Starting phenix.real_space_refine on Fri Mar 6 11:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.map" model { file = "/net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sud_25440/03_2026/7sud_25440.cif" } resolution = 3.6 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 195 5.16 5 C 19210 2.51 5 N 5085 2.21 5 O 5482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29980 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 29880 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3740, 29845 Classifications: {'peptide': 3740} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3579} Chain breaks: 17 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 7, 'ASP:plan': 2, 'ARG:plan': 2, 'TPO:plan-1': 4} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 3740, 29845 Classifications: {'peptide': 3740} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3579} Chain breaks: 17 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 7, 'ASP:plan': 2, 'ARG:plan': 2, 'TPO:plan-1': 4} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 30420 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 70 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 70 " occ=0.50 residue: pdb=" N AARG A 257 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 257 " occ=0.50 Time building chain proxies: 11.77, per 1000 atoms: 0.39 Number of scatterers: 29980 At special positions: 0 Unit cell: (154.938, 155.771, 180.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 195 16.00 P 7 15.00 Mg 1 11.99 O 5482 8.00 N 5085 7.00 C 19210 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: 2.50 Conformation dependent library (CDL) restraints added in 2.3 seconds 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 5 sheets defined 68.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 27 through 43 Processing helix chain 'A' and resid 49 through 59 removed outlier: 4.452A pdb=" N LEU A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.528A pdb=" N MET A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 120 through 138 removed outlier: 4.015A pdb=" N LYS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 148 through 162 removed outlier: 3.805A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 4.066A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.397A pdb=" N GLU A 188 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN A 191 " --> pdb=" O GLU A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 191' Processing helix chain 'A' and resid 192 through 207 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.873A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 306 through 328 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.535A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 453 through 470 removed outlier: 3.771A pdb=" N ARG A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 removed outlier: 3.953A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.567A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.727A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 681 through 685 removed outlier: 4.470A pdb=" N GLY A 685 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 715 removed outlier: 3.551A pdb=" N CYS A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 removed outlier: 3.504A pdb=" N ALA A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.748A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 3.556A pdb=" N GLN A 786 " --> pdb=" O ARG A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.540A pdb=" N ILE A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 797 through 802 removed outlier: 3.705A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.958A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 removed outlier: 4.481A pdb=" N ILE A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.700A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 4.223A pdb=" N SER A 882 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 923 through 945 Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.875A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.514A pdb=" N VAL A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1043 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1055 through 1068 removed outlier: 3.611A pdb=" N ARG A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1065 " --> pdb=" O LYS A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 removed outlier: 3.641A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.831A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A1100 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.171A pdb=" N ASN A1146 " --> pdb=" O HIS A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.995A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.198A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1273 removed outlier: 3.891A pdb=" N THR A1253 " --> pdb=" O SER A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1301 Processing helix chain 'A' and resid 1307 through 1312 removed outlier: 3.537A pdb=" N LYS A1311 " --> pdb=" O ILE A1307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A1312 " --> pdb=" O ALA A1308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1307 through 1312' Processing helix chain 'A' and resid 1323 through 1352 removed outlier: 3.584A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A1352 " --> pdb=" O LEU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1361 removed outlier: 3.742A pdb=" N TRP A1356 " --> pdb=" O PRO A1353 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A1357 " --> pdb=" O GLU A1354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1358 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A1360 " --> pdb=" O LYS A1357 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A1361 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1378 Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1390 through 1393 Processing helix chain 'A' and resid 1394 through 1406 Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1431 through 1434 removed outlier: 3.908A pdb=" N VAL A1434 " --> pdb=" O LEU A1431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1431 through 1434' Processing helix chain 'A' and resid 1444 through 1462 removed outlier: 4.155A pdb=" N ALA A1449 " --> pdb=" O ARG A1445 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 5.029A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1521 removed outlier: 4.078A pdb=" N LYS A1508 " --> pdb=" O ASP A1504 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 4.004A pdb=" N LEU A1528 " --> pdb=" O LEU A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.663A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 Processing helix chain 'A' and resid 1574 through 1583 removed outlier: 3.826A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 4.524A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1623 Processing helix chain 'A' and resid 1638 through 1653 Processing helix chain 'A' and resid 1667 through 1678 removed outlier: 4.809A pdb=" N THR A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.909A pdb=" N THR A1700 " --> pdb=" O PRO A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1720 removed outlier: 4.466A pdb=" N GLU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 3.851A pdb=" N LEU A1752 " --> pdb=" O ASP A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1766 removed outlier: 3.666A pdb=" N GLU A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.920A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 4.035A pdb=" N VAL A1795 " --> pdb=" O CYS A1791 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1807 " --> pdb=" O GLU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1822 removed outlier: 4.275A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1831 removed outlier: 4.169A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS A1831 " --> pdb=" O LEU A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1852 removed outlier: 4.468A pdb=" N VAL A1844 " --> pdb=" O PHE A1840 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1883 removed outlier: 3.740A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1900 Processing helix chain 'A' and resid 1910 through 1924 Processing helix chain 'A' and resid 1933 through 1953 Processing helix chain 'A' and resid 1958 through 1965 removed outlier: 4.149A pdb=" N TYR A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A1963 " --> pdb=" O LEU A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 Processing helix chain 'A' and resid 1997 through 2013 removed outlier: 3.848A pdb=" N LYS A2001 " --> pdb=" O PRO A1997 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS A2002 " --> pdb=" O MET A1998 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A2012 " --> pdb=" O ARG A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2105 removed outlier: 3.966A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A2102 " --> pdb=" O THR A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2134 removed outlier: 3.589A pdb=" N LEU A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A2134 " --> pdb=" O HIS A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.670A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 Processing helix chain 'A' and resid 2183 through 2194 Processing helix chain 'A' and resid 2201 through 2204 removed outlier: 4.342A pdb=" N GLY A2204 " --> pdb=" O THR A2201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2201 through 2204' Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2255 through 2261 removed outlier: 3.770A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2282 removed outlier: 3.836A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 removed outlier: 3.687A pdb=" N LEU A2303 " --> pdb=" O TYR A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2309 removed outlier: 3.539A pdb=" N PHE A2309 " --> pdb=" O ASN A2306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2306 through 2309' Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.290A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A2325 " --> pdb=" O GLU A2321 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 3.937A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2371 removed outlier: 3.720A pdb=" N PHE A2360 " --> pdb=" O MET A2356 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.624A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 4.025A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A2396 " --> pdb=" O VAL A2392 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A2401 " --> pdb=" O CYS A2397 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.809A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2456 Processing helix chain 'A' and resid 2458 through 2462 removed outlier: 4.160A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.547A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2534 through 2542 removed outlier: 3.666A pdb=" N LEU A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2546 removed outlier: 3.900A pdb=" N TYR A2546 " --> pdb=" O ASN A2543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2543 through 2546' Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.068A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2584 removed outlier: 3.519A pdb=" N GLU A2583 " --> pdb=" O PRO A2580 " (cutoff:3.500A) Processing helix chain 'A' and resid 2594 through 2601 removed outlier: 3.584A pdb=" N ARG A2598 " --> pdb=" O ASP A2594 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2827 through 2847 Processing helix chain 'A' and resid 2851 through 2861 Processing helix chain 'A' and resid 2867 through 2871 removed outlier: 4.297A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A2871 " --> pdb=" O LEU A2868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2867 through 2871' Processing helix chain 'A' and resid 2872 through 2884 removed outlier: 3.506A pdb=" N SER A2877 " --> pdb=" O PRO A2873 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.556A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2933 removed outlier: 3.999A pdb=" N LEU A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.749A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 4.198A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2976 removed outlier: 4.454A pdb=" N GLN A2971 " --> pdb=" O GLU A2967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.567A pdb=" N TRP A2994 " --> pdb=" O GLU A2990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3017 removed outlier: 4.067A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3031 removed outlier: 3.686A pdb=" N LYS A3029 " --> pdb=" O ASP A3026 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A3030 " --> pdb=" O LEU A3027 " (cutoff:3.500A) Processing helix chain 'A' and resid 3033 through 3040 removed outlier: 4.130A pdb=" N GLN A3037 " --> pdb=" O GLU A3033 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A3038 " --> pdb=" O PRO A3034 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3053 Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3074 through 3082 removed outlier: 3.985A pdb=" N GLU A3079 " --> pdb=" O LYS A3075 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A3080 " --> pdb=" O ALA A3076 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.590A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.549A pdb=" N MET A3111 " --> pdb=" O ILE A3107 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.889A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3152 Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3196 Processing helix chain 'A' and resid 3227 through 3248 removed outlier: 3.660A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 3.574A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 removed outlier: 3.677A pdb=" N SER A3275 " --> pdb=" O ASP A3271 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3300 removed outlier: 3.743A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3308 removed outlier: 4.424A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A3308 " --> pdb=" O VAL A3304 " (cutoff:3.500A) Processing helix chain 'A' and resid 3311 through 3319 removed outlier: 3.612A pdb=" N TYR A3315 " --> pdb=" O ASN A3311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A3317 " --> pdb=" O SER A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3344 removed outlier: 3.860A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3364 removed outlier: 3.778A pdb=" N GLY A3364 " --> pdb=" O LEU A3360 " (cutoff:3.500A) Processing helix chain 'A' and resid 3370 through 3392 Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.620A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.503A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3475 removed outlier: 3.734A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3481 through 3488 Processing helix chain 'A' and resid 3491 through 3497 removed outlier: 3.878A pdb=" N PHE A3495 " --> pdb=" O CYS A3492 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A3496 " --> pdb=" O TRP A3493 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.795A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A3503 " --> pdb=" O ILE A3499 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 4.575A pdb=" N HIS A3516 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.873A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3563 removed outlier: 3.707A pdb=" N HIS A3549 " --> pdb=" O THR A3545 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A3563 " --> pdb=" O LYS A3559 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 removed outlier: 3.605A pdb=" N ASP A3570 " --> pdb=" O GLY A3566 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3597 removed outlier: 4.719A pdb=" N GLU A3595 " --> pdb=" O ASP A3591 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3618 removed outlier: 3.629A pdb=" N LYS A3608 " --> pdb=" O LYS A3604 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3637 Processing helix chain 'A' and resid 3638 through 3643 Processing helix chain 'A' and resid 3657 through 3674 removed outlier: 4.348A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A3674 " --> pdb=" O MET A3670 " (cutoff:3.500A) Processing helix chain 'A' and resid 3679 through 3683 Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3758 through 3775 Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 4.698A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A3841 " --> pdb=" O CYS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3853 No H-bonds generated for 'chain 'A' and resid 3851 through 3853' Processing helix chain 'A' and resid 3854 through 3862 removed outlier: 4.929A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3874 removed outlier: 3.608A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3891 removed outlier: 3.686A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.704A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 3.928A 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 3948 through 3953 removed outlier: 3.768A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3970 removed outlier: 3.695A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.630A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4007 removed outlier: 3.654A pdb=" N ASN A4000 " --> pdb=" O GLY A3996 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A4001 " --> pdb=" O LEU A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 4.008A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4033 through 4037 removed outlier: 3.668A pdb=" N ASN A4037 " --> pdb=" O ALA A4034 " (cutoff:3.500A) Processing helix chain 'A' and resid 4042 through 4053 Processing helix chain 'A' and resid 4055 through 4065 removed outlier: 3.520A pdb=" N ILE A4059 " --> pdb=" O ASN A4055 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4083 removed outlier: 3.817A pdb=" N GLY A4083 " --> pdb=" O ALA A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.652A pdb=" N GLN A4110 " --> pdb=" O CYS A4106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'C' and resid 725 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 2635 through 2636 removed outlier: 3.579A pdb=" N ILE A2635 " --> pdb=" O ARG A2773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3728 removed outlier: 4.740A pdb=" N ILE A3739 " --> pdb=" O ASP A3723 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A3725 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A3737 " --> pdb=" O ARG A3725 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3809 through 3811 1581 hydrogen bonds defined for protein. 4670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8532 1.33 - 1.46: 6308 1.46 - 1.58: 15439 1.58 - 1.70: 17 1.70 - 1.82: 304 Bond restraints: 30600 Sorted by residual: bond pdb=" C4 ATP A4202 " pdb=" C5 ATP A4202 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.98e+01 bond pdb=" OG1 TPO A2638 " pdb=" P TPO A2638 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" OG1 TPO A2645 " pdb=" P TPO A2645 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C4 ATP A4202 " pdb=" N9 ATP A4202 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" C5 ATP A4202 " pdb=" C6 ATP A4202 " ideal model delta sigma weight residual 1.409 1.462 -0.053 1.00e-02 1.00e+04 2.79e+01 ... (remaining 30595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 40448 3.43 - 6.86: 792 6.86 - 10.29: 119 10.29 - 13.72: 19 13.72 - 17.16: 6 Bond angle restraints: 41384 Sorted by residual: angle pdb=" PB ATP A4202 " pdb=" O3B ATP A4202 " pdb=" PG ATP A4202 " ideal model delta sigma weight residual 139.87 122.71 17.16 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PA ATP A4202 " pdb=" O3A ATP A4202 " pdb=" PB ATP A4202 " ideal model delta sigma weight residual 136.83 124.07 12.76 1.00e+00 1.00e+00 1.63e+02 angle pdb=" C5 ATP A4202 " pdb=" C4 ATP A4202 " pdb=" N3 ATP A4202 " ideal model delta sigma weight residual 126.80 119.48 7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" N3 ATP A4202 " pdb=" C4 ATP A4202 " pdb=" N9 ATP A4202 " ideal model delta sigma weight residual 127.04 134.47 -7.43 1.15e+00 7.59e-01 4.19e+01 angle pdb=" C ASP A3369 " pdb=" N SER A3370 " pdb=" CA SER A3370 " ideal model delta sigma weight residual 121.54 133.32 -11.78 1.91e+00 2.74e-01 3.80e+01 ... (remaining 41379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16404 18.00 - 36.00: 1880 36.00 - 54.00: 307 54.00 - 72.01: 58 72.01 - 90.01: 31 Dihedral angle restraints: 18680 sinusoidal: 7634 harmonic: 11046 Sorted by residual: dihedral pdb=" CA ILE A1306 " pdb=" C ILE A1306 " pdb=" N ILE A1307 " pdb=" CA ILE A1307 " ideal model delta harmonic sigma weight residual -180.00 -128.27 -51.73 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA PRO A3600 " pdb=" C PRO A3600 " pdb=" N VAL A3601 " pdb=" CA VAL A3601 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA TYR A 385 " pdb=" C TYR A 385 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " ideal model delta harmonic sigma weight residual 180.00 141.05 38.95 0 5.00e+00 4.00e-02 6.07e+01 ... (remaining 18677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3537 0.067 - 0.134: 962 0.134 - 0.201: 159 0.201 - 0.268: 30 0.268 - 0.335: 6 Chirality restraints: 4694 Sorted by residual: chirality pdb=" CA PHE A1553 " pdb=" N PHE A1553 " pdb=" C PHE A1553 " pdb=" CB PHE A1553 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL A2330 " pdb=" CA VAL A2330 " pdb=" CG1 VAL A2330 " pdb=" CG2 VAL A2330 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE A 256 " pdb=" CA ILE A 256 " pdb=" CG1 ILE A 256 " pdb=" CG2 ILE A 256 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 4691 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A3370 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C SER A3370 " -0.065 2.00e-02 2.50e+03 pdb=" O SER A3370 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A3371 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ARG A 9 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 9 " 0.024 2.00e-02 2.50e+03 pdb=" N CYS A 10 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A3622 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A3623 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A3623 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A3623 " 0.048 5.00e-02 4.00e+02 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 374 2.63 - 3.19: 25835 3.19 - 3.76: 47110 3.76 - 4.33: 62988 4.33 - 4.90: 102676 Nonbonded interactions: 238983 Sorted by model distance: nonbonded pdb=" OD1 ASN A3927 " pdb="MG MG A4201 " model vdw 2.056 2.170 nonbonded pdb=" OD2 ASP A3941 " pdb="MG MG A4201 " model vdw 2.068 2.170 nonbonded pdb=" O GLY A1796 " pdb=" OG SER A1800 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A1424 " pdb=" OG SER A1427 " model vdw 2.242 3.040 nonbonded pdb="MG MG A4201 " pdb=" O1G ATP A4202 " model vdw 2.252 2.170 ... (remaining 238978 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=0.50 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: 9.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.009 0.147 30600 Z= 0.411 Angle : 1.236 17.156 41384 Z= 0.675 Chirality : 0.063 0.335 4694 Planarity : 0.008 0.089 5241 Dihedral : 15.596 90.008 11486 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.65 % Favored : 90.11 % Rotamer: Outliers : 0.09 % Allowed : 8.06 % Favored : 91.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.34 % 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: -4.69 (0.10), residues: 3709 helix: -2.71 (0.08), residues: 2330 sheet: -2.03 (0.68), residues: 47 loop : -3.68 (0.14), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3696 TYR 0.037 0.003 TYR A 366 PHE 0.040 0.003 PHE A1923 TRP 0.036 0.003 TRP A4027 HIS 0.020 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00914 (30600) covalent geometry : angle 1.23563 (41384) hydrogen bonds : bond 0.14156 ( 1581) hydrogen bonds : angle 6.40184 ( 4670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 382 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.2336 (mpp) cc_final: 0.1262 (mmp) REVERT: A 441 MET cc_start: 0.6622 (mmm) cc_final: 0.6381 (mmm) REVERT: A 484 HIS cc_start: 0.7684 (t70) cc_final: 0.7464 (t-170) REVERT: A 532 ARG cc_start: 0.7626 (mtp180) cc_final: 0.7069 (mtm-85) REVERT: A 1369 MET cc_start: 0.7785 (mmm) cc_final: 0.7447 (mmm) REVERT: A 1552 HIS cc_start: 0.3299 (m-70) cc_final: 0.2704 (m90) REVERT: A 1764 GLU cc_start: 0.7564 (tp30) cc_final: 0.7030 (tp30) REVERT: A 1774 MET cc_start: 0.6741 (pmm) cc_final: 0.5825 (pmm) REVERT: A 1778 PHE cc_start: 0.6943 (m-80) cc_final: 0.6737 (m-80) REVERT: A 1961 PHE cc_start: 0.6858 (m-10) cc_final: 0.6275 (m-80) REVERT: A 2006 GLU cc_start: 0.7187 (tp30) cc_final: 0.6931 (tp30) REVERT: A 2145 PHE cc_start: 0.5634 (t80) cc_final: 0.5374 (t80) REVERT: A 2185 MET cc_start: 0.7925 (tpp) cc_final: 0.7393 (mpp) REVERT: A 2188 GLU cc_start: 0.7503 (pt0) cc_final: 0.6814 (tp30) REVERT: A 2347 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7651 (tptm) REVERT: A 2431 ARG cc_start: 0.5724 (ttm170) cc_final: 0.5318 (ttp-110) REVERT: A 3450 MET cc_start: 0.7710 (ttm) cc_final: 0.7454 (mtt) REVERT: C 731 MET cc_start: 0.5933 (mtp) cc_final: 0.5714 (mtt) outliers start: 3 outliers final: 0 residues processed: 385 average time/residue: 0.2055 time to fit residues: 124.6577 Evaluate side-chains 255 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 390 GLN A 394 GLN A 415 GLN A 485 GLN A 771 ASN A 960 GLN A 997 ASN A1043 GLN A1280 GLN A1350 ASN A1442 GLN A1466 ASN A1716 GLN A1898 GLN A2130 HIS A2152 ASN ** A2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 ASN A2365 ASN A2414 GLN A2475 ASN A2518 GLN A2553 HIS A2560 ASN A2859 GLN A3296 GLN A3524 ASN A3664 ASN A3908 HIS A3924 HIS ** A4042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.125387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097058 restraints weight = 201037.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096894 restraints weight = 92016.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097116 restraints weight = 70450.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097162 restraints weight = 64877.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097421 restraints weight = 52546.425| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30600 Z= 0.170 Angle : 0.725 13.030 41384 Z= 0.374 Chirality : 0.043 0.225 4694 Planarity : 0.006 0.081 5241 Dihedral : 6.885 88.236 4076 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.97 % Favored : 91.84 % Rotamer: Outliers : 1.15 % Allowed : 12.14 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.11 % 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: -2.88 (0.13), residues: 3709 helix: -1.14 (0.10), residues: 2376 sheet: -1.74 (0.71), residues: 47 loop : -3.30 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1727 TYR 0.024 0.002 TYR A2184 PHE 0.028 0.002 PHE A3636 TRP 0.025 0.001 TRP A4027 HIS 0.016 0.001 HIS A2225 Details of bonding type rmsd covalent geometry : bond 0.00383 (30600) covalent geometry : angle 0.72493 (41384) hydrogen bonds : bond 0.04463 ( 1581) hydrogen bonds : angle 4.70398 ( 4670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.3169 (pt0) cc_final: 0.2758 (pt0) REVERT: A 410 MET cc_start: 0.2293 (mpp) cc_final: 0.0753 (tpt) REVERT: A 441 MET cc_start: 0.6643 (mmm) cc_final: 0.6288 (mmm) REVERT: A 445 SER cc_start: 0.5479 (t) cc_final: 0.5157 (p) REVERT: A 532 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7235 (mtm-85) REVERT: A 662 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6467 (pp) REVERT: A 1369 MET cc_start: 0.7823 (mmm) cc_final: 0.7334 (mmm) REVERT: A 1486 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6194 (tt) REVERT: A 1581 GLU cc_start: 0.6831 (tt0) cc_final: 0.6377 (pt0) REVERT: A 1592 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.5960 (mmm) REVERT: A 1643 MET cc_start: 0.5671 (tmm) cc_final: 0.5446 (tmm) REVERT: A 1764 GLU cc_start: 0.7459 (tp30) cc_final: 0.6957 (tp30) REVERT: A 1774 MET cc_start: 0.6210 (pmm) cc_final: 0.5676 (pmm) REVERT: A 1778 PHE cc_start: 0.6931 (m-80) cc_final: 0.6655 (m-80) REVERT: A 1900 PHE cc_start: 0.6683 (t80) cc_final: 0.6347 (m-80) REVERT: A 2097 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7411 (tp) REVERT: A 2145 PHE cc_start: 0.6027 (t80) cc_final: 0.5719 (t80) REVERT: A 2185 MET cc_start: 0.8177 (tpp) cc_final: 0.7923 (mpp) REVERT: A 2188 GLU cc_start: 0.7771 (pt0) cc_final: 0.7188 (tp30) REVERT: A 2347 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7604 (tptm) REVERT: A 2420 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6915 (t80) REVERT: A 2431 ARG cc_start: 0.6023 (ttm170) cc_final: 0.5623 (ttp-110) outliers start: 38 outliers final: 20 residues processed: 342 average time/residue: 0.1849 time to fit residues: 104.2442 Evaluate side-chains 272 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1592 MET Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2384 PHE Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3230 LEU Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 0.0770 chunk 235 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 371 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 484 HIS A 656 GLN A 997 ASN ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 HIS A2275 GLN A2456 ASN A2518 GLN ** A3081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3944 HIS ** A4042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.127165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098626 restraints weight = 211641.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098889 restraints weight = 95851.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098806 restraints weight = 72037.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.099160 restraints weight = 70211.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099390 restraints weight = 54507.155| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30600 Z= 0.125 Angle : 0.655 10.118 41384 Z= 0.332 Chirality : 0.041 0.306 4694 Planarity : 0.005 0.075 5241 Dihedral : 6.219 88.677 4076 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer: Outliers : 1.33 % Allowed : 13.77 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.11 % 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: -1.97 (0.13), residues: 3709 helix: -0.36 (0.10), residues: 2381 sheet: -1.53 (0.70), residues: 47 loop : -3.11 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2485 TYR 0.017 0.001 TYR A2299 PHE 0.035 0.001 PHE A3636 TRP 0.030 0.001 TRP A4027 HIS 0.007 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00261 (30600) covalent geometry : angle 0.65512 (41384) hydrogen bonds : bond 0.03737 ( 1581) hydrogen bonds : angle 4.28458 ( 4670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6726 (mmm) cc_final: 0.6482 (mmm) REVERT: A 445 SER cc_start: 0.5667 (t) cc_final: 0.5370 (p) REVERT: A 475 LEU cc_start: 0.6158 (tt) cc_final: 0.5903 (mt) REVERT: A 532 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7215 (mtm-85) REVERT: A 562 HIS cc_start: 0.6256 (OUTLIER) cc_final: 0.5718 (t-170) REVERT: A 653 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 879 MET cc_start: 0.5484 (ttm) cc_final: 0.5266 (ptm) REVERT: A 880 MET cc_start: 0.7753 (mmm) cc_final: 0.7337 (mmp) REVERT: A 1064 TYR cc_start: 0.8059 (m-10) cc_final: 0.7574 (m-10) REVERT: A 1108 MET cc_start: 0.7838 (mtp) cc_final: 0.7607 (mtp) REVERT: A 1486 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5962 (tt) REVERT: A 1581 GLU cc_start: 0.6713 (tt0) cc_final: 0.6501 (pt0) REVERT: A 1583 MET cc_start: 0.5619 (mtt) cc_final: 0.4481 (ptt) REVERT: A 1592 MET cc_start: 0.7105 (ttp) cc_final: 0.5898 (mmm) REVERT: A 1626 TRP cc_start: 0.5980 (m100) cc_final: 0.5742 (m100) REVERT: A 1643 MET cc_start: 0.5672 (tmm) cc_final: 0.5394 (tmm) REVERT: A 1757 MET cc_start: 0.6814 (mmt) cc_final: 0.6575 (mmp) REVERT: A 1778 PHE cc_start: 0.6871 (m-80) cc_final: 0.6632 (m-80) REVERT: A 1873 TYR cc_start: 0.6667 (m-80) cc_final: 0.6259 (m-10) REVERT: A 1900 PHE cc_start: 0.6658 (t80) cc_final: 0.6313 (m-80) REVERT: A 1962 TYR cc_start: 0.6647 (m-10) cc_final: 0.5875 (m-80) REVERT: A 2097 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tp) REVERT: A 2145 PHE cc_start: 0.5960 (t80) cc_final: 0.5732 (t80) REVERT: A 2185 MET cc_start: 0.8156 (tpp) cc_final: 0.7787 (mpp) REVERT: A 2188 GLU cc_start: 0.7762 (pt0) cc_final: 0.7128 (tp30) REVERT: A 2275 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7017 (tp-100) REVERT: A 2328 ARG cc_start: 0.7704 (tpt-90) cc_final: 0.7482 (tpp80) REVERT: A 2331 MET cc_start: 0.6896 (tpt) cc_final: 0.6568 (tpt) REVERT: A 2347 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7452 (tptm) REVERT: A 2408 MET cc_start: 0.5411 (mmm) cc_final: 0.2357 (tpt) REVERT: A 2443 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: A 3613 MET cc_start: 0.8814 (tmm) cc_final: 0.8591 (tmm) outliers start: 44 outliers final: 18 residues processed: 336 average time/residue: 0.1843 time to fit residues: 102.8903 Evaluate side-chains 281 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2360 PHE Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3429 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 245 optimal weight: 0.0980 chunk 240 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 189 optimal weight: 0.2980 chunk 159 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 142 optimal weight: 0.0170 overall best weight: 2.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN A2163 HIS A2177 ASN A2275 GLN A2426 HIS ** A3081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.125786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096815 restraints weight = 223092.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097500 restraints weight = 93344.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097565 restraints weight = 66721.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097755 restraints weight = 59750.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098026 restraints weight = 48177.056| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30600 Z= 0.150 Angle : 0.676 11.446 41384 Z= 0.339 Chirality : 0.043 0.308 4694 Planarity : 0.005 0.068 5241 Dihedral : 6.117 86.794 4076 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.08 % Favored : 91.81 % Rotamer: Outliers : 1.66 % Allowed : 15.07 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.62 (0.14), residues: 3709 helix: -0.09 (0.11), residues: 2393 sheet: -1.55 (0.68), residues: 47 loop : -2.98 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1727 TYR 0.025 0.002 TYR A2184 PHE 0.025 0.001 PHE A2260 TRP 0.023 0.001 TRP A4027 HIS 0.011 0.001 HIS A2225 Details of bonding type rmsd covalent geometry : bond 0.00344 (30600) covalent geometry : angle 0.67638 (41384) hydrogen bonds : bond 0.03839 ( 1581) hydrogen bonds : angle 4.24840 ( 4670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.3046 (pt0) cc_final: 0.2790 (pt0) REVERT: A 445 SER cc_start: 0.5642 (t) cc_final: 0.5306 (p) REVERT: A 532 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7220 (mtm-85) REVERT: A 562 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5643 (t-170) REVERT: A 653 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 880 MET cc_start: 0.7796 (mmm) cc_final: 0.7489 (mmp) REVERT: A 1486 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5982 (tt) REVERT: A 1581 GLU cc_start: 0.6764 (tt0) cc_final: 0.6543 (pt0) REVERT: A 1583 MET cc_start: 0.5543 (mtt) cc_final: 0.4428 (ptt) REVERT: A 2145 PHE cc_start: 0.5948 (t80) cc_final: 0.5711 (t80) REVERT: A 2188 GLU cc_start: 0.7783 (pt0) cc_final: 0.7110 (tp30) REVERT: A 2275 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6986 (tp-100) REVERT: A 2331 MET cc_start: 0.6881 (tpt) cc_final: 0.6543 (tpt) REVERT: A 2347 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7438 (tptm) REVERT: A 2408 MET cc_start: 0.5517 (mmm) cc_final: 0.2351 (tpt) REVERT: A 3614 TYR cc_start: 0.6866 (t80) cc_final: 0.6396 (t80) outliers start: 53 outliers final: 32 residues processed: 307 average time/residue: 0.1741 time to fit residues: 89.8891 Evaluate side-chains 284 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2360 PHE Chi-restraints excluded: chain A residue 2384 PHE Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3968 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 77 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 352 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 212 optimal weight: 0.0060 chunk 308 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 292 optimal weight: 0.0770 overall best weight: 0.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 394 GLN ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS A2275 GLN A2787 HIS A2859 GLN ** A3081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.127259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097799 restraints weight = 171225.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098702 restraints weight = 82864.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099321 restraints weight = 49404.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099469 restraints weight = 50201.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099378 restraints weight = 38957.171| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30600 Z= 0.113 Angle : 0.639 10.790 41384 Z= 0.319 Chirality : 0.042 0.291 4694 Planarity : 0.004 0.067 5241 Dihedral : 5.819 87.538 4076 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.92 % Favored : 92.97 % Rotamer: Outliers : 1.60 % Allowed : 15.74 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.30 (0.14), residues: 3709 helix: 0.17 (0.11), residues: 2397 sheet: -1.15 (0.71), residues: 45 loop : -2.90 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2328 TYR 0.019 0.001 TYR A2184 PHE 0.027 0.001 PHE A2260 TRP 0.022 0.001 TRP A4027 HIS 0.012 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00245 (30600) covalent geometry : angle 0.63931 (41384) hydrogen bonds : bond 0.03515 ( 1581) hydrogen bonds : angle 4.09821 ( 4670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7197 (mtm-85) REVERT: A 562 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5673 (t-170) REVERT: A 653 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 879 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.4749 (ttp) REVERT: A 1064 TYR cc_start: 0.8105 (m-10) cc_final: 0.7612 (m-10) REVERT: A 1108 MET cc_start: 0.7813 (mtp) cc_final: 0.7590 (mtp) REVERT: A 1486 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5873 (tt) REVERT: A 1583 MET cc_start: 0.5376 (mtt) cc_final: 0.4219 (ptm) REVERT: A 1592 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.5580 (mmp) REVERT: A 1900 PHE cc_start: 0.6474 (t80) cc_final: 0.6169 (m-80) REVERT: A 2188 GLU cc_start: 0.7743 (pt0) cc_final: 0.7065 (tp30) REVERT: A 2275 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6943 (tp-100) REVERT: A 2328 ARG cc_start: 0.7842 (ttt90) cc_final: 0.7394 (tpt-90) REVERT: A 2347 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7395 (tptm) REVERT: A 2408 MET cc_start: 0.5443 (mmm) cc_final: 0.2385 (tpt) REVERT: A 3613 MET cc_start: 0.8789 (tmm) cc_final: 0.8517 (tmm) REVERT: A 3614 TYR cc_start: 0.6757 (t80) cc_final: 0.6416 (t80) REVERT: A 3962 ARG cc_start: 0.8899 (tpt170) cc_final: 0.8409 (tpt170) REVERT: A 4039 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.4869 (p90) outliers start: 51 outliers final: 33 residues processed: 314 average time/residue: 0.1806 time to fit residues: 95.7375 Evaluate side-chains 294 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1592 MET Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2384 PHE Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 256 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 151 optimal weight: 0.2980 chunk 258 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 192 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS A2859 GLN ** A3081 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098393 restraints weight = 207822.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099458 restraints weight = 94663.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.099257 restraints weight = 64417.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099814 restraints weight = 60767.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100002 restraints weight = 47420.422| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30600 Z= 0.111 Angle : 0.629 10.557 41384 Z= 0.312 Chirality : 0.041 0.280 4694 Planarity : 0.004 0.065 5241 Dihedral : 5.630 87.593 4076 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.11 % Favored : 92.79 % Rotamer: Outliers : 1.57 % Allowed : 16.28 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.05 (0.14), residues: 3709 helix: 0.37 (0.11), residues: 2411 sheet: -1.03 (0.71), residues: 45 loop : -2.83 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2328 TYR 0.020 0.001 TYR A1920 PHE 0.041 0.001 PHE A1961 TRP 0.021 0.001 TRP A2479 HIS 0.011 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00241 (30600) covalent geometry : angle 0.62896 (41384) hydrogen bonds : bond 0.03362 ( 1581) hydrogen bonds : angle 4.00668 ( 4670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7189 (mtm-85) REVERT: A 562 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.5658 (t-170) REVERT: A 653 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 880 MET cc_start: 0.7754 (mmm) cc_final: 0.7432 (mmm) REVERT: A 1064 TYR cc_start: 0.8049 (m-10) cc_final: 0.7547 (m-10) REVERT: A 1108 MET cc_start: 0.7770 (mtp) cc_final: 0.7529 (mtp) REVERT: A 1218 SER cc_start: 0.8670 (m) cc_final: 0.8299 (p) REVERT: A 1583 MET cc_start: 0.5407 (mtt) cc_final: 0.4218 (ptm) REVERT: A 1592 MET cc_start: 0.6849 (ttp) cc_final: 0.5615 (mmp) REVERT: A 1642 LYS cc_start: 0.6355 (mttm) cc_final: 0.5835 (mtpt) REVERT: A 1900 PHE cc_start: 0.6534 (t80) cc_final: 0.6210 (m-80) REVERT: A 2126 MET cc_start: 0.5054 (mmt) cc_final: 0.4768 (mmm) REVERT: A 2145 PHE cc_start: 0.5778 (t80) cc_final: 0.5513 (m-80) REVERT: A 2188 GLU cc_start: 0.7770 (pt0) cc_final: 0.7113 (tp30) REVERT: A 2328 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7342 (tpt-90) REVERT: A 2420 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6458 (t80) REVERT: A 3614 TYR cc_start: 0.6720 (t80) cc_final: 0.6428 (t80) REVERT: A 3962 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8392 (tpt170) REVERT: A 4039 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.4752 (p90) outliers start: 50 outliers final: 36 residues processed: 320 average time/residue: 0.1810 time to fit residues: 98.0309 Evaluate side-chains 292 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2310 VAL Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2360 PHE Chi-restraints excluded: chain A residue 2384 PHE Chi-restraints excluded: chain A residue 2390 HIS Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2590 THR Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 369 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 256 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 230 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A1280 GLN ** A1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1574 ASN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096556 restraints weight = 203746.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097534 restraints weight = 87296.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099231 restraints weight = 57395.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098488 restraints weight = 53015.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098577 restraints weight = 43961.189| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30600 Z= 0.139 Angle : 0.653 13.559 41384 Z= 0.325 Chirality : 0.042 0.260 4694 Planarity : 0.004 0.063 5241 Dihedral : 5.666 84.730 4076 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.70 % Favored : 92.16 % Rotamer: Outliers : 1.90 % Allowed : 16.70 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.05 (0.14), residues: 3709 helix: 0.35 (0.11), residues: 2424 sheet: -1.35 (0.68), residues: 47 loop : -2.80 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2328 TYR 0.022 0.001 TYR A1920 PHE 0.032 0.001 PHE A1965 TRP 0.017 0.001 TRP A2479 HIS 0.010 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00319 (30600) covalent geometry : angle 0.65287 (41384) hydrogen bonds : bond 0.03583 ( 1581) hydrogen bonds : angle 4.05771 ( 4670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: -0.1508 (mmt) cc_final: -0.2726 (tpt) REVERT: A 532 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7256 (mtm-85) REVERT: A 562 HIS cc_start: 0.6239 (OUTLIER) cc_final: 0.5701 (t-170) REVERT: A 1064 TYR cc_start: 0.8200 (m-10) cc_final: 0.7778 (m-10) REVERT: A 1448 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 1583 MET cc_start: 0.5388 (mtt) cc_final: 0.4239 (ptm) REVERT: A 1592 MET cc_start: 0.6687 (ttp) cc_final: 0.5562 (mmm) REVERT: A 1900 PHE cc_start: 0.6432 (t80) cc_final: 0.6110 (m-80) REVERT: A 2145 PHE cc_start: 0.5679 (t80) cc_final: 0.5397 (m-80) REVERT: A 2188 GLU cc_start: 0.7769 (pt0) cc_final: 0.7068 (tp30) REVERT: A 2295 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 2328 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7374 (tpt-90) REVERT: A 2420 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 3614 TYR cc_start: 0.6869 (t80) cc_final: 0.6409 (t80) REVERT: A 4039 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.4740 (p90) outliers start: 61 outliers final: 44 residues processed: 299 average time/residue: 0.1718 time to fit residues: 87.6166 Evaluate side-chains 290 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1574 ASN Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2310 VAL Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2590 THR Chi-restraints excluded: chain A residue 2608 GLU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 230 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 372 optimal weight: 0.0040 chunk 242 optimal weight: 10.0000 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A1280 GLN ** A1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3081 HIS ** 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 = 0.4069 r_free = 0.4069 target = 0.126151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097536 restraints weight = 203481.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098169 restraints weight = 92489.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098142 restraints weight = 65559.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098534 restraints weight = 58154.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098672 restraints weight = 47272.693| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30600 Z= 0.137 Angle : 0.662 16.300 41384 Z= 0.328 Chirality : 0.042 0.274 4694 Planarity : 0.004 0.063 5241 Dihedral : 5.640 84.077 4076 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.46 % Favored : 92.41 % Rotamer: Outliers : 1.81 % Allowed : 17.12 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.98 (0.14), residues: 3709 helix: 0.40 (0.11), residues: 2419 sheet: -1.35 (0.69), residues: 47 loop : -2.76 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2328 TYR 0.020 0.001 TYR A 340 PHE 0.027 0.001 PHE A1965 TRP 0.017 0.001 TRP A2164 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00312 (30600) covalent geometry : angle 0.66214 (41384) hydrogen bonds : bond 0.03561 ( 1581) hydrogen bonds : angle 4.09254 ( 4670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: -0.1589 (mmt) cc_final: -0.2741 (tpt) REVERT: A 344 GLN cc_start: 0.4173 (pm20) cc_final: 0.2314 (mm-40) REVERT: A 532 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7235 (mtm-85) REVERT: A 562 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5686 (t-170) REVERT: A 1064 TYR cc_start: 0.8134 (m-10) cc_final: 0.7720 (m-10) REVERT: A 1448 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 1570 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6719 (tm-30) REVERT: A 1583 MET cc_start: 0.5382 (mtt) cc_final: 0.4193 (ptm) REVERT: A 1900 PHE cc_start: 0.6562 (t80) cc_final: 0.6130 (m-80) REVERT: A 2126 MET cc_start: 0.4980 (mmt) cc_final: 0.4680 (mmm) REVERT: A 2145 PHE cc_start: 0.5972 (t80) cc_final: 0.5619 (m-80) REVERT: A 2188 GLU cc_start: 0.7838 (pt0) cc_final: 0.7172 (tp30) REVERT: A 2295 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 2328 ARG cc_start: 0.7871 (ttt90) cc_final: 0.7539 (tpt-90) REVERT: A 2420 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6507 (t80) REVERT: A 3614 TYR cc_start: 0.6923 (t80) cc_final: 0.6413 (t80) REVERT: A 4039 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.4681 (p90) outliers start: 58 outliers final: 45 residues processed: 296 average time/residue: 0.1662 time to fit residues: 83.4008 Evaluate side-chains 293 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2310 VAL Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2590 THR Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 147 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 326 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 363 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3081 HIS ** 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 = 0.4073 r_free = 0.4073 target = 0.126435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098489 restraints weight = 189795.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097967 restraints weight = 88829.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098379 restraints weight = 68434.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.098460 restraints weight = 61811.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098754 restraints weight = 51095.705| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30600 Z= 0.130 Angle : 0.655 13.394 41384 Z= 0.325 Chirality : 0.042 0.262 4694 Planarity : 0.004 0.063 5241 Dihedral : 5.557 83.938 4076 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.65 % Favored : 92.22 % Rotamer: Outliers : 1.69 % Allowed : 17.52 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.14), residues: 3709 helix: 0.48 (0.11), residues: 2418 sheet: -1.14 (0.71), residues: 45 loop : -2.70 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2328 TYR 0.021 0.001 TYR A1739 PHE 0.023 0.001 PHE A2260 TRP 0.015 0.001 TRP A2479 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00294 (30600) covalent geometry : angle 0.65511 (41384) hydrogen bonds : bond 0.03463 ( 1581) hydrogen bonds : angle 4.06068 ( 4670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: -0.1623 (mmt) cc_final: -0.2703 (tpt) REVERT: A 344 GLN cc_start: 0.4320 (pm20) cc_final: 0.3687 (pm20) REVERT: A 453 MET cc_start: 0.5165 (mtp) cc_final: 0.4829 (mmm) REVERT: A 532 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7239 (mtm-85) REVERT: A 562 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5617 (t-170) REVERT: A 1004 GLN cc_start: 0.7955 (pt0) cc_final: 0.7338 (mp10) REVERT: A 1064 TYR cc_start: 0.8170 (m-10) cc_final: 0.7708 (m-10) REVERT: A 1182 GLU cc_start: 0.7008 (tp30) cc_final: 0.6759 (tp30) REVERT: A 1448 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7286 (mm) REVERT: A 1583 MET cc_start: 0.5362 (mtt) cc_final: 0.4151 (ptm) REVERT: A 1900 PHE cc_start: 0.6467 (t80) cc_final: 0.6090 (m-80) REVERT: A 2145 PHE cc_start: 0.5889 (t80) cc_final: 0.5541 (m-80) REVERT: A 2188 GLU cc_start: 0.7844 (pt0) cc_final: 0.7146 (tp30) REVERT: A 2295 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 2328 ARG cc_start: 0.7873 (ttt90) cc_final: 0.7395 (tpt-90) REVERT: A 2420 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 3614 TYR cc_start: 0.6925 (t80) cc_final: 0.6399 (t80) REVERT: A 4039 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.4627 (p90) outliers start: 54 outliers final: 42 residues processed: 298 average time/residue: 0.1732 time to fit residues: 87.9475 Evaluate side-chains 291 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2310 VAL Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2590 THR Chi-restraints excluded: chain A residue 2608 GLU Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 84 optimal weight: 7.9990 chunk 289 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 358 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS ** A1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 GLN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS A2183 HIS ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.124805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096084 restraints weight = 164197.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096627 restraints weight = 81583.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096342 restraints weight = 58804.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096720 restraints weight = 59920.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097184 restraints weight = 44763.023| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30600 Z= 0.184 Angle : 0.713 11.562 41384 Z= 0.356 Chirality : 0.044 0.243 4694 Planarity : 0.005 0.062 5241 Dihedral : 5.790 81.969 4076 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.70 % Favored : 91.16 % Rotamer: Outliers : 1.69 % Allowed : 17.58 % Favored : 80.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.08 (0.14), residues: 3709 helix: 0.29 (0.11), residues: 2432 sheet: -1.51 (0.68), residues: 47 loop : -2.74 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1727 TYR 0.024 0.002 TYR A 408 PHE 0.024 0.002 PHE A1965 TRP 0.016 0.002 TRP A2245 HIS 0.009 0.001 HIS A1665 Details of bonding type rmsd covalent geometry : bond 0.00426 (30600) covalent geometry : angle 0.71265 (41384) hydrogen bonds : bond 0.03912 ( 1581) hydrogen bonds : angle 4.24625 ( 4670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: -0.1605 (mmt) cc_final: -0.2652 (tpt) REVERT: A 344 GLN cc_start: 0.4320 (pm20) cc_final: 0.3617 (pm20) REVERT: A 532 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7287 (mtm-85) REVERT: A 1448 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7311 (mm) REVERT: A 1583 MET cc_start: 0.5358 (mtt) cc_final: 0.4187 (ptm) REVERT: A 1900 PHE cc_start: 0.6529 (t80) cc_final: 0.6059 (m-80) REVERT: A 2145 PHE cc_start: 0.6036 (t80) cc_final: 0.5641 (m-80) REVERT: A 2185 MET cc_start: 0.8183 (tpp) cc_final: 0.7890 (mpp) REVERT: A 2188 GLU cc_start: 0.7859 (pt0) cc_final: 0.7095 (tp30) REVERT: A 2295 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 2328 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7483 (tpt-90) REVERT: A 2420 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 2442 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6588 (tmm) REVERT: A 4039 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.4549 (p90) outliers start: 54 outliers final: 47 residues processed: 285 average time/residue: 0.1696 time to fit residues: 82.8707 Evaluate side-chains 288 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1322 THR Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1795 VAL Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1977 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2310 VAL Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2360 PHE Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2420 PHE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2590 THR Chi-restraints excluded: chain A residue 2608 GLU Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3429 GLU Chi-restraints excluded: chain A residue 3547 THR Chi-restraints excluded: chain A residue 3852 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 20 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1574 ASN A1963 GLN ** A1980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2163 HIS ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3081 HIS ** 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 = 0.4063 r_free = 0.4063 target = 0.125776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097926 restraints weight = 216350.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097821 restraints weight = 95543.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097623 restraints weight = 77445.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097957 restraints weight = 66331.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098217 restraints weight = 52626.705| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30600 Z= 0.138 Angle : 0.672 11.398 41384 Z= 0.335 Chirality : 0.042 0.245 4694 Planarity : 0.004 0.063 5241 Dihedral : 5.669 83.671 4076 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.73 % Favored : 92.14 % Rotamer: Outliers : 1.69 % Allowed : 17.70 % Favored : 80.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.95 (0.14), residues: 3709 helix: 0.42 (0.11), residues: 2413 sheet: -1.50 (0.68), residues: 47 loop : -2.71 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2328 TYR 0.021 0.001 TYR A1739 PHE 0.023 0.001 PHE A2260 TRP 0.015 0.001 TRP A2479 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00313 (30600) covalent geometry : angle 0.67224 (41384) hydrogen bonds : bond 0.03608 ( 1581) hydrogen bonds : angle 4.14271 ( 4670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.08 seconds wall clock time: 101 minutes 38.43 seconds (6098.43 seconds total)