Starting phenix.real_space_refine on Mon Sep 14 10:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1b_22623/09_2026/7k1b_22623.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 185 5.16 5 C 18651 2.51 5 N 4987 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 28343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3589, 28343 Classifications: {'peptide': 3589} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 146, 'TRANS': 3441} Chain breaks: 21 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 39, 'ARG:plan': 7, 'ASP:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'TYR:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 298 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 6.34, per 1000 atoms: 0.22 Number of scatterers: 29321 At special positions: 0 Unit cell: (124.12, 147.32, 183.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 185 16.00 P 46 15.00 O 5452 8.00 N 4987 7.00 C 18651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 4 sheets defined 67.0% alpha, 1.2% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.592A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.516A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 96 removed outlier: 3.835A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.975A pdb=" N ALA A 127 " --> pdb=" O CYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.566A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 4.020A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.957A pdb=" N GLU A 188 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.852A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.147A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.930A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.865A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A 288 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.275A pdb=" N LYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.110A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.950A pdb=" N VAL A 375 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 376 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 396 removed outlier: 4.995A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.647A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.996A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.793A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.719A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.656A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.662A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 removed outlier: 4.449A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.875A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.234A pdb=" N SER A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 removed outlier: 3.722A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.322A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 4.118A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 847 through 862 removed outlier: 4.176A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.789A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 910 through 920 removed outlier: 4.291A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 944 removed outlier: 4.257A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 947 No H-bonds generated for 'chain 'A' and resid 945 through 947' Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.905A pdb=" N LYS A 963 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.540A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.967A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1042 removed outlier: 3.573A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1067 removed outlier: 3.639A pdb=" N LEU A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 removed outlier: 4.275A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 Processing helix chain 'A' and resid 1122 through 1139 removed outlier: 3.601A pdb=" N ARG A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 3.590A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1213 removed outlier: 3.663A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1219 through 1226 Processing helix chain 'A' and resid 1241 through 1245 Processing helix chain 'A' and resid 1252 through 1273 removed outlier: 4.066A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A1270 " --> pdb=" O CYS A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1300 Processing helix chain 'A' and resid 1326 through 1336 removed outlier: 3.604A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1350 Processing helix chain 'A' and resid 1352 through 1356 removed outlier: 4.362A pdb=" N GLY A1355 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.239A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1407 Proline residue: A1396 - end of helix removed outlier: 3.679A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A1403 " --> pdb=" O CYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1431 removed outlier: 3.802A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1462 Processing helix chain 'A' and resid 1477 through 1490 Processing helix chain 'A' and resid 1505 through 1520 Processing helix chain 'A' and resid 1524 through 1532 removed outlier: 3.830A pdb=" N LEU A1528 " --> pdb=" O LEU A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1563 removed outlier: 3.947A pdb=" N TYR A1560 " --> pdb=" O GLY A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.837A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1585 removed outlier: 3.549A pdb=" N GLU A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.749A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1610 No H-bonds generated for 'chain 'A' and resid 1608 through 1610' Processing helix chain 'A' and resid 1613 through 1624 Processing helix chain 'A' and resid 1625 through 1629 removed outlier: 3.552A pdb=" N LYS A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1625 through 1629' Processing helix chain 'A' and resid 1640 through 1655 Processing helix chain 'A' and resid 1667 through 1678 Processing helix chain 'A' and resid 1688 through 1700 removed outlier: 3.941A pdb=" N ALA A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1705 through 1722 removed outlier: 3.889A pdb=" N ALA A1720 " --> pdb=" O GLN A1716 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1751 removed outlier: 3.879A pdb=" N ASN A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 3.901A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.966A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.534A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A1795 " --> pdb=" O CYS A1791 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.738A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1848 removed outlier: 3.806A pdb=" N ALA A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 5.239A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1900 removed outlier: 3.611A pdb=" N ASN A1897 " --> pdb=" O GLU A1893 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A1898 " --> pdb=" O SER A1894 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1899 " --> pdb=" O LYS A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1922 removed outlier: 3.712A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE A1916 " --> pdb=" O THR A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1955 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 4.497A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2048 removed outlier: 4.110A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2132 Processing helix chain 'A' and resid 2139 through 2151 removed outlier: 3.797A pdb=" N LEU A2149 " --> pdb=" O PHE A2145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.771A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2161 No H-bonds generated for 'chain 'A' and resid 2159 through 2161' Processing helix chain 'A' and resid 2165 through 2173 Processing helix chain 'A' and resid 2182 through 2194 Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 removed outlier: 3.910A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A2232 " --> pdb=" O ARG A2228 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N HIS A2233 " --> pdb=" O ALA A2229 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2295 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.517A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2354 removed outlier: 3.621A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2371 removed outlier: 3.676A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.887A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.638A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 removed outlier: 3.589A pdb=" N LEU A2415 " --> pdb=" O LEU A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.679A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2442 removed outlier: 3.641A pdb=" N GLN A2432 " --> pdb=" O ASP A2428 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2446 Processing helix chain 'A' and resid 2447 through 2455 removed outlier: 3.534A pdb=" N LEU A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2462 removed outlier: 3.663A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.783A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2509 removed outlier: 4.115A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2536 through 2543 removed outlier: 4.123A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2790 through 2799 removed outlier: 3.559A pdb=" N GLN A2795 " --> pdb=" O ILE A2791 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 4.114A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.834A pdb=" N LYS A2829 " --> pdb=" O THR A2825 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 3.729A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2883 removed outlier: 4.059A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 4.112A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2931 Processing helix chain 'A' and resid 2935 through 2943 removed outlier: 3.924A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2962 removed outlier: 3.793A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2972 through 2977 removed outlier: 3.844A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.737A pdb=" N LYS A2991 " --> pdb=" O THR A2987 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A3005 " --> pdb=" O CYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3018 removed outlier: 3.680A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A3018 " --> pdb=" O CYS A3014 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.801A pdb=" N GLU A3038 " --> pdb=" O PRO A3034 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.701A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.808A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3077 through 3082 removed outlier: 3.688A pdb=" N TYR A3082 " --> pdb=" O LEU A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.802A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 4.091A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3263 removed outlier: 3.952A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3291 removed outlier: 3.832A pdb=" N SER A3290 " --> pdb=" O CYS A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3306 removed outlier: 3.847A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3307 through 3309 No H-bonds generated for 'chain 'A' and resid 3307 through 3309' Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 4.023A pdb=" N SER A3342 " --> pdb=" O ALA A3338 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3361 Processing helix chain 'A' and resid 3373 through 3391 Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.666A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.634A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 4.298A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 Processing helix chain 'A' and resid 3498 through 3503 removed outlier: 4.027A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3525 through 3539 removed outlier: 4.345A pdb=" N ILE A3529 " --> pdb=" O TYR A3525 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR A3531 " --> pdb=" O GLN A3527 " (cutoff:3.500A) Proline residue: A3532 - end of helix removed outlier: 4.011A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3546 through 3562 removed outlier: 4.019A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3596 removed outlier: 3.824A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.377A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3641 through 3651 removed outlier: 3.862A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3670 Processing helix chain 'A' and resid 3759 through 3775 Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.224A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.626A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3846 Processing helix chain 'A' and resid 3853 through 3858 Processing helix chain 'A' and resid 3865 through 3876 removed outlier: 3.615A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3892 removed outlier: 3.834A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A3892 " --> pdb=" O VAL A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3918 removed outlier: 4.188A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.534A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.949A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4013 through 4023 Processing helix chain 'A' and resid 4041 through 4052 Processing helix chain 'A' and resid 4057 through 4068 removed outlier: 3.828A pdb=" N CYS A4061 " --> pdb=" O ALA A4057 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4093 removed outlier: 3.792A pdb=" N GLN A4092 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4121 through 4125 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 3.812A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 4.016A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 1451 hydrogen bonds defined for protein. 4299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 9.73 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8455 1.34 - 1.46: 6629 1.46 - 1.58: 14538 1.58 - 1.70: 91 1.70 - 1.83: 287 Bond restraints: 30000 Sorted by residual: bond pdb=" C PRO A2372 " pdb=" N PRO A2373 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.01e+01 bond pdb=" C LEU A 793 " pdb=" N PRO A 794 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.06e+01 bond pdb=" C3' DG D 1 " pdb=" C2' DG D 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC D 14 " pdb=" C2' DC D 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.04e+00 ... (remaining 29995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 40152 3.44 - 6.88: 517 6.88 - 10.32: 98 10.32 - 13.76: 12 13.76 - 17.20: 1 Bond angle restraints: 40780 Sorted by residual: angle pdb=" C PRO A3676 " pdb=" N PRO A3677 " pdb=" CA PRO A3677 " ideal model delta sigma weight residual 119.84 108.48 11.36 1.25e+00 6.40e-01 8.25e+01 angle pdb=" N TRP A4038 " pdb=" CA TRP A4038 " pdb=" C TRP A4038 " ideal model delta sigma weight residual 111.04 99.67 11.37 1.55e+00 4.16e-01 5.38e+01 angle pdb=" C GLU A1002 " pdb=" N SER A1003 " pdb=" CA SER A1003 " ideal model delta sigma weight residual 122.73 132.97 -10.24 1.62e+00 3.81e-01 4.00e+01 angle pdb=" C ALA A 266 " pdb=" N VAL A 267 " pdb=" CA VAL A 267 " ideal model delta sigma weight residual 120.24 124.12 -3.88 6.30e-01 2.52e+00 3.78e+01 angle pdb=" C ASP A4012 " pdb=" N TRP A4013 " pdb=" CA TRP A4013 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 ... (remaining 40775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15495 17.98 - 35.95: 2002 35.95 - 53.93: 481 53.93 - 71.91: 124 71.91 - 89.89: 28 Dihedral angle restraints: 18130 sinusoidal: 7574 harmonic: 10556 Sorted by residual: dihedral pdb=" CA ASP A 607 " pdb=" C ASP A 607 " pdb=" N PRO A 608 " pdb=" CA PRO A 608 " ideal model delta harmonic sigma weight residual 180.00 116.97 63.03 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA PRO A 608 " pdb=" C PRO A 608 " pdb=" N ALA A 609 " pdb=" CA ALA A 609 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ASN A2534 " pdb=" C ASN A2534 " pdb=" N THR A2535 " pdb=" CA THR A2535 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 18127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3595 0.062 - 0.124: 914 0.124 - 0.186: 151 0.186 - 0.248: 19 0.248 - 0.310: 5 Chirality restraints: 4684 Sorted by residual: chirality pdb=" CA TRP A4038 " pdb=" N TRP A4038 " pdb=" C TRP A4038 " pdb=" CB TRP A4038 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE A3719 " pdb=" CA ILE A3719 " pdb=" CG1 ILE A3719 " pdb=" CG2 ILE A3719 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 4681 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2182 " -0.020 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE A2182 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE A2182 " -0.029 2.00e-02 2.50e+03 pdb=" N HIS A2183 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1002 " -0.017 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLU A1002 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU A1002 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A1003 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 385 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C TYR A 385 " -0.066 2.00e-02 2.50e+03 pdb=" O TYR A 385 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A 386 " 0.022 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7739 2.79 - 3.32: 28165 3.32 - 3.85: 48638 3.85 - 4.37: 53922 4.37 - 4.90: 87356 Nonbonded interactions: 225820 Sorted by model distance: nonbonded pdb=" O ASP A3180 " pdb=" OG1 THR A3184 " model vdw 2.268 3.040 nonbonded pdb=" O ARG A2842 " pdb=" OG1 THR A2846 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A2955 " pdb=" OE1 GLN A2971 " model vdw 2.275 3.040 nonbonded pdb=" O LYS A 133 " pdb=" OG1 THR A 137 " model vdw 2.276 3.040 nonbonded pdb=" O ARG A 532 " pdb=" OG SER A 536 " model vdw 2.278 3.040 ... (remaining 225815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30000 Z= 0.300 Angle : 1.063 17.196 40780 Z= 0.602 Chirality : 0.056 0.310 4684 Planarity : 0.008 0.090 5000 Dihedral : 17.491 89.886 11246 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.21 % Favored : 87.53 % Rotamer: Outliers : 0.55 % Allowed : 11.57 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.11), residues: 3545 helix: -2.72 (0.08), residues: 2244 sheet: -2.91 (0.88), residues: 32 loop : -4.14 (0.14), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A3741 TYR 0.021 0.002 TYR A2316 PHE 0.038 0.002 PHE A1089 TRP 0.048 0.002 TRP A1039 HIS 0.011 0.001 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.30 (30000) covalent geometry : angle 1.06324 / 0.60 (40780) hydrogen bonds : bond 0.11559 / 7.28 ( 1505) hydrogen bonds : angle 6.20136 / 4.31 ( 4411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 441 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8753 (m-80) cc_final: 0.8025 (m-10) REVERT: A 238 MET cc_start: 0.8091 (mmt) cc_final: 0.7817 (mmm) REVERT: A 326 MET cc_start: 0.8263 (ptm) cc_final: 0.7913 (ppp) REVERT: A 338 LEU cc_start: 0.9132 (tp) cc_final: 0.8805 (pp) REVERT: A 359 LEU cc_start: 0.8560 (mt) cc_final: 0.8226 (pt) REVERT: A 441 MET cc_start: 0.8427 (tpt) cc_final: 0.7710 (tpp) REVERT: A 959 TYR cc_start: 0.7909 (p90) cc_final: 0.7621 (p90) REVERT: A 961 LEU cc_start: 0.9091 (tp) cc_final: 0.8796 (tt) REVERT: A 963 LYS cc_start: 0.8327 (mttt) cc_final: 0.7302 (tttp) REVERT: A 966 PHE cc_start: 0.8830 (m-10) cc_final: 0.8524 (m-80) REVERT: A 1369 MET cc_start: 0.8792 (mmt) cc_final: 0.8453 (mmp) REVERT: A 1392 MET cc_start: 0.8229 (mtp) cc_final: 0.7994 (mtp) REVERT: A 1804 MET cc_start: 0.9080 (ptm) cc_final: 0.8833 (ptm) REVERT: A 2126 MET cc_start: 0.6213 (ttt) cc_final: 0.5848 (ttm) REVERT: A 2220 MET cc_start: 0.9088 (mtt) cc_final: 0.8881 (mtm) REVERT: A 2255 LEU cc_start: 0.8394 (pt) cc_final: 0.8110 (pt) REVERT: A 2274 ILE cc_start: 0.9241 (pt) cc_final: 0.8988 (pt) REVERT: A 2307 MET cc_start: 0.8146 (tmm) cc_final: 0.7875 (tmm) REVERT: A 2546 TYR cc_start: 0.8264 (t80) cc_final: 0.7931 (t80) REVERT: A 3235 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8312 (mtmm) REVERT: A 3239 LYS cc_start: 0.8606 (mttm) cc_final: 0.8395 (mttm) REVERT: A 3315 TYR cc_start: 0.5277 (t80) cc_final: 0.4801 (t80) REVERT: A 3621 LYS cc_start: 0.9054 (tppt) cc_final: 0.8840 (tppt) REVERT: A 3741 ARG cc_start: 0.7109 (ptp90) cc_final: 0.6336 (ptp90) REVERT: A 3774 ILE cc_start: 0.9156 (mt) cc_final: 0.8948 (mt) outliers start: 17 outliers final: 3 residues processed: 455 average time/residue: 0.1879 time to fit residues: 138.8438 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 54 GLN A 109 ASN A 136 GLN A 207 GLN A 355 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 484 HIS ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS A1071 ASN A1083 ASN A1325 GLN A1598 ASN A1611 GLN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 HIS A2270 ASN A2352 HIS A2354 ASN A2432 GLN A2475 ASN ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2831 ASN A3054 GLN A3139 GLN A3263 HIS A3327 ASN A3422 GLN A3423 GLN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3573 ASN A3590 ASN A3671 ASN ** A3716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3908 HIS A3924 HIS A4088 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067053 restraints weight = 159910.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.068366 restraints weight = 104368.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069297 restraints weight = 75864.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069963 restraints weight = 59623.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070444 restraints weight = 49765.109| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30000 Z= 0.181 Angle : 0.770 11.041 40780 Z= 0.405 Chirality : 0.044 0.197 4684 Planarity : 0.006 0.109 5000 Dihedral : 13.951 68.197 4358 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.59 % Favored : 88.35 % Rotamer: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.12), residues: 3545 helix: -1.54 (0.10), residues: 2267 sheet: -2.64 (0.88), residues: 31 loop : -3.84 (0.15), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 70 TYR 0.035 0.002 TYR A2288 PHE 0.046 0.002 PHE A1060 TRP 0.033 0.002 TRP A3164 HIS 0.007 0.001 HIS A1687 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (30000) covalent geometry : angle 0.77043 / 0.40 (40780) hydrogen bonds : bond 0.04898 / 3.24 ( 1505) hydrogen bonds : angle 5.22045 / 3.66 ( 4411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8680 (m-80) cc_final: 0.8158 (m-80) REVERT: A 189 MET cc_start: 0.4065 (mtm) cc_final: 0.3712 (mpp) REVERT: A 238 MET cc_start: 0.7952 (mmt) cc_final: 0.7681 (mmm) REVERT: A 326 MET cc_start: 0.8514 (ptm) cc_final: 0.8076 (ppp) REVERT: A 338 LEU cc_start: 0.9250 (tp) cc_final: 0.8972 (pp) REVERT: A 359 LEU cc_start: 0.8853 (mt) cc_final: 0.8388 (pt) REVERT: A 441 MET cc_start: 0.8370 (tpt) cc_final: 0.7953 (tpp) REVERT: A 652 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7830 (tp30) REVERT: A 963 LYS cc_start: 0.8363 (mttt) cc_final: 0.7280 (tttp) REVERT: A 966 PHE cc_start: 0.8759 (m-10) cc_final: 0.8389 (m-80) REVERT: A 1194 PHE cc_start: 0.7922 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1369 MET cc_start: 0.8675 (mmt) cc_final: 0.8220 (mmp) REVERT: A 1688 LEU cc_start: 0.8533 (mp) cc_final: 0.8183 (mp) REVERT: A 1743 MET cc_start: 0.8382 (mmt) cc_final: 0.8117 (tpp) REVERT: A 1804 MET cc_start: 0.9103 (ptm) cc_final: 0.8851 (ptm) REVERT: A 2098 THR cc_start: 0.9106 (t) cc_final: 0.8901 (t) REVERT: A 2102 LYS cc_start: 0.9403 (mttt) cc_final: 0.9082 (mtmm) REVERT: A 2126 MET cc_start: 0.6134 (ttt) cc_final: 0.5846 (ttm) REVERT: A 2220 MET cc_start: 0.9385 (mtt) cc_final: 0.9170 (mtm) REVERT: A 2307 MET cc_start: 0.8658 (tmm) cc_final: 0.8306 (tmm) REVERT: A 2340 SER cc_start: 0.8616 (t) cc_final: 0.8384 (m) REVERT: A 2546 TYR cc_start: 0.8330 (t80) cc_final: 0.8001 (t80) REVERT: A 2937 ASP cc_start: 0.8971 (m-30) cc_final: 0.8208 (t0) REVERT: A 3235 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8620 (mtpt) REVERT: A 3239 LYS cc_start: 0.8818 (mttm) cc_final: 0.8574 (ptpt) REVERT: A 3315 TYR cc_start: 0.5242 (t80) cc_final: 0.4822 (t80) REVERT: A 3808 ASN cc_start: 0.8006 (t0) cc_final: 0.7328 (p0) REVERT: A 3941 ASP cc_start: 0.8954 (t0) cc_final: 0.8716 (t0) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.1775 time to fit residues: 114.9632 Evaluate side-chains 286 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 17 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS A 611 ASN A 738 HIS ** A1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN ** A1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1859 ASN ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1980 ASN A1989 ASN A2103 HIS ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN A2865 HIS A3059 GLN A3148 GLN ** A3423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3716 HIS ** A3748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3787 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.079402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065353 restraints weight = 165444.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066672 restraints weight = 107964.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067591 restraints weight = 78418.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068234 restraints weight = 61540.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068714 restraints weight = 51415.600| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 30000 Z= 0.266 Angle : 0.818 12.498 40780 Z= 0.432 Chirality : 0.046 0.190 4684 Planarity : 0.006 0.070 5000 Dihedral : 13.865 68.615 4358 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.15 % Favored : 86.83 % Rotamer: Outliers : 0.06 % Allowed : 6.49 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.13), residues: 3545 helix: -1.16 (0.10), residues: 2270 sheet: -2.33 (0.90), residues: 31 loop : -3.81 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1608 TYR 0.033 0.002 TYR A 527 PHE 0.036 0.002 PHE A1060 TRP 0.018 0.002 TRP A3164 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.27 (30000) covalent geometry : angle 0.81846 / 0.43 (40780) hydrogen bonds : bond 0.05013 / 3.30 ( 1505) hydrogen bonds : angle 5.28169 / 3.70 ( 4411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8717 (m-80) cc_final: 0.8210 (m-80) REVERT: A 238 MET cc_start: 0.8023 (mmt) cc_final: 0.7818 (mmm) REVERT: A 338 LEU cc_start: 0.9371 (tp) cc_final: 0.9060 (pp) REVERT: A 359 LEU cc_start: 0.8883 (mt) cc_final: 0.8438 (pt) REVERT: A 441 MET cc_start: 0.8382 (tpt) cc_final: 0.7961 (tpp) REVERT: A 963 LYS cc_start: 0.8513 (mttt) cc_final: 0.7611 (tttp) REVERT: A 1194 PHE cc_start: 0.8130 (m-80) cc_final: 0.7860 (m-80) REVERT: A 1369 MET cc_start: 0.8668 (mmt) cc_final: 0.8192 (mmp) REVERT: A 1743 MET cc_start: 0.8371 (mmt) cc_final: 0.8097 (tpp) REVERT: A 2098 THR cc_start: 0.9092 (t) cc_final: 0.8881 (t) REVERT: A 2100 LEU cc_start: 0.9360 (tt) cc_final: 0.8715 (tt) REVERT: A 2102 LYS cc_start: 0.9407 (mttt) cc_final: 0.9095 (mtmm) REVERT: A 2126 MET cc_start: 0.6503 (ttt) cc_final: 0.6114 (ttm) REVERT: A 2255 LEU cc_start: 0.8835 (pt) cc_final: 0.8304 (pt) REVERT: A 2306 ASN cc_start: 0.9025 (m-40) cc_final: 0.8787 (m110) REVERT: A 2323 LEU cc_start: 0.9226 (mt) cc_final: 0.9026 (mt) REVERT: A 2340 SER cc_start: 0.8661 (t) cc_final: 0.8435 (m) REVERT: A 2546 TYR cc_start: 0.8496 (t80) cc_final: 0.8192 (t80) REVERT: A 2937 ASP cc_start: 0.9021 (m-30) cc_final: 0.8274 (t0) REVERT: A 3235 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8673 (mtpt) REVERT: A 3238 MET cc_start: 0.8530 (mtp) cc_final: 0.8321 (mtp) REVERT: A 3239 LYS cc_start: 0.8811 (mttm) cc_final: 0.8445 (mttm) REVERT: A 3315 TYR cc_start: 0.5669 (t80) cc_final: 0.5179 (t80) REVERT: A 3808 ASN cc_start: 0.8027 (t0) cc_final: 0.7319 (p0) REVERT: A 4020 MET cc_start: 0.8910 (ttm) cc_final: 0.8530 (ttm) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.1790 time to fit residues: 108.3707 Evaluate side-chains 267 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 201 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067224 restraints weight = 159792.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068575 restraints weight = 103547.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069529 restraints weight = 74633.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070198 restraints weight = 58272.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070694 restraints weight = 48515.991| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30000 Z= 0.157 Angle : 0.730 13.933 40780 Z= 0.380 Chirality : 0.044 0.182 4684 Planarity : 0.005 0.072 5000 Dihedral : 13.666 71.371 4358 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.42 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.13), residues: 3545 helix: -0.79 (0.10), residues: 2279 sheet: -2.23 (0.89), residues: 31 loop : -3.67 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2254 TYR 0.022 0.002 TYR A2484 PHE 0.043 0.002 PHE A 251 TRP 0.014 0.001 TRP A3164 HIS 0.014 0.001 HIS A3716 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (30000) covalent geometry : angle 0.73050 / 0.38 (40780) hydrogen bonds : bond 0.04421 / 2.89 ( 1505) hydrogen bonds : angle 4.92793 / 3.46 ( 4411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8675 (m-80) cc_final: 0.8149 (m-80) REVERT: A 189 MET cc_start: 0.6397 (mpp) cc_final: 0.5797 (mpp) REVERT: A 326 MET cc_start: 0.8725 (ptt) cc_final: 0.8076 (ppp) REVERT: A 338 LEU cc_start: 0.9198 (tp) cc_final: 0.8933 (pp) REVERT: A 359 LEU cc_start: 0.8851 (mt) cc_final: 0.8385 (pt) REVERT: A 413 PHE cc_start: 0.8158 (m-10) cc_final: 0.7938 (m-10) REVERT: A 441 MET cc_start: 0.8249 (tpt) cc_final: 0.7874 (tpp) REVERT: A 941 MET cc_start: 0.8546 (ptp) cc_final: 0.8267 (ppp) REVERT: A 963 LYS cc_start: 0.8322 (mttt) cc_final: 0.7294 (tttp) REVERT: A 966 PHE cc_start: 0.8865 (m-10) cc_final: 0.8458 (m-80) REVERT: A 1108 MET cc_start: 0.8869 (mtp) cc_final: 0.8614 (mtm) REVERT: A 1194 PHE cc_start: 0.8080 (m-80) cc_final: 0.7704 (m-80) REVERT: A 1369 MET cc_start: 0.8632 (mmt) cc_final: 0.8161 (mmp) REVERT: A 1757 MET cc_start: 0.5974 (tpt) cc_final: 0.5158 (tpt) REVERT: A 1804 MET cc_start: 0.9086 (ptm) cc_final: 0.8486 (ptt) REVERT: A 1871 MET cc_start: 0.8812 (ttp) cc_final: 0.8430 (ptm) REVERT: A 2040 MET cc_start: 0.8568 (tpt) cc_final: 0.8115 (tpp) REVERT: A 2098 THR cc_start: 0.9045 (t) cc_final: 0.8568 (t) REVERT: A 2100 LEU cc_start: 0.9234 (tt) cc_final: 0.8606 (tt) REVERT: A 2102 LYS cc_start: 0.9380 (mttt) cc_final: 0.9090 (mttt) REVERT: A 2126 MET cc_start: 0.6400 (ttt) cc_final: 0.6021 (ttm) REVERT: A 2306 ASN cc_start: 0.8871 (m-40) cc_final: 0.8519 (m110) REVERT: A 2323 LEU cc_start: 0.9169 (mt) cc_final: 0.8914 (mt) REVERT: A 2340 SER cc_start: 0.8600 (t) cc_final: 0.8394 (m) REVERT: A 2546 TYR cc_start: 0.8416 (t80) cc_final: 0.8142 (t80) REVERT: A 2925 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8034 (mt-10) REVERT: A 2937 ASP cc_start: 0.9009 (m-30) cc_final: 0.8219 (t0) REVERT: A 3235 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8479 (mtmt) REVERT: A 3238 MET cc_start: 0.8499 (mtp) cc_final: 0.8299 (mtp) REVERT: A 3239 LYS cc_start: 0.8786 (mttm) cc_final: 0.8404 (mttm) REVERT: A 3315 TYR cc_start: 0.5462 (t80) cc_final: 0.5014 (t80) REVERT: A 3808 ASN cc_start: 0.7993 (t0) cc_final: 0.7335 (p0) REVERT: A 3941 ASP cc_start: 0.8914 (t0) cc_final: 0.8683 (t0) REVERT: A 4020 MET cc_start: 0.8925 (ttm) cc_final: 0.8498 (ttm) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1759 time to fit residues: 109.7793 Evaluate side-chains 276 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1890 HIS A2089 ASN ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2514 ASN ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4087 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066624 restraints weight = 158896.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067954 restraints weight = 102634.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068895 restraints weight = 74016.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069562 restraints weight = 57797.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070045 restraints weight = 47954.053| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30000 Z= 0.179 Angle : 0.729 14.218 40780 Z= 0.381 Chirality : 0.044 0.260 4684 Planarity : 0.005 0.086 5000 Dihedral : 13.557 72.944 4358 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.99 % Favored : 87.98 % Rotamer: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.14), residues: 3545 helix: -0.68 (0.11), residues: 2282 sheet: -2.11 (0.93), residues: 30 loop : -3.55 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3763 TYR 0.042 0.002 TYR A2288 PHE 0.038 0.002 PHE A 251 TRP 0.039 0.002 TRP A1039 HIS 0.009 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (30000) covalent geometry : angle 0.72926 / 0.38 (40780) hydrogen bonds : bond 0.04337 / 2.86 ( 1505) hydrogen bonds : angle 4.92420 / 3.46 ( 4411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4943 (tpp) cc_final: 0.3959 (tpp) REVERT: A 103 TYR cc_start: 0.8589 (m-80) cc_final: 0.8069 (m-80) REVERT: A 189 MET cc_start: 0.6426 (mpp) cc_final: 0.6005 (mpp) REVERT: A 326 MET cc_start: 0.8800 (ptt) cc_final: 0.8169 (ppp) REVERT: A 338 LEU cc_start: 0.9275 (tp) cc_final: 0.9017 (pp) REVERT: A 357 LYS cc_start: 0.8181 (mttp) cc_final: 0.7885 (mmtt) REVERT: A 359 LEU cc_start: 0.8889 (mt) cc_final: 0.8431 (pt) REVERT: A 441 MET cc_start: 0.8210 (tpt) cc_final: 0.7773 (tpp) REVERT: A 652 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7993 (tp30) REVERT: A 726 LEU cc_start: 0.9135 (tt) cc_final: 0.8879 (tt) REVERT: A 963 LYS cc_start: 0.8337 (mttt) cc_final: 0.7234 (tttp) REVERT: A 966 PHE cc_start: 0.8855 (m-10) cc_final: 0.8426 (m-80) REVERT: A 1369 MET cc_start: 0.8546 (mmt) cc_final: 0.8088 (mmp) REVERT: A 1757 MET cc_start: 0.6018 (tpt) cc_final: 0.5280 (tpt) REVERT: A 1804 MET cc_start: 0.9285 (ptm) cc_final: 0.8831 (ptt) REVERT: A 1871 MET cc_start: 0.8704 (ttp) cc_final: 0.8282 (ptm) REVERT: A 2102 LYS cc_start: 0.9394 (mttt) cc_final: 0.9085 (mtmm) REVERT: A 2126 MET cc_start: 0.6312 (ttt) cc_final: 0.5905 (ttm) REVERT: A 2306 ASN cc_start: 0.8944 (m-40) cc_final: 0.8622 (m110) REVERT: A 2340 SER cc_start: 0.8639 (t) cc_final: 0.8436 (m) REVERT: A 2546 TYR cc_start: 0.8457 (t80) cc_final: 0.8238 (t80) REVERT: A 2925 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8086 (tt0) REVERT: A 2937 ASP cc_start: 0.9002 (m-30) cc_final: 0.8233 (t0) REVERT: A 3235 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8539 (mtmt) REVERT: A 3239 LYS cc_start: 0.8742 (mttm) cc_final: 0.8381 (mttm) REVERT: A 3315 TYR cc_start: 0.5597 (t80) cc_final: 0.5139 (t80) REVERT: A 3414 MET cc_start: 0.8789 (tpp) cc_final: 0.8122 (mmm) REVERT: A 3808 ASN cc_start: 0.8013 (t0) cc_final: 0.7240 (p0) REVERT: A 3932 MET cc_start: 0.9080 (mtm) cc_final: 0.8642 (mtt) REVERT: A 4020 MET cc_start: 0.8941 (ttm) cc_final: 0.8514 (ttm) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.1738 time to fit residues: 107.1025 Evaluate side-chains 271 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 86 optimal weight: 0.6980 chunk 243 optimal weight: 0.1980 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 0.0010 chunk 3 optimal weight: 8.9990 chunk 146 optimal weight: 0.0370 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 335 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 overall best weight: 0.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 GLN A1830 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS A3510 GLN ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.082995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068991 restraints weight = 153862.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070351 restraints weight = 100875.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071292 restraints weight = 73091.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071963 restraints weight = 57184.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072440 restraints weight = 47604.072| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30000 Z= 0.132 Angle : 0.725 15.466 40780 Z= 0.365 Chirality : 0.043 0.248 4684 Planarity : 0.005 0.070 5000 Dihedral : 13.344 74.195 4358 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.13 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.14), residues: 3545 helix: -0.42 (0.11), residues: 2290 sheet: -2.10 (0.92), residues: 30 loop : -3.46 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3763 TYR 0.025 0.001 TYR A1558 PHE 0.041 0.001 PHE A 251 TRP 0.085 0.002 TRP A3164 HIS 0.012 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (30000) covalent geometry : angle 0.72475 / 0.36 (40780) hydrogen bonds : bond 0.03908 / 2.58 ( 1505) hydrogen bonds : angle 4.62518 / 3.26 ( 4411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5173 (tpp) cc_final: 0.4905 (mmm) REVERT: A 103 TYR cc_start: 0.8602 (m-80) cc_final: 0.8065 (m-80) REVERT: A 109 ASN cc_start: 0.8612 (t0) cc_final: 0.8334 (p0) REVERT: A 189 MET cc_start: 0.5890 (mpp) cc_final: 0.5517 (mpp) REVERT: A 326 MET cc_start: 0.8817 (ptt) cc_final: 0.8242 (ppp) REVERT: A 357 LYS cc_start: 0.8062 (mttp) cc_final: 0.7804 (mmtt) REVERT: A 359 LEU cc_start: 0.8790 (mt) cc_final: 0.8415 (pt) REVERT: A 441 MET cc_start: 0.8254 (tpt) cc_final: 0.7806 (tpp) REVERT: A 652 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7689 (tp30) REVERT: A 725 LEU cc_start: 0.8155 (pt) cc_final: 0.7838 (pt) REVERT: A 963 LYS cc_start: 0.8156 (mttt) cc_final: 0.7099 (tttp) REVERT: A 966 PHE cc_start: 0.8789 (m-10) cc_final: 0.8459 (m-80) REVERT: A 1369 MET cc_start: 0.8401 (mmt) cc_final: 0.7921 (mmp) REVERT: A 1757 MET cc_start: 0.5962 (tpt) cc_final: 0.5290 (tpt) REVERT: A 1804 MET cc_start: 0.9254 (ptm) cc_final: 0.8805 (ptt) REVERT: A 2098 THR cc_start: 0.8989 (t) cc_final: 0.8772 (t) REVERT: A 2102 LYS cc_start: 0.9363 (mttt) cc_final: 0.9041 (mtmm) REVERT: A 2126 MET cc_start: 0.6187 (ttt) cc_final: 0.5829 (ttm) REVERT: A 2925 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8006 (tt0) REVERT: A 3195 GLU cc_start: 0.6967 (pp20) cc_final: 0.6644 (mm-30) REVERT: A 3235 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8524 (mtmt) REVERT: A 3239 LYS cc_start: 0.8721 (mttm) cc_final: 0.8326 (mttm) REVERT: A 3256 MET cc_start: 0.8052 (tpt) cc_final: 0.7680 (mmm) REVERT: A 3577 GLN cc_start: 0.8131 (pp30) cc_final: 0.7925 (pp30) REVERT: A 3808 ASN cc_start: 0.8066 (t0) cc_final: 0.7295 (p0) REVERT: A 3932 MET cc_start: 0.9050 (mtm) cc_final: 0.8634 (mtt) REVERT: A 3941 ASP cc_start: 0.8781 (t0) cc_final: 0.8546 (t0) REVERT: A 3974 MET cc_start: 0.8313 (mpp) cc_final: 0.7601 (mpp) REVERT: A 4020 MET cc_start: 0.8925 (ttm) cc_final: 0.8475 (ttm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1680 time to fit residues: 113.9244 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 121 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 250 optimal weight: 0.0870 chunk 252 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 258 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 216 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1465 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3037 GLN A3059 GLN A3423 GLN ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3760 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.083835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069602 restraints weight = 158165.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070955 restraints weight = 103638.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071892 restraints weight = 75448.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072566 restraints weight = 59424.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073051 restraints weight = 49622.096| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30000 Z= 0.126 Angle : 0.698 14.622 40780 Z= 0.352 Chirality : 0.043 0.333 4684 Planarity : 0.004 0.069 5000 Dihedral : 13.137 75.033 4358 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 3545 helix: -0.25 (0.11), residues: 2299 sheet: -2.05 (0.90), residues: 30 loop : -3.43 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3763 TYR 0.015 0.001 TYR A3002 PHE 0.037 0.001 PHE A 251 TRP 0.091 0.001 TRP A3164 HIS 0.006 0.001 HIS A1890 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (30000) covalent geometry : angle 0.69766 / 0.35 (40780) hydrogen bonds : bond 0.03714 / 2.46 ( 1505) hydrogen bonds : angle 4.50592 / 3.17 ( 4411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5062 (tpp) cc_final: 0.4851 (mmm) REVERT: A 103 TYR cc_start: 0.8555 (m-80) cc_final: 0.7938 (m-10) REVERT: A 109 ASN cc_start: 0.8542 (t0) cc_final: 0.8307 (p0) REVERT: A 189 MET cc_start: 0.5992 (mpp) cc_final: 0.5581 (mpp) REVERT: A 326 MET cc_start: 0.8867 (ptt) cc_final: 0.8195 (ppp) REVERT: A 357 LYS cc_start: 0.8156 (mttp) cc_final: 0.7898 (mmtt) REVERT: A 359 LEU cc_start: 0.8827 (mt) cc_final: 0.8493 (pt) REVERT: A 441 MET cc_start: 0.8157 (tpt) cc_final: 0.7779 (tpp) REVERT: A 652 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7549 (tp30) REVERT: A 725 LEU cc_start: 0.8332 (pt) cc_final: 0.8061 (pt) REVERT: A 963 LYS cc_start: 0.8148 (mttt) cc_final: 0.7081 (tttp) REVERT: A 966 PHE cc_start: 0.8803 (m-10) cc_final: 0.8438 (m-80) REVERT: A 1369 MET cc_start: 0.8376 (mmt) cc_final: 0.8051 (mmp) REVERT: A 1757 MET cc_start: 0.5871 (tpt) cc_final: 0.5245 (tpt) REVERT: A 1804 MET cc_start: 0.9251 (ptm) cc_final: 0.8695 (ptt) REVERT: A 1933 LEU cc_start: 0.8128 (mt) cc_final: 0.7715 (mt) REVERT: A 2098 THR cc_start: 0.8984 (t) cc_final: 0.8728 (t) REVERT: A 2102 LYS cc_start: 0.9395 (mttt) cc_final: 0.9088 (mtmm) REVERT: A 2126 MET cc_start: 0.6211 (ttt) cc_final: 0.5818 (ttm) REVERT: A 2307 MET cc_start: 0.8474 (tpp) cc_final: 0.8018 (tpp) REVERT: A 2379 MET cc_start: 0.8371 (ptp) cc_final: 0.7933 (mtt) REVERT: A 2385 LEU cc_start: 0.8307 (tp) cc_final: 0.7810 (tp) REVERT: A 2389 PHE cc_start: 0.7933 (m-10) cc_final: 0.7608 (m-10) REVERT: A 2925 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7942 (tt0) REVERT: A 3084 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 3195 GLU cc_start: 0.6936 (pp20) cc_final: 0.6633 (mm-30) REVERT: A 3239 LYS cc_start: 0.8737 (mttm) cc_final: 0.8389 (mttm) REVERT: A 3808 ASN cc_start: 0.7983 (t0) cc_final: 0.7294 (p0) REVERT: A 3932 MET cc_start: 0.9038 (mtm) cc_final: 0.8624 (mtt) REVERT: A 3941 ASP cc_start: 0.8796 (t0) cc_final: 0.8546 (t0) REVERT: A 3974 MET cc_start: 0.8347 (mpp) cc_final: 0.7714 (mpp) REVERT: A 4020 MET cc_start: 0.8970 (ttm) cc_final: 0.8467 (ttm) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.1749 time to fit residues: 121.6642 Evaluate side-chains 296 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 55 optimal weight: 0.0970 chunk 309 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 254 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN A1624 GLN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.084020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069795 restraints weight = 157488.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071150 restraints weight = 102822.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072100 restraints weight = 74718.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.072784 restraints weight = 58778.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073268 restraints weight = 49028.491| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30000 Z= 0.124 Angle : 0.693 15.346 40780 Z= 0.351 Chirality : 0.042 0.216 4684 Planarity : 0.005 0.072 5000 Dihedral : 13.021 74.825 4358 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3545 helix: -0.16 (0.11), residues: 2293 sheet: -1.66 (0.90), residues: 31 loop : -3.41 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3741 TYR 0.040 0.001 TYR A2288 PHE 0.035 0.001 PHE A3991 TRP 0.092 0.001 TRP A3164 HIS 0.006 0.001 HIS A1890 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (30000) covalent geometry : angle 0.69345 / 0.35 (40780) hydrogen bonds : bond 0.03613 / 2.39 ( 1505) hydrogen bonds : angle 4.46419 / 3.14 ( 4411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8510 (m-80) cc_final: 0.7908 (m-10) REVERT: A 109 ASN cc_start: 0.8535 (t0) cc_final: 0.8307 (p0) REVERT: A 189 MET cc_start: 0.5967 (mpp) cc_final: 0.5533 (mpp) REVERT: A 326 MET cc_start: 0.8851 (ptt) cc_final: 0.8153 (ppp) REVERT: A 357 LYS cc_start: 0.8169 (mttp) cc_final: 0.7902 (mmtt) REVERT: A 359 LEU cc_start: 0.8815 (mt) cc_final: 0.8515 (pt) REVERT: A 395 MET cc_start: 0.8392 (ppp) cc_final: 0.7963 (ppp) REVERT: A 441 MET cc_start: 0.8210 (tpt) cc_final: 0.7837 (tpp) REVERT: A 652 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7924 (tp30) REVERT: A 725 LEU cc_start: 0.8333 (pt) cc_final: 0.8085 (pt) REVERT: A 963 LYS cc_start: 0.8129 (mttt) cc_final: 0.7202 (tttp) REVERT: A 966 PHE cc_start: 0.8765 (m-10) cc_final: 0.8317 (m-10) REVERT: A 1369 MET cc_start: 0.8405 (mmt) cc_final: 0.8084 (mmp) REVERT: A 1804 MET cc_start: 0.9224 (ptm) cc_final: 0.8774 (ptt) REVERT: A 1933 LEU cc_start: 0.8149 (mt) cc_final: 0.7736 (mt) REVERT: A 2098 THR cc_start: 0.8972 (t) cc_final: 0.8712 (t) REVERT: A 2102 LYS cc_start: 0.9427 (mttt) cc_final: 0.9105 (mtmm) REVERT: A 2126 MET cc_start: 0.6197 (ttt) cc_final: 0.5811 (ttm) REVERT: A 2306 ASN cc_start: 0.8829 (m110) cc_final: 0.8575 (m-40) REVERT: A 2307 MET cc_start: 0.8311 (tpp) cc_final: 0.7922 (tpp) REVERT: A 2379 MET cc_start: 0.8408 (ptp) cc_final: 0.8003 (mtt) REVERT: A 2385 LEU cc_start: 0.8345 (tp) cc_final: 0.7853 (tp) REVERT: A 2389 PHE cc_start: 0.7966 (m-10) cc_final: 0.7607 (m-10) REVERT: A 2925 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7929 (tt0) REVERT: A 3084 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 3235 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8643 (mtmt) REVERT: A 3238 MET cc_start: 0.8363 (mtp) cc_final: 0.8092 (mtp) REVERT: A 3239 LYS cc_start: 0.8754 (mttm) cc_final: 0.8387 (mttm) REVERT: A 3808 ASN cc_start: 0.7984 (t0) cc_final: 0.7332 (p0) REVERT: A 3932 MET cc_start: 0.9044 (mtm) cc_final: 0.8627 (mtt) REVERT: A 3941 ASP cc_start: 0.8849 (t0) cc_final: 0.8582 (t0) REVERT: A 3974 MET cc_start: 0.8332 (mpp) cc_final: 0.7754 (mpp) REVERT: A 4020 MET cc_start: 0.8974 (ttm) cc_final: 0.8505 (ttm) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1737 time to fit residues: 114.7191 Evaluate side-chains 298 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 218 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1610 ASN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 HIS ** A2426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.084525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070277 restraints weight = 157191.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071632 restraints weight = 102769.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072601 restraints weight = 74694.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073298 restraints weight = 58649.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.073779 restraints weight = 48886.458| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30000 Z= 0.124 Angle : 0.705 14.846 40780 Z= 0.354 Chirality : 0.043 0.203 4684 Planarity : 0.004 0.068 5000 Dihedral : 12.894 74.824 4358 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.87 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3545 helix: -0.07 (0.11), residues: 2293 sheet: -1.58 (0.91), residues: 31 loop : -3.40 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3741 TYR 0.027 0.001 TYR A1558 PHE 0.038 0.001 PHE A 251 TRP 0.097 0.001 TRP A3164 HIS 0.009 0.001 HIS A2426 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (30000) covalent geometry : angle 0.70458 / 0.35 (40780) hydrogen bonds : bond 0.03492 / 2.31 ( 1505) hydrogen bonds : angle 4.41574 / 3.09 ( 4411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8617 (m-80) cc_final: 0.7992 (m-10) REVERT: A 109 ASN cc_start: 0.8611 (t0) cc_final: 0.8294 (p0) REVERT: A 189 MET cc_start: 0.5912 (mpp) cc_final: 0.5460 (mpp) REVERT: A 326 MET cc_start: 0.8883 (ptt) cc_final: 0.8188 (ppp) REVERT: A 357 LYS cc_start: 0.8200 (mttp) cc_final: 0.7935 (mmtt) REVERT: A 359 LEU cc_start: 0.8810 (mt) cc_final: 0.8543 (pt) REVERT: A 395 MET cc_start: 0.8562 (ppp) cc_final: 0.8140 (ppp) REVERT: A 441 MET cc_start: 0.8287 (tpt) cc_final: 0.7837 (tpp) REVERT: A 652 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7776 (tp30) REVERT: A 963 LYS cc_start: 0.8056 (mttt) cc_final: 0.7119 (tttp) REVERT: A 966 PHE cc_start: 0.8724 (m-10) cc_final: 0.8289 (m-10) REVERT: A 1369 MET cc_start: 0.8381 (mmt) cc_final: 0.8066 (mmp) REVERT: A 1757 MET cc_start: 0.5656 (tpt) cc_final: 0.4880 (tpt) REVERT: A 1804 MET cc_start: 0.9201 (ptm) cc_final: 0.8664 (ptt) REVERT: A 1933 LEU cc_start: 0.8216 (mt) cc_final: 0.7828 (mt) REVERT: A 2098 THR cc_start: 0.8985 (t) cc_final: 0.8732 (t) REVERT: A 2102 LYS cc_start: 0.9433 (mttt) cc_final: 0.9110 (mtmm) REVERT: A 2126 MET cc_start: 0.6244 (ttt) cc_final: 0.5848 (ttm) REVERT: A 2306 ASN cc_start: 0.8842 (m110) cc_final: 0.8584 (m-40) REVERT: A 2379 MET cc_start: 0.8543 (ptp) cc_final: 0.8154 (mtt) REVERT: A 2385 LEU cc_start: 0.8345 (tp) cc_final: 0.7852 (tp) REVERT: A 2389 PHE cc_start: 0.7986 (m-10) cc_final: 0.7675 (m-10) REVERT: A 2843 PHE cc_start: 0.8290 (m-10) cc_final: 0.7875 (m-80) REVERT: A 2925 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7915 (tt0) REVERT: A 3084 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8450 (tm-30) REVERT: A 3238 MET cc_start: 0.8349 (mtp) cc_final: 0.8064 (mtp) REVERT: A 3239 LYS cc_start: 0.8744 (mttm) cc_final: 0.8375 (mttm) REVERT: A 3741 ARG cc_start: 0.6487 (ptp-170) cc_final: 0.6255 (ptp-170) REVERT: A 3808 ASN cc_start: 0.8095 (t0) cc_final: 0.7364 (p0) REVERT: A 3932 MET cc_start: 0.9039 (mtm) cc_final: 0.8602 (mtt) REVERT: A 3941 ASP cc_start: 0.8848 (t0) cc_final: 0.8570 (t0) REVERT: A 3959 MET cc_start: 0.8978 (pmm) cc_final: 0.8706 (pmm) REVERT: A 3974 MET cc_start: 0.8342 (mpp) cc_final: 0.7752 (mpp) REVERT: A 4020 MET cc_start: 0.8979 (ttm) cc_final: 0.8463 (ttm) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.1632 time to fit residues: 111.0966 Evaluate side-chains 305 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 235 optimal weight: 6.9990 chunk 287 optimal weight: 0.7980 chunk 296 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN ** A3501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.084079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069885 restraints weight = 156724.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071218 restraints weight = 102806.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072174 restraints weight = 74951.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072843 restraints weight = 59025.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073327 restraints weight = 49476.140| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30000 Z= 0.128 Angle : 0.704 14.511 40780 Z= 0.356 Chirality : 0.043 0.198 4684 Planarity : 0.005 0.073 5000 Dihedral : 12.848 74.667 4358 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3545 helix: 0.03 (0.11), residues: 2286 sheet: -1.68 (0.89), residues: 31 loop : -3.37 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3741 TYR 0.040 0.001 TYR A2288 PHE 0.040 0.001 PHE A1839 TRP 0.095 0.001 TRP A3164 HIS 0.008 0.001 HIS A3501 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (30000) covalent geometry : angle 0.70366 / 0.36 (40780) hydrogen bonds : bond 0.03467 / 2.29 ( 1505) hydrogen bonds : angle 4.41147 / 3.10 ( 4411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8517 (m-80) cc_final: 0.7961 (m-10) REVERT: A 109 ASN cc_start: 0.8589 (t0) cc_final: 0.8284 (p0) REVERT: A 189 MET cc_start: 0.5968 (mpp) cc_final: 0.5542 (mpp) REVERT: A 326 MET cc_start: 0.8874 (ptt) cc_final: 0.8213 (ppp) REVERT: A 357 LYS cc_start: 0.8174 (mttp) cc_final: 0.7911 (mmtt) REVERT: A 359 LEU cc_start: 0.8814 (mt) cc_final: 0.8551 (pt) REVERT: A 395 MET cc_start: 0.8566 (ppp) cc_final: 0.8174 (ppp) REVERT: A 406 ARG cc_start: 0.7684 (mpt180) cc_final: 0.7442 (pmt170) REVERT: A 652 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7710 (tp30) REVERT: A 963 LYS cc_start: 0.8060 (mttt) cc_final: 0.7136 (tttp) REVERT: A 966 PHE cc_start: 0.8773 (m-10) cc_final: 0.8311 (m-10) REVERT: A 1369 MET cc_start: 0.8330 (mmt) cc_final: 0.8036 (mmp) REVERT: A 1757 MET cc_start: 0.5661 (tpt) cc_final: 0.4903 (tpt) REVERT: A 1804 MET cc_start: 0.9214 (ptm) cc_final: 0.8576 (ptt) REVERT: A 1933 LEU cc_start: 0.8226 (mt) cc_final: 0.7836 (mt) REVERT: A 2098 THR cc_start: 0.9006 (t) cc_final: 0.8753 (t) REVERT: A 2102 LYS cc_start: 0.9422 (mttt) cc_final: 0.9110 (mtmm) REVERT: A 2126 MET cc_start: 0.6147 (ttt) cc_final: 0.5740 (ttm) REVERT: A 2306 ASN cc_start: 0.8882 (m110) cc_final: 0.8615 (m110) REVERT: A 2379 MET cc_start: 0.8576 (ptp) cc_final: 0.8220 (mtt) REVERT: A 2385 LEU cc_start: 0.8344 (tp) cc_final: 0.7857 (tp) REVERT: A 2389 PHE cc_start: 0.7928 (m-10) cc_final: 0.7505 (m-10) REVERT: A 2843 PHE cc_start: 0.8288 (m-10) cc_final: 0.7878 (m-80) REVERT: A 2925 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7941 (tt0) REVERT: A 3084 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 3239 LYS cc_start: 0.8762 (mttm) cc_final: 0.8455 (mttm) REVERT: A 3672 LYS cc_start: 0.8005 (mppt) cc_final: 0.6656 (tptm) REVERT: A 3741 ARG cc_start: 0.6409 (ptp-170) cc_final: 0.6144 (ptp-170) REVERT: A 3808 ASN cc_start: 0.8072 (t0) cc_final: 0.7357 (p0) REVERT: A 3932 MET cc_start: 0.9065 (mtm) cc_final: 0.8626 (mtt) REVERT: A 3941 ASP cc_start: 0.8860 (t0) cc_final: 0.8581 (t0) REVERT: A 3959 MET cc_start: 0.9020 (pmm) cc_final: 0.8739 (pmm) REVERT: A 3974 MET cc_start: 0.8352 (mpp) cc_final: 0.7658 (mpp) REVERT: A 4020 MET cc_start: 0.8984 (ttm) cc_final: 0.8509 (ttm) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1739 time to fit residues: 115.2588 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 154 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.083101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068924 restraints weight = 159615.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070247 restraints weight = 104096.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071198 restraints weight = 75801.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071877 restraints weight = 59655.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072355 restraints weight = 49758.726| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30000 Z= 0.147 Angle : 0.714 14.013 40780 Z= 0.363 Chirality : 0.043 0.204 4684 Planarity : 0.005 0.138 5000 Dihedral : 12.858 74.321 4358 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.58 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3545 helix: 0.02 (0.11), residues: 2301 sheet: -1.82 (0.88), residues: 31 loop : -3.35 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3629 TYR 0.018 0.001 TYR A2316 PHE 0.024 0.002 PHE A 396 TRP 0.093 0.002 TRP A3164 HIS 0.007 0.001 HIS A2426 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (30000) covalent geometry : angle 0.71381 / 0.36 (40780) hydrogen bonds : bond 0.03559 / 2.34 ( 1505) hydrogen bonds : angle 4.46011 / 3.13 ( 4411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4804.71 seconds wall clock time: 84 minutes 15.32 seconds (5055.32 seconds total)