA ALA A2716 " pdb=" C ALA A2716 " pdb=" N ARG A2717 " pdb=" CA ARG A2717 " ideal model delta harmonic sigma weight residual -180.00 -148.73 -31.27 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA CYS A 799 " pdb=" C CYS A 799 " pdb=" N GLY A 800 " pdb=" CA GLY A 800 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2654 0.040 - 0.081: 684 0.081 - 0.121: 145 0.121 - 0.162: 12 0.162 - 0.202: 5 Chirality restraints: 3500 Sorted by residual: chirality pdb=" CB ILE A3099 " pdb=" CA ILE A3099 " pdb=" CG1 ILE A3099 " pdb=" CG2 ILE A3099 " 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 ARG A2522 " pdb=" N ARG A2522 " pdb=" C ARG A2522 " pdb=" CB ARG A2522 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CB ILE A1041 " pdb=" CA ILE A1041 " pdb=" CG1 ILE A1041 " pdb=" CG2 ILE A1041 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 3497 not shown) Planarity restraints: 3713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A3074 " -0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PRO A3075 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A3075 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A3075 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 128 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 129 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2803 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A2804 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A2804 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2804 " 0.028 5.00e-02 4.00e+02 ... (remaining 3710 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 572 2.71 - 3.26: 21833 3.26 - 3.80: 34971 3.80 - 4.35: 46618 4.35 - 4.90: 75495 Nonbonded interactions: 179489 Sorted by model distance: nonbonded pdb=" O LEU A2731 " pdb=" OG SER A2735 " model vdw 2.160 3.040 nonbonded pdb=" O ARG A1708 " pdb=" OG SER A1712 " model vdw 2.172 3.040 nonbonded pdb=" O LYS A3045 " pdb=" OG1 THR A3049 " model vdw 2.181 3.040 nonbonded pdb=" N GLU A2753 " pdb=" OE1 GLU A2753 " model vdw 2.187 3.120 nonbonded pdb=" OD2 ASP A1184 " pdb=" OG SER A1326 " model vdw 2.188 3.040 ... (remaining 179484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 1.660 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: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 46.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.004 0.174 21654 Z= 0.183 Angle : 0.614 12.350 29410 Z= 0.308 Chirality : 0.037 0.202 3500 Planarity : 0.004 0.090 3713 Dihedral : 18.286 89.673 7992 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.73 % Allowed : 27.26 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2668 helix: 0.95 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2126 HIS 0.005 0.001 HIS A 222 PHE 0.023 0.001 PHE A3014 TYR 0.018 0.001 TYR A2748 ARG 0.017 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.24359 ( 1353) hydrogen bonds : angle 6.86971 ( 3963) SS BOND : bond 0.00480 ( 2) SS BOND : angle 2.34704 ( 4) covalent geometry : bond 0.00389 (21652) covalent geometry : angle 0.61374 (29406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 158 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1516 GLU cc_start: 0.8525 (tt0) cc_final: 0.8249 (mp0) REVERT: A 2055 MET cc_start: 0.8696 (mtm) cc_final: 0.8404 (tpt) REVERT: A 2764 ILE cc_start: 0.8958 (tt) cc_final: 0.8635 (tp) REVERT: B 148 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7575 (ttm110) outliers start: 88 outliers final: 75 residues processed: 244 average time/residue: 1.0517 time to fit residues: 303.3953 Evaluate side-chains 216 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 141 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1570 GLN Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1786 GLN Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 1986 SER Chi-restraints excluded: chain A residue 2024 LEU Chi-restraints excluded: chain A residue 2025 CYS Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2120 VAL Chi-restraints excluded: chain A residue 2131 VAL Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2434 SER Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2611 SER Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2638 SER Chi-restraints excluded: chain A residue 2640 LYS Chi-restraints excluded: chain A residue 2697 SER Chi-restraints excluded: chain A residue 2711 LEU Chi-restraints excluded: chain A residue 2735 SER Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2847 CYS Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2874 VAL Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2934 VAL Chi-restraints excluded: chain A residue 2951 THR Chi-restraints excluded: chain A residue 2987 VAL Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3103 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073981 restraints weight = 42024.135| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.75 r_work: 0.2960 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21654 Z= 0.218 Angle : 0.645 10.045 29410 Z= 0.323 Chirality : 0.041 0.215 3500 Planarity : 0.005 0.062 3713 Dihedral : 7.573 59.748 3038 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.13 % Allowed : 24.25 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.17), residues: 2668 helix: 1.33 (0.12), residues: 1935 sheet: None (None), residues: 0 loop : -0.08 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1877 HIS 0.005 0.001 HIS A1812 PHE 0.017 0.002 PHE A3014 TYR 0.019 0.001 TYR A2748 ARG 0.006 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 1353) hydrogen bonds : angle 4.52081 ( 3963) SS BOND : bond 0.00339 ( 2) SS BOND : angle 3.84834 ( 4) covalent geometry : bond 0.00519 (21652) covalent geometry : angle 0.64382 (29406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 170 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7876 (pttp) REVERT: A 200 GLU cc_start: 0.8771 (tp30) cc_final: 0.8386 (tp30) REVERT: A 845 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8530 (pp20) REVERT: A 915 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 1449 ILE cc_start: 0.8367 (tt) cc_final: 0.8147 (mp) REVERT: A 1497 VAL cc_start: 0.8969 (p) cc_final: 0.8759 (m) REVERT: A 1516 GLU cc_start: 0.8546 (tt0) cc_final: 0.8181 (mp0) REVERT: A 1570 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: A 2022 ARG cc_start: 0.9097 (mtp180) cc_final: 0.8374 (mtt90) REVERT: A 2145 GLU cc_start: 0.8859 (mp0) cc_final: 0.8541 (mp0) REVERT: A 2243 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7697 (pp30) REVERT: A 2690 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7590 (mmp80) REVERT: A 2700 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: A 2986 SER cc_start: 0.8650 (m) cc_final: 0.8222 (p) REVERT: A 3020 ILE cc_start: 0.8264 (mm) cc_final: 0.8049 (pp) REVERT: B 110 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8047 (pp20) outliers start: 121 outliers final: 57 residues processed: 276 average time/residue: 1.1530 time to fit residues: 369.4484 Evaluate side-chains 212 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1570 GLN Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1786 GLN Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2243 GLN Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2434 SER Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2535 SER Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2735 SER Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain A residue 2782 MET Chi-restraints excluded: chain A residue 2803 LEU Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2847 CYS Chi-restraints excluded: chain A residue 2859 MET Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2951 THR Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 2987 VAL Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 241 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 233 optimal weight: 0.0040 chunk 137 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.106331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076860 restraints weight = 41571.114| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.73 r_work: 0.3020 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21654 Z= 0.119 Angle : 0.577 10.589 29410 Z= 0.280 Chirality : 0.038 0.195 3500 Planarity : 0.004 0.065 3713 Dihedral : 6.246 58.759 2984 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.20 % Allowed : 23.82 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2668 helix: 1.60 (0.12), residues: 1938 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1877 HIS 0.005 0.001 HIS A1259 PHE 0.026 0.001 PHE B 115 TYR 0.016 0.001 TYR A2748 ARG 0.009 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1353) hydrogen bonds : angle 4.10101 ( 3963) SS BOND : bond 0.01864 ( 2) SS BOND : angle 2.69514 ( 4) covalent geometry : bond 0.00262 (21652) covalent geometry : angle 0.57589 (29406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 190 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8485 (p0) REVERT: A 200 GLU cc_start: 0.8723 (tp30) cc_final: 0.8318 (tp30) REVERT: A 915 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 968 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9006 (mtmm) REVERT: A 1449 ILE cc_start: 0.8419 (tt) cc_final: 0.8207 (mp) REVERT: A 1495 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: A 1516 GLU cc_start: 0.8466 (tt0) cc_final: 0.8037 (mp0) REVERT: A 2022 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8337 (mtt90) REVERT: A 2145 GLU cc_start: 0.8886 (mp0) cc_final: 0.8433 (mp0) REVERT: A 2569 ARG cc_start: 0.8639 (tmm160) cc_final: 0.8387 (tmm-80) REVERT: A 2690 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7688 (mmt180) REVERT: A 2700 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: A 2802 HIS cc_start: 0.7155 (t-90) cc_final: 0.6416 (t-90) REVERT: A 2949 MET cc_start: 0.8391 (ttp) cc_final: 0.8049 (OUTLIER) REVERT: A 2986 SER cc_start: 0.8702 (m) cc_final: 0.8220 (p) REVERT: A 3070 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (t80) outliers start: 99 outliers final: 35 residues processed: 274 average time/residue: 1.1437 time to fit residues: 364.0006 Evaluate side-chains 192 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1786 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2434 SER Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2486 THR Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2525 ILE Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3130 ILE Chi-restraints excluded: chain B residue 211 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 166 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074325 restraints weight = 42233.716| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.77 r_work: 0.2964 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21654 Z= 0.188 Angle : 0.613 9.457 29410 Z= 0.297 Chirality : 0.040 0.194 3500 Planarity : 0.004 0.064 3713 Dihedral : 5.818 56.935 2965 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.41 % Allowed : 24.29 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2668 helix: 1.69 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -0.03 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1877 HIS 0.010 0.001 HIS A2855 PHE 0.020 0.001 PHE A3070 TYR 0.014 0.001 TYR A2748 ARG 0.010 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1353) hydrogen bonds : angle 4.08105 ( 3963) SS BOND : bond 0.00522 ( 2) SS BOND : angle 4.32144 ( 4) covalent geometry : bond 0.00456 (21652) covalent geometry : angle 0.61074 (29406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 168 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 845 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: A 915 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8339 (mm-30) REVERT: A 968 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9008 (mtmm) REVERT: A 1516 GLU cc_start: 0.8563 (tt0) cc_final: 0.8171 (mp0) REVERT: A 1964 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 2022 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8310 (mtt90) REVERT: A 2055 MET cc_start: 0.8870 (mtm) cc_final: 0.8427 (tpt) REVERT: A 2145 GLU cc_start: 0.8892 (mp0) cc_final: 0.8423 (mp0) REVERT: A 2567 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8313 (p0) REVERT: A 2572 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7635 (mtm-85) REVERT: A 2690 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7657 (mmt180) REVERT: A 2700 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: A 2764 ILE cc_start: 0.8786 (tt) cc_final: 0.8484 (pp) REVERT: A 2774 CYS cc_start: 0.8764 (m) cc_final: 0.8390 (m) REVERT: A 2819 CYS cc_start: 0.8030 (t) cc_final: 0.7757 (t) REVERT: A 2910 GLU cc_start: 0.8602 (tt0) cc_final: 0.8218 (mt-10) REVERT: A 2982 MET cc_start: 0.8855 (mmm) cc_final: 0.8540 (mmm) REVERT: A 2983 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8451 (mp0) REVERT: A 2986 SER cc_start: 0.8753 (m) cc_final: 0.8146 (p) REVERT: A 3070 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (t80) REVERT: B 110 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7959 (pp20) outliers start: 104 outliers final: 48 residues processed: 252 average time/residue: 1.2446 time to fit residues: 362.8033 Evaluate side-chains 210 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1786 GLN Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2572 ARG Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2711 LEU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2803 LEU Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2951 THR Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 245 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076716 restraints weight = 42132.702| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.76 r_work: 0.3015 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21654 Z= 0.118 Angle : 0.576 10.108 29410 Z= 0.276 Chirality : 0.038 0.187 3500 Planarity : 0.004 0.060 3713 Dihedral : 5.532 53.289 2962 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.15 % Allowed : 24.80 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2668 helix: 1.81 (0.12), residues: 1941 sheet: None (None), residues: 0 loop : 0.02 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 215 HIS 0.006 0.001 HIS A2855 PHE 0.020 0.001 PHE A3070 TYR 0.013 0.001 TYR A2748 ARG 0.012 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1353) hydrogen bonds : angle 3.90690 ( 3963) SS BOND : bond 0.00503 ( 2) SS BOND : angle 3.06488 ( 4) covalent geometry : bond 0.00270 (21652) covalent geometry : angle 0.57476 (29406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 178 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8295 (mm-30) REVERT: A 968 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9000 (mtmm) REVERT: A 1516 GLU cc_start: 0.8479 (tt0) cc_final: 0.8049 (mp0) REVERT: A 1964 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: A 2022 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8110 (mtt90) REVERT: A 2055 MET cc_start: 0.8888 (mtm) cc_final: 0.8397 (tpt) REVERT: A 2690 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7528 (mmp80) REVERT: A 2700 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: A 2764 ILE cc_start: 0.8794 (tt) cc_final: 0.8508 (pp) REVERT: A 2774 CYS cc_start: 0.8771 (m) cc_final: 0.8386 (m) REVERT: A 2910 GLU cc_start: 0.8526 (tt0) cc_final: 0.8268 (mt-10) REVERT: A 2982 MET cc_start: 0.8995 (mmm) cc_final: 0.8753 (mmm) REVERT: A 2983 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8444 (mp0) REVERT: A 2986 SER cc_start: 0.8715 (m) cc_final: 0.8115 (p) REVERT: A 3070 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8124 (t80) outliers start: 98 outliers final: 47 residues processed: 255 average time/residue: 1.1745 time to fit residues: 348.2160 Evaluate side-chains 207 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1786 GLN Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2803 LEU Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2853 GLN Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2931 VAL Chi-restraints excluded: chain A residue 2951 THR Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 41 optimal weight: 0.0070 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 264 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076640 restraints weight = 42355.026| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.83 r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21654 Z= 0.111 Angle : 0.579 9.886 29410 Z= 0.275 Chirality : 0.038 0.194 3500 Planarity : 0.004 0.060 3713 Dihedral : 5.272 52.111 2957 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.15 % Allowed : 24.80 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2668 helix: 1.93 (0.12), residues: 1941 sheet: None (None), residues: 0 loop : 0.04 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1699 HIS 0.004 0.000 HIS A1812 PHE 0.029 0.001 PHE B 115 TYR 0.012 0.001 TYR A2382 ARG 0.013 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1353) hydrogen bonds : angle 3.81646 ( 3963) SS BOND : bond 0.00445 ( 2) SS BOND : angle 2.82363 ( 4) covalent geometry : bond 0.00252 (21652) covalent geometry : angle 0.57827 (29406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 180 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 919 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7470 (mtt180) REVERT: A 968 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9009 (mtmm) REVERT: A 1516 GLU cc_start: 0.8467 (tt0) cc_final: 0.8049 (mp0) REVERT: A 1964 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: A 2022 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8111 (mtt90) REVERT: A 2050 ASN cc_start: 0.8235 (t0) cc_final: 0.7980 (t0) REVERT: A 2055 MET cc_start: 0.8876 (mtm) cc_final: 0.8386 (tpt) REVERT: A 2138 ARG cc_start: 0.8075 (mmp80) cc_final: 0.7702 (mmp-170) REVERT: A 2444 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8722 (ptpp) REVERT: A 2690 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7500 (mmp80) REVERT: A 2700 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: A 2764 ILE cc_start: 0.8847 (tt) cc_final: 0.8500 (pp) REVERT: A 2774 CYS cc_start: 0.8779 (m) cc_final: 0.8393 (m) REVERT: A 2877 GLU cc_start: 0.8013 (pm20) cc_final: 0.7713 (pp20) REVERT: A 2982 MET cc_start: 0.9007 (mmm) cc_final: 0.8710 (mmm) REVERT: A 2983 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8598 (mp0) REVERT: A 2986 SER cc_start: 0.8701 (m) cc_final: 0.8390 (m) REVERT: A 3070 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8062 (t80) outliers start: 98 outliers final: 47 residues processed: 259 average time/residue: 1.1726 time to fit residues: 354.0194 Evaluate side-chains 217 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2177 SER Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2444 LYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2525 ILE Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2572 ARG Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2709 TRP Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain A residue 2811 HIS Chi-restraints excluded: chain A residue 2815 TYR Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2853 GLN Chi-restraints excluded: chain A residue 2859 MET Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain B residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 42 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 245 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.104686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075259 restraints weight = 41945.466| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.72 r_work: 0.2981 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21654 Z= 0.176 Angle : 0.623 10.024 29410 Z= 0.297 Chirality : 0.040 0.231 3500 Planarity : 0.004 0.063 3713 Dihedral : 5.026 51.585 2950 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.86 % Allowed : 25.10 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2668 helix: 1.93 (0.12), residues: 1941 sheet: None (None), residues: 0 loop : 0.04 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1699 HIS 0.004 0.001 HIS A1812 PHE 0.018 0.001 PHE A3070 TYR 0.013 0.001 TYR A2382 ARG 0.015 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1353) hydrogen bonds : angle 3.91405 ( 3963) SS BOND : bond 0.00306 ( 2) SS BOND : angle 4.04339 ( 4) covalent geometry : bond 0.00425 (21652) covalent geometry : angle 0.62117 (29406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 168 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 968 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9004 (mtmm) REVERT: A 1516 GLU cc_start: 0.8513 (tt0) cc_final: 0.8124 (mp0) REVERT: A 1964 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 2022 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8327 (mtt90) REVERT: A 2050 ASN cc_start: 0.8285 (t0) cc_final: 0.7995 (t0) REVERT: A 2055 MET cc_start: 0.8883 (mtm) cc_final: 0.8414 (tpt) REVERT: A 2444 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8735 (ptpp) REVERT: A 2690 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7541 (mmp80) REVERT: A 2700 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: A 2764 ILE cc_start: 0.8915 (tt) cc_final: 0.8507 (pp) REVERT: A 2774 CYS cc_start: 0.8765 (m) cc_final: 0.8419 (m) REVERT: A 2877 GLU cc_start: 0.8074 (pm20) cc_final: 0.7775 (pp20) REVERT: A 2885 MET cc_start: 0.6752 (ttt) cc_final: 0.6386 (ttt) REVERT: A 2982 MET cc_start: 0.9033 (mmm) cc_final: 0.8754 (mmm) REVERT: A 2983 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8616 (mp0) REVERT: A 2986 SER cc_start: 0.8698 (m) cc_final: 0.8353 (m) REVERT: A 3070 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 110 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7897 (pp20) outliers start: 91 outliers final: 46 residues processed: 237 average time/residue: 1.1873 time to fit residues: 325.5114 Evaluate side-chains 207 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2177 SER Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2444 LYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2853 GLN Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2931 VAL Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 35 optimal weight: 0.6980 chunk 239 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 80 optimal weight: 0.0270 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077360 restraints weight = 41880.229| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.75 r_work: 0.3033 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21654 Z= 0.113 Angle : 0.594 10.471 29410 Z= 0.284 Chirality : 0.038 0.201 3500 Planarity : 0.004 0.058 3713 Dihedral : 4.753 49.004 2947 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 25.82 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.17), residues: 2668 helix: 2.01 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : 0.09 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 215 HIS 0.004 0.000 HIS A1812 PHE 0.018 0.001 PHE A3070 TYR 0.012 0.001 TYR A2382 ARG 0.016 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1353) hydrogen bonds : angle 3.79617 ( 3963) SS BOND : bond 0.00808 ( 2) SS BOND : angle 3.37356 ( 4) covalent geometry : bond 0.00259 (21652) covalent geometry : angle 0.59259 (29406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8254 (mm-30) REVERT: A 968 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9000 (mtmm) REVERT: A 1516 GLU cc_start: 0.8460 (tt0) cc_final: 0.8031 (mp0) REVERT: A 1780 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: A 1964 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: A 2022 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8120 (mtt90) REVERT: A 2055 MET cc_start: 0.8849 (mtm) cc_final: 0.8387 (tpt) REVERT: A 2572 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: A 2690 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7483 (mmp80) REVERT: A 2700 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: A 2764 ILE cc_start: 0.8840 (tt) cc_final: 0.8492 (pp) REVERT: A 2774 CYS cc_start: 0.8781 (m) cc_final: 0.8422 (m) REVERT: A 2885 MET cc_start: 0.6650 (ttt) cc_final: 0.6369 (ttt) REVERT: A 2982 MET cc_start: 0.8985 (mmm) cc_final: 0.8681 (tpp) REVERT: A 2983 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8643 (mp0) REVERT: A 2986 SER cc_start: 0.8665 (m) cc_final: 0.8337 (m) REVERT: A 3070 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8026 (t80) outliers start: 77 outliers final: 39 residues processed: 223 average time/residue: 1.3301 time to fit residues: 340.6504 Evaluate side-chains 202 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2177 SER Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2572 ARG Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2640 LYS Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2853 GLN Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3070 PHE Chi-restraints excluded: chain A residue 3071 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 126 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 161 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.076776 restraints weight = 41908.540| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.74 r_work: 0.3025 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21654 Z= 0.125 Angle : 0.610 12.656 29410 Z= 0.289 Chirality : 0.038 0.201 3500 Planarity : 0.004 0.057 3713 Dihedral : 4.718 48.823 2947 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.42 % Allowed : 26.45 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2668 helix: 2.05 (0.12), residues: 1937 sheet: None (None), residues: 0 loop : 0.04 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1699 HIS 0.004 0.001 HIS A1812 PHE 0.018 0.001 PHE A3070 TYR 0.012 0.001 TYR A2382 ARG 0.010 0.000 ARG A3137 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1353) hydrogen bonds : angle 3.79730 ( 3963) SS BOND : bond 0.00912 ( 2) SS BOND : angle 3.71035 ( 4) covalent geometry : bond 0.00296 (21652) covalent geometry : angle 0.60843 (29406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8291 (mm-30) REVERT: A 968 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8999 (mtmm) REVERT: A 1516 GLU cc_start: 0.8474 (tt0) cc_final: 0.8106 (mp0) REVERT: A 1780 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: A 1964 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: A 2022 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8146 (mtt90) REVERT: A 2055 MET cc_start: 0.8830 (mtm) cc_final: 0.8460 (tpt) REVERT: A 2567 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8304 (p0) REVERT: A 2572 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7853 (mtm-85) REVERT: A 2690 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7510 (mmp80) REVERT: A 2700 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: A 2764 ILE cc_start: 0.8847 (tt) cc_final: 0.8504 (pp) REVERT: A 2774 CYS cc_start: 0.8814 (m) cc_final: 0.8451 (m) REVERT: A 2877 GLU cc_start: 0.8201 (pm20) cc_final: 0.7802 (pp20) REVERT: A 2885 MET cc_start: 0.6712 (ttt) cc_final: 0.6364 (ttt) REVERT: A 2982 MET cc_start: 0.8962 (mmm) cc_final: 0.8647 (tpp) REVERT: A 2986 SER cc_start: 0.8690 (m) cc_final: 0.8339 (m) REVERT: B 110 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7848 (pp20) outliers start: 57 outliers final: 36 residues processed: 208 average time/residue: 1.2537 time to fit residues: 301.5587 Evaluate side-chains 197 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2177 SER Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2406 LYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2572 ARG Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain B residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 238 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077456 restraints weight = 41898.446| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.74 r_work: 0.3033 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21654 Z= 0.116 Angle : 0.615 14.914 29410 Z= 0.290 Chirality : 0.038 0.221 3500 Planarity : 0.004 0.057 3713 Dihedral : 4.657 47.612 2947 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.20 % Allowed : 26.66 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.17), residues: 2668 helix: 2.11 (0.12), residues: 1931 sheet: None (None), residues: 0 loop : 0.04 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 215 HIS 0.004 0.000 HIS A1812 PHE 0.031 0.001 PHE A3070 TYR 0.012 0.001 TYR A2382 ARG 0.009 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1353) hydrogen bonds : angle 3.77654 ( 3963) SS BOND : bond 0.00647 ( 2) SS BOND : angle 3.26103 ( 4) covalent geometry : bond 0.00271 (21652) covalent geometry : angle 0.61401 (29406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 968 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8994 (mtmm) REVERT: A 1516 GLU cc_start: 0.8476 (tt0) cc_final: 0.8059 (mp0) REVERT: A 1780 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: A 1964 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: A 2022 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8142 (mtt90) REVERT: A 2055 MET cc_start: 0.8834 (mtm) cc_final: 0.8532 (tpt) REVERT: A 2567 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8205 (p0) REVERT: A 2572 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7856 (mtm-85) REVERT: A 2690 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7498 (mmp80) REVERT: A 2700 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: A 2764 ILE cc_start: 0.8847 (tt) cc_final: 0.8516 (pp) REVERT: A 2774 CYS cc_start: 0.8836 (m) cc_final: 0.8466 (m) REVERT: A 2877 GLU cc_start: 0.8271 (pm20) cc_final: 0.7762 (pp20) REVERT: A 2885 MET cc_start: 0.6725 (ttt) cc_final: 0.6460 (ttt) REVERT: A 2982 MET cc_start: 0.8955 (mmm) cc_final: 0.8646 (tpp) REVERT: A 2986 SER cc_start: 0.8691 (m) cc_final: 0.8339 (m) outliers start: 52 outliers final: 38 residues processed: 203 average time/residue: 1.2330 time to fit residues: 288.8899 Evaluate side-chains 203 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1780 GLU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1964 GLN Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2022 ARG Chi-restraints excluded: chain A residue 2177 SER Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 CYS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2543 VAL Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2572 ARG Chi-restraints excluded: chain A residue 2590 SER Chi-restraints excluded: chain A residue 2700 GLN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2859 MET Chi-restraints excluded: chain A residue 2926 LEU Chi-restraints excluded: chain A residue 2979 ILE Chi-restraints excluded: chain A residue 3041 THR Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3156 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 261 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076370 restraints weight = 42289.039| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.75 r_work: 0.3018 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21654 Z= 0.135 Angle : 0.628 16.126 29410 Z= 0.295 Chirality : 0.039 0.251 3500 Planarity : 0.004 0.057 3713 Dihedral : 4.679 47.350 2947 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.29 % Allowed : 26.62 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.17), residues: 2668 helix: 2.08 (0.12), residues: 1937 sheet: None (None), residues: 0 loop : 0.05 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1699 HIS 0.006 0.001 HIS A 222 PHE 0.027 0.001 PHE A3070 TYR 0.012 0.001 TYR A2382 ARG 0.008 0.000 ARG A1820 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1353) hydrogen bonds : angle 3.80848 ( 3963) SS BOND : bond 0.00522 ( 2) SS BOND : angle 3.60085 ( 4) covalent geometry : bond 0.00325 (21652) covalent geometry : angle 0.62653 (29406) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 13219.51 seconds wall clock time: 227 minutes 32.69 seconds (13652.69 seconds total)