Starting phenix.real_space_refine on Thu Jun 4 20:16:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vs3_65295/06_2026/9vs3_65295.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 9555 2.51 5 N 2478 2.21 5 O 2750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1833, 14876 Classifications: {'peptide': 1833} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1769} Chain breaks: 15 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14876 At special positions: 0 Unit cell: (106.4, 114.95, 142.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 2750 8.00 N 2478 7.00 C 9555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 713.2 milliseconds 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 16 sheets defined 52.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.527A pdb=" N GLU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 45 removed outlier: 3.563A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.624A pdb=" N TYR A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.851A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 215 through 227 removed outlier: 4.074A pdb=" N SER A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.581A pdb=" N LEU A 240 " --> pdb=" O TRP A 236 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.521A pdb=" N HIS A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.685A pdb=" N ASN A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.642A pdb=" N ASP A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.746A pdb=" N SER A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.676A pdb=" N ALA A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.620A pdb=" N TYR A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.527A pdb=" N THR A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.920A pdb=" N ALA A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 523 removed outlier: 3.771A pdb=" N THR A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.781A pdb=" N GLN A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.805A pdb=" N LEU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 4.028A pdb=" N ASN A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 removed outlier: 3.946A pdb=" N LEU A 647 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.529A pdb=" N ILE A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 4.080A pdb=" N PHE A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 697 Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.945A pdb=" N ASN A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 752 removed outlier: 3.552A pdb=" N PHE A 752 " --> pdb=" O PRO A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 749 through 752' Processing helix chain 'A' and resid 766 through 782 removed outlier: 3.915A pdb=" N GLU A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 815 removed outlier: 4.003A pdb=" N ARG A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 removed outlier: 3.508A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 941 removed outlier: 3.585A pdb=" N GLN A 933 " --> pdb=" O PRO A 929 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 939 " --> pdb=" O MET A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 985 removed outlier: 3.947A pdb=" N CYS A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 975 " --> pdb=" O CYS A 971 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1024 removed outlier: 3.504A pdb=" N GLU A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 4.113A pdb=" N LYS A1049 " --> pdb=" O VAL A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1050 through 1055 removed outlier: 3.503A pdb=" N VAL A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A1055 " --> pdb=" O PHE A1051 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1050 through 1055' Processing helix chain 'A' and resid 1061 through 1076 removed outlier: 3.826A pdb=" N LYS A1066 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1091 removed outlier: 3.568A pdb=" N LEU A1087 " --> pdb=" O PRO A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1125 through 1151 removed outlier: 3.696A pdb=" N SER A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1130 " --> pdb=" O ASN A1126 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1132 " --> pdb=" O MET A1128 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1151 " --> pdb=" O ALA A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1197 removed outlier: 3.719A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A1192 " --> pdb=" O LYS A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1234 removed outlier: 4.122A pdb=" N LEU A1233 " --> pdb=" O TYR A1229 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1234' Processing helix chain 'A' and resid 1244 through 1262 removed outlier: 4.214A pdb=" N SER A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A1260 " --> pdb=" O ALA A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1284 removed outlier: 4.331A pdb=" N TYR A1284 " --> pdb=" O THR A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1324 Processing helix chain 'A' and resid 1326 through 1342 removed outlier: 4.470A pdb=" N ASN A1330 " --> pdb=" O ILE A1326 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1347 removed outlier: 3.586A pdb=" N LYS A1346 " --> pdb=" O PRO A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1357 removed outlier: 4.346A pdb=" N THR A1356 " --> pdb=" O GLN A1352 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1357 " --> pdb=" O THR A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1378 removed outlier: 3.686A pdb=" N ARG A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1415 removed outlier: 3.682A pdb=" N LEU A1414 " --> pdb=" O THR A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1428 removed outlier: 4.196A pdb=" N ASN A1428 " --> pdb=" O LYS A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1442 removed outlier: 4.078A pdb=" N GLU A1434 " --> pdb=" O ASN A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1447 removed outlier: 3.688A pdb=" N VAL A1447 " --> pdb=" O GLU A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 3.942A pdb=" N TYR A1464 " --> pdb=" O ILE A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1473 Processing helix chain 'A' and resid 1479 through 1489 removed outlier: 4.200A pdb=" N LEU A1487 " --> pdb=" O VAL A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1537 removed outlier: 4.615A pdb=" N GLN A1529 " --> pdb=" O PRO A1525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A1530 " --> pdb=" O GLN A1526 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A1537 " --> pdb=" O ARG A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1551 removed outlier: 3.870A pdb=" N LYS A1546 " --> pdb=" O ILE A1542 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A1548 " --> pdb=" O ASP A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1569 removed outlier: 3.815A pdb=" N CYS A1569 " --> pdb=" O THR A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1635 removed outlier: 3.991A pdb=" N GLU A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A1633 " --> pdb=" O GLU A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1639 removed outlier: 3.752A pdb=" N LYS A1639 " --> pdb=" O ILE A1636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1636 through 1639' Processing helix chain 'A' and resid 1640 through 1646 Processing helix chain 'A' and resid 1653 through 1676 removed outlier: 3.937A pdb=" N LEU A1657 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A1671 " --> pdb=" O LEU A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1705 removed outlier: 3.589A pdb=" N THR A1705 " --> pdb=" O ILE A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1754 removed outlier: 4.279A pdb=" N ARG A1745 " --> pdb=" O ALA A1741 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A1749 " --> pdb=" O ARG A1745 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A1754 " --> pdb=" O PHE A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1759 Processing helix chain 'A' and resid 1760 through 1769 removed outlier: 3.570A pdb=" N LEU A1764 " --> pdb=" O ARG A1760 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP A1769 " --> pdb=" O ASN A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1788 Processing helix chain 'A' and resid 1789 through 1793 removed outlier: 4.477A pdb=" N LEU A1792 " --> pdb=" O SER A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1801 removed outlier: 3.852A pdb=" N LEU A1798 " --> pdb=" O PHE A1794 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A1799 " --> pdb=" O ILE A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1814 removed outlier: 3.561A pdb=" N ASN A1810 " --> pdb=" O GLN A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1881 Processing helix chain 'A' and resid 1921 through 1927 Processing helix chain 'A' and resid 1961 through 1966 removed outlier: 4.474A pdb=" N VAL A1964 " --> pdb=" O MET A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1994 through 1996 No H-bonds generated for 'chain 'A' and resid 1994 through 1996' Processing helix chain 'A' and resid 2023 through 2029 Processing helix chain 'A' and resid 2031 through 2038 removed outlier: 4.171A pdb=" N PHE A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A2037 " --> pdb=" O ILE A2033 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A2038 " --> pdb=" O PRO A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2103 removed outlier: 3.532A pdb=" N VAL A2093 " --> pdb=" O ILE A2089 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A2098 " --> pdb=" O ALA A2094 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A2099 " --> pdb=" O ASN A2095 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A2103 " --> pdb=" O GLU A2099 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.920A pdb=" N ALA A 79 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 91 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 81 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 89 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N CYS A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 90 " --> pdb=" O CYS A 127 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA A 131 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS A 94 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 5.811A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 534 removed outlier: 4.168A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 591 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 579 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 531 through 534 removed outlier: 4.168A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AA7, first strand: chain 'A' and resid 843 through 847 removed outlier: 3.595A pdb=" N ILE A 908 " --> pdb=" O LYS A 846 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 963 through 964 removed outlier: 5.983A pdb=" N PHE A 946 " --> pdb=" O ILE A1081 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1158 through 1159 removed outlier: 3.688A pdb=" N SER A1169 " --> pdb=" O ASN A1158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB2, first strand: chain 'A' and resid 1581 through 1584 Processing sheet with id=AB3, first strand: chain 'A' and resid 1772 through 1773 Processing sheet with id=AB4, first strand: chain 'A' and resid 1821 through 1823 removed outlier: 3.690A pdb=" N SER A1847 " --> pdb=" O THR A1863 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU A1853 " --> pdb=" O LEU A1857 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A1857 " --> pdb=" O GLU A1853 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LYS A1856 " --> pdb=" O VAL A1945 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A1858 " --> pdb=" O PRO A1947 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL A1949 " --> pdb=" O LYS A1858 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A1860 " --> pdb=" O VAL A1949 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER A1951 " --> pdb=" O ALA A1860 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A1862 " --> pdb=" O SER A1951 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A1904 " --> pdb=" O VAL A1945 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A1902 " --> pdb=" O PRO A1947 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1977 through 1980 removed outlier: 6.604A pdb=" N GLU A1983 " --> pdb=" O VAL A1979 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2004 through 2005 removed outlier: 3.813A pdb=" N ILE A2008 " --> pdb=" O ALA A2005 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2058 through 2062 625 hydrogen bonds defined for protein. 1776 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: 3.28 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2435 1.30 - 1.43: 3954 1.43 - 1.56: 8625 1.56 - 1.69: 1 1.69 - 1.82: 156 Bond restraints: 15171 Sorted by residual: bond pdb=" C GLU A2063 " pdb=" O GLU A2063 " ideal model delta sigma weight residual 1.235 1.174 0.062 1.14e-02 7.69e+03 2.92e+01 bond pdb=" C THR A2072 " pdb=" O THR A2072 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.13e-02 7.83e+03 2.36e+01 bond pdb=" N ASP A1556 " pdb=" CA ASP A1556 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.97e+01 bond pdb=" C TYR A1012 " pdb=" O TYR A1012 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" N ILE A 991 " pdb=" CA ILE A 991 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.17e-02 7.31e+03 1.32e+01 ... (remaining 15166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 20031 2.72 - 5.45: 390 5.45 - 8.17: 68 8.17 - 10.89: 15 10.89 - 13.62: 4 Bond angle restraints: 20508 Sorted by residual: angle pdb=" C THR A2060 " pdb=" CA THR A2060 " pdb=" CB THR A2060 " ideal model delta sigma weight residual 109.54 95.92 13.62 1.84e+00 2.95e-01 5.48e+01 angle pdb=" CA GLY A 995 " pdb=" C GLY A 995 " pdb=" O GLY A 995 " ideal model delta sigma weight residual 121.41 116.81 4.60 8.80e-01 1.29e+00 2.73e+01 angle pdb=" C PHE A2071 " pdb=" N THR A2072 " pdb=" CA THR A2072 " ideal model delta sigma weight residual 122.86 115.61 7.25 1.42e+00 4.96e-01 2.61e+01 angle pdb=" CA LYS A2077 " pdb=" C LYS A2077 " pdb=" O LYS A2077 " ideal model delta sigma weight residual 120.32 114.69 5.63 1.11e+00 8.12e-01 2.57e+01 angle pdb=" C TYR A2075 " pdb=" CA TYR A2075 " pdb=" CB TYR A2075 " ideal model delta sigma weight residual 109.56 98.36 11.20 2.22e+00 2.03e-01 2.54e+01 ... (remaining 20503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7828 17.94 - 35.88: 1019 35.88 - 53.81: 313 53.81 - 71.75: 64 71.75 - 89.69: 10 Dihedral angle restraints: 9234 sinusoidal: 3776 harmonic: 5458 Sorted by residual: dihedral pdb=" C TYR A2075 " pdb=" N TYR A2075 " pdb=" CA TYR A2075 " pdb=" CB TYR A2075 " ideal model delta harmonic sigma weight residual -122.60 -106.05 -16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C THR A2060 " pdb=" N THR A2060 " pdb=" CA THR A2060 " pdb=" CB THR A2060 " ideal model delta harmonic sigma weight residual -122.00 -106.96 -15.04 0 2.50e+00 1.60e-01 3.62e+01 dihedral pdb=" C ASN A2087 " pdb=" N ASN A2087 " pdb=" CA ASN A2087 " pdb=" CB ASN A2087 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 9231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2075 0.083 - 0.166: 223 0.166 - 0.250: 31 0.250 - 0.333: 8 0.333 - 0.416: 3 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CA TYR A2075 " pdb=" N TYR A2075 " pdb=" C TYR A2075 " pdb=" CB TYR A2075 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA LYS A2077 " pdb=" N LYS A2077 " pdb=" C LYS A2077 " pdb=" CB LYS A2077 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA ASN A2087 " pdb=" N ASN A2087 " pdb=" C ASN A2087 " pdb=" CB ASN A2087 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 2337 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2071 " -0.044 2.00e-02 2.50e+03 3.36e-02 1.98e+01 pdb=" CG PHE A2071 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A2071 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE A2071 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A2071 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE A2071 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A2071 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A2067 " -0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C SER A2067 " 0.072 2.00e-02 2.50e+03 pdb=" O SER A2067 " -0.027 2.00e-02 2.50e+03 pdb=" N MET A2068 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1231 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ARG A1231 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG A1231 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A1232 " -0.023 2.00e-02 2.50e+03 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 2 2.03 - 2.75: 1358 2.75 - 3.46: 21225 3.46 - 4.18: 33428 4.18 - 4.90: 60644 Nonbonded interactions: 116657 Sorted by model distance: nonbonded pdb=" O GLU A2055 " pdb=" CG2 THR A2084 " model vdw 1.309 3.460 nonbonded pdb=" O LEU A2022 " pdb=" O GLU A2058 " model vdw 1.813 3.040 nonbonded pdb=" NH1 ARG A1000 " pdb=" OE1 GLN A1584 " model vdw 2.045 3.120 nonbonded pdb=" O SER A1236 " pdb=" OG SER A1236 " model vdw 2.129 3.040 nonbonded pdb=" O THR A2072 " pdb=" OG1 THR A2072 " model vdw 2.185 3.040 ... (remaining 116652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.005 0.062 15171 Z= 0.304 Angle : 0.914 13.619 20508 Z= 0.528 Chirality : 0.057 0.416 2340 Planarity : 0.006 0.077 2583 Dihedral : 17.864 89.687 5672 Min Nonbonded Distance : 1.309 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.03 % Allowed : 29.17 % Favored : 68.80 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.18), residues: 1801 helix: -0.37 (0.17), residues: 863 sheet: -0.73 (0.48), residues: 113 loop : -1.92 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 982 TYR 0.021 0.001 TYR A1906 PHE 0.045 0.002 PHE A2071 TRP 0.021 0.001 TRP A 786 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.30 (15171) covalent geometry : angle 0.91446 / 0.53 (20508) hydrogen bonds : bond 0.15827 / 10.49 ( 616) hydrogen bonds : angle 6.15847 / 4.62 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1226 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 1439 MET cc_start: 0.7786 (mmt) cc_final: 0.7447 (mmt) REVERT: A 2099 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7568 (mt-10) outliers start: 34 outliers final: 13 residues processed: 294 average time/residue: 0.1012 time to fit residues: 46.3199 Evaluate side-chains 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2084 THR Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2089 ILE Chi-restraints excluded: chain A residue 2099 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 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 815 HIS A 820 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2095 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117256 restraints weight = 19121.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121199 restraints weight = 10685.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123656 restraints weight = 7531.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124934 restraints weight = 6177.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125908 restraints weight = 5544.630| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15171 Z= 0.153 Angle : 0.577 7.789 20508 Z= 0.297 Chirality : 0.042 0.177 2340 Planarity : 0.004 0.049 2583 Dihedral : 5.417 56.212 2000 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 3.77 % Allowed : 27.20 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1801 helix: 0.15 (0.18), residues: 865 sheet: -0.70 (0.45), residues: 131 loop : -1.78 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 596 TYR 0.012 0.001 TYR A 254 PHE 0.016 0.001 PHE A 752 TRP 0.013 0.001 TRP A 83 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (15171) covalent geometry : angle 0.57727 / 0.30 (20508) hydrogen bonds : bond 0.04212 / 2.85 ( 616) hydrogen bonds : angle 4.54117 / 3.38 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.8110 (tpp) cc_final: 0.7753 (tpp) REVERT: A 213 SER cc_start: 0.8471 (t) cc_final: 0.8161 (p) REVERT: A 1369 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 1439 MET cc_start: 0.7930 (mmt) cc_final: 0.7512 (mmt) REVERT: A 1625 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7580 (mp) REVERT: A 1766 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 1767 ILE cc_start: 0.8349 (tt) cc_final: 0.8043 (tt) REVERT: A 1781 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5832 (tt) REVERT: A 1855 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6837 (t0) outliers start: 63 outliers final: 28 residues processed: 312 average time/residue: 0.0978 time to fit residues: 48.3700 Evaluate side-chains 283 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1288 HIS Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1925 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2097 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118420 restraints weight = 19228.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120665 restraints weight = 10409.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121747 restraints weight = 7344.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122981 restraints weight = 6595.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122795 restraints weight = 5898.806| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15171 Z= 0.157 Angle : 0.568 10.772 20508 Z= 0.288 Chirality : 0.042 0.166 2340 Planarity : 0.004 0.045 2583 Dihedral : 4.430 59.037 1977 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 4.06 % Allowed : 28.03 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1801 helix: 0.30 (0.18), residues: 874 sheet: -0.63 (0.46), residues: 129 loop : -1.82 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 596 TYR 0.013 0.001 TYR A 254 PHE 0.017 0.001 PHE A 530 TRP 0.012 0.001 TRP A 83 HIS 0.005 0.001 HIS A1715 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (15171) covalent geometry : angle 0.56813 / 0.29 (20508) hydrogen bonds : bond 0.03929 / 2.63 ( 616) hydrogen bonds : angle 4.30994 / 3.17 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.390 Fit side-chains REVERT: A 69 MET cc_start: 0.7372 (mmt) cc_final: 0.7080 (mmm) REVERT: A 161 PHE cc_start: 0.7398 (m-80) cc_final: 0.7185 (m-10) REVERT: A 167 MET cc_start: 0.8121 (tpp) cc_final: 0.7758 (tpp) REVERT: A 275 ASP cc_start: 0.8492 (t0) cc_final: 0.8288 (t0) REVERT: A 1057 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: A 1205 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7722 (mttp) REVERT: A 1369 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: A 1454 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: A 1625 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 1781 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5757 (tt) REVERT: A 1855 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6627 (t0) outliers start: 68 outliers final: 40 residues processed: 313 average time/residue: 0.0934 time to fit residues: 45.9085 Evaluate side-chains 300 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1288 HIS Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2097 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118111 restraints weight = 19082.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119668 restraints weight = 11101.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120673 restraints weight = 7766.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120955 restraints weight = 7129.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121415 restraints weight = 6756.819| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15171 Z= 0.165 Angle : 0.580 10.887 20508 Z= 0.291 Chirality : 0.042 0.173 2340 Planarity : 0.003 0.044 2583 Dihedral : 4.326 52.568 1976 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 5.38 % Allowed : 27.20 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1801 helix: 0.41 (0.18), residues: 875 sheet: -0.58 (0.47), residues: 129 loop : -1.82 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 596 TYR 0.013 0.001 TYR A 254 PHE 0.020 0.001 PHE A 530 TRP 0.011 0.001 TRP A 83 HIS 0.005 0.001 HIS A1715 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (15171) covalent geometry : angle 0.58045 / 0.29 (20508) hydrogen bonds : bond 0.03784 / 2.51 ( 616) hydrogen bonds : angle 4.23097 / 3.10 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 265 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 161 PHE cc_start: 0.7381 (m-80) cc_final: 0.7159 (m-10) REVERT: A 167 MET cc_start: 0.8139 (tpp) cc_final: 0.7798 (tpp) REVERT: A 275 ASP cc_start: 0.8626 (t0) cc_final: 0.8425 (t0) REVERT: A 565 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6963 (p90) REVERT: A 579 THR cc_start: 0.8354 (p) cc_final: 0.8087 (p) REVERT: A 1057 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: A 1205 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7658 (mttp) REVERT: A 1441 MET cc_start: 0.8319 (tpt) cc_final: 0.8050 (tpt) REVERT: A 1454 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: A 1781 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5671 (tt) REVERT: A 1855 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6685 (t0) outliers start: 90 outliers final: 55 residues processed: 327 average time/residue: 0.0895 time to fit residues: 46.6025 Evaluate side-chains 315 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2087 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 128 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 815 HIS A 820 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN ** A2080 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.172607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118588 restraints weight = 19067.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122724 restraints weight = 10282.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125316 restraints weight = 7139.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126709 restraints weight = 5790.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127443 restraints weight = 5156.291| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15171 Z= 0.101 Angle : 0.537 9.332 20508 Z= 0.269 Chirality : 0.041 0.179 2340 Planarity : 0.003 0.044 2583 Dihedral : 4.087 45.831 1976 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 3.83 % Allowed : 29.47 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1801 helix: 0.75 (0.18), residues: 856 sheet: -0.54 (0.47), residues: 129 loop : -1.77 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 596 TYR 0.014 0.001 TYR A 36 PHE 0.021 0.001 PHE A 530 TRP 0.011 0.001 TRP A 83 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (15171) covalent geometry : angle 0.53717 / 0.27 (20508) hydrogen bonds : bond 0.03229 / 2.15 ( 616) hydrogen bonds : angle 3.98969 / 2.94 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.544 Fit side-chains REVERT: A 5 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6343 (ppp) REVERT: A 161 PHE cc_start: 0.7451 (m-80) cc_final: 0.7229 (m-10) REVERT: A 167 MET cc_start: 0.8138 (tpp) cc_final: 0.7782 (tpp) REVERT: A 180 MET cc_start: 0.8663 (tpt) cc_final: 0.8440 (tpp) REVERT: A 501 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7869 (pttp) REVERT: A 565 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.6989 (p90) REVERT: A 578 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 1369 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 1441 MET cc_start: 0.8331 (tpt) cc_final: 0.8126 (tpt) REVERT: A 1625 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 1781 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5653 (tt) REVERT: A 1855 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6882 (t0) REVERT: A 1995 MET cc_start: 0.7987 (tpt) cc_final: 0.7755 (tpt) REVERT: A 2083 MET cc_start: 0.7304 (mtt) cc_final: 0.6556 (mpp) outliers start: 64 outliers final: 38 residues processed: 308 average time/residue: 0.0959 time to fit residues: 47.0224 Evaluate side-chains 296 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1288 HIS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 0.2980 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN A2023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117434 restraints weight = 18921.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121489 restraints weight = 10326.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123726 restraints weight = 7216.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125450 restraints weight = 5910.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126067 restraints weight = 5239.085| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15171 Z= 0.120 Angle : 0.542 9.552 20508 Z= 0.272 Chirality : 0.041 0.165 2340 Planarity : 0.003 0.042 2583 Dihedral : 3.929 22.857 1974 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 4.00 % Allowed : 29.29 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1801 helix: 0.76 (0.18), residues: 862 sheet: -0.58 (0.47), residues: 129 loop : -1.74 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 821 TYR 0.011 0.001 TYR A 63 PHE 0.022 0.001 PHE A 530 TRP 0.012 0.001 TRP A 786 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15171) covalent geometry : angle 0.54216 / 0.27 (20508) hydrogen bonds : bond 0.03267 / 2.16 ( 616) hydrogen bonds : angle 3.98766 / 2.93 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 0.606 Fit side-chains REVERT: A 5 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6372 (ppp) REVERT: A 155 GLU cc_start: 0.7573 (mp0) cc_final: 0.6677 (pt0) REVERT: A 161 PHE cc_start: 0.7443 (m-80) cc_final: 0.7239 (m-10) REVERT: A 167 MET cc_start: 0.8171 (tpp) cc_final: 0.7831 (tpp) REVERT: A 501 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7881 (pttp) REVERT: A 565 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7031 (p90) REVERT: A 1057 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8417 (t0) REVERT: A 1369 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 1441 MET cc_start: 0.8313 (tpt) cc_final: 0.8022 (tpt) REVERT: A 1625 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 1781 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5675 (tt) REVERT: A 1855 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6827 (t0) REVERT: A 1995 MET cc_start: 0.8037 (tpt) cc_final: 0.7793 (tpt) REVERT: A 2085 TYR cc_start: 0.8241 (t80) cc_final: 0.7815 (t80) outliers start: 67 outliers final: 39 residues processed: 298 average time/residue: 0.0934 time to fit residues: 44.2655 Evaluate side-chains 294 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1916 TYR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 153 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 170 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 109 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.171260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117034 restraints weight = 18966.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121082 restraints weight = 10330.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123614 restraints weight = 7229.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125106 restraints weight = 5860.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125403 restraints weight = 5212.973| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15171 Z= 0.127 Angle : 0.565 10.021 20508 Z= 0.279 Chirality : 0.041 0.154 2340 Planarity : 0.003 0.042 2583 Dihedral : 3.934 22.417 1974 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.39 % Rotamer: Outliers : 3.95 % Allowed : 29.65 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1801 helix: 0.78 (0.18), residues: 866 sheet: -0.58 (0.47), residues: 129 loop : -1.74 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 596 TYR 0.015 0.001 TYR A 36 PHE 0.015 0.001 PHE A1750 TRP 0.012 0.001 TRP A 786 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (15171) covalent geometry : angle 0.56479 / 0.28 (20508) hydrogen bonds : bond 0.03288 / 2.17 ( 616) hydrogen bonds : angle 3.98558 / 2.93 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 0.576 Fit side-chains REVERT: A 5 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6359 (ppp) REVERT: A 161 PHE cc_start: 0.7453 (m-80) cc_final: 0.7246 (m-10) REVERT: A 167 MET cc_start: 0.8170 (tpp) cc_final: 0.7851 (tpp) REVERT: A 501 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7901 (pttp) REVERT: A 565 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7074 (p90) REVERT: A 1369 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: A 1441 MET cc_start: 0.8320 (tpt) cc_final: 0.7983 (tpt) REVERT: A 1781 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5686 (tt) REVERT: A 1855 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6858 (t0) REVERT: A 1962 GLN cc_start: 0.8815 (mp10) cc_final: 0.8175 (mm-40) REVERT: A 2085 TYR cc_start: 0.8350 (t80) cc_final: 0.7901 (t80) REVERT: A 2090 ARG cc_start: 0.6539 (ttm170) cc_final: 0.6089 (mmt180) outliers start: 66 outliers final: 42 residues processed: 298 average time/residue: 0.0954 time to fit residues: 45.0010 Evaluate side-chains 293 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1288 HIS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 3.9990 chunk 155 optimal weight: 0.0670 chunk 167 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 0.0670 overall best weight: 1.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.170863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120934 restraints weight = 19020.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121468 restraints weight = 10443.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122484 restraints weight = 7639.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123470 restraints weight = 7473.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123388 restraints weight = 6495.087| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15171 Z= 0.149 Angle : 0.586 11.270 20508 Z= 0.290 Chirality : 0.042 0.175 2340 Planarity : 0.003 0.042 2583 Dihedral : 3.993 21.984 1974 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.39 % Rotamer: Outliers : 3.35 % Allowed : 30.13 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1801 helix: 0.73 (0.18), residues: 872 sheet: -0.61 (0.47), residues: 129 loop : -1.70 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 596 TYR 0.013 0.001 TYR A 93 PHE 0.025 0.001 PHE A 530 TRP 0.011 0.001 TRP A 83 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (15171) covalent geometry : angle 0.58650 / 0.29 (20508) hydrogen bonds : bond 0.03443 / 2.27 ( 616) hydrogen bonds : angle 4.05009 / 2.97 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 0.487 Fit side-chains REVERT: A 5 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6410 (ppp) REVERT: A 163 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7969 (pp20) REVERT: A 167 MET cc_start: 0.8205 (tpp) cc_final: 0.7840 (tpp) REVERT: A 501 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7961 (pttp) REVERT: A 531 ARG cc_start: 0.7517 (mtt-85) cc_final: 0.7269 (mtt-85) REVERT: A 565 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.6951 (p90) REVERT: A 1289 ASP cc_start: 0.7633 (p0) cc_final: 0.7028 (t0) REVERT: A 1369 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: A 1374 LYS cc_start: 0.8023 (mttt) cc_final: 0.7569 (mptt) REVERT: A 1781 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5773 (tt) REVERT: A 1855 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6715 (t0) REVERT: A 1962 GLN cc_start: 0.8851 (mp10) cc_final: 0.8098 (mm-40) REVERT: A 2085 TYR cc_start: 0.8418 (t80) cc_final: 0.8118 (t80) REVERT: A 2090 ARG cc_start: 0.6639 (ttm170) cc_final: 0.6158 (mpt180) outliers start: 56 outliers final: 43 residues processed: 293 average time/residue: 0.0983 time to fit residues: 45.0442 Evaluate side-chains 298 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 126 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117291 restraints weight = 19110.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119081 restraints weight = 11163.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119716 restraints weight = 7899.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120916 restraints weight = 7191.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120967 restraints weight = 6452.994| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15171 Z= 0.184 Angle : 0.627 12.295 20508 Z= 0.310 Chirality : 0.043 0.168 2340 Planarity : 0.003 0.044 2583 Dihedral : 4.153 23.540 1974 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 3.89 % Allowed : 29.89 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1801 helix: 0.67 (0.18), residues: 863 sheet: -0.65 (0.47), residues: 129 loop : -1.75 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 596 TYR 0.015 0.001 TYR A 36 PHE 0.021 0.002 PHE A 530 TRP 0.012 0.001 TRP A 83 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 (15171) covalent geometry : angle 0.62671 / 0.31 (20508) hydrogen bonds : bond 0.03715 / 2.45 ( 616) hydrogen bonds : angle 4.18726 / 3.06 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 251 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6420 (ppp) REVERT: A 86 ASP cc_start: 0.7804 (p0) cc_final: 0.7576 (p0) REVERT: A 163 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7992 (pp20) REVERT: A 167 MET cc_start: 0.8186 (tpp) cc_final: 0.7843 (tpp) REVERT: A 501 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (pttp) REVERT: A 531 ARG cc_start: 0.7543 (mtt-85) cc_final: 0.6961 (mtt-85) REVERT: A 565 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 1057 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8331 (t0) REVERT: A 1369 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: A 1781 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5688 (tt) REVERT: A 1855 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6767 (t0) REVERT: A 2085 TYR cc_start: 0.8475 (t80) cc_final: 0.8121 (t80) REVERT: A 2086 LYS cc_start: 0.7127 (ttpp) cc_final: 0.5330 (mmtt) REVERT: A 2090 ARG cc_start: 0.6714 (ttm170) cc_final: 0.6262 (mpt180) outliers start: 65 outliers final: 47 residues processed: 298 average time/residue: 0.1066 time to fit residues: 49.3816 Evaluate side-chains 299 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1906 TYR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2060 THR Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 113 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.172116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121045 restraints weight = 18997.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122907 restraints weight = 10125.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124405 restraints weight = 7117.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124656 restraints weight = 6439.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124967 restraints weight = 6029.148| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15171 Z= 0.111 Angle : 0.585 13.169 20508 Z= 0.289 Chirality : 0.041 0.167 2340 Planarity : 0.003 0.041 2583 Dihedral : 3.957 22.457 1974 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.39 % Rotamer: Outliers : 2.81 % Allowed : 30.96 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1801 helix: 0.79 (0.18), residues: 866 sheet: -0.59 (0.47), residues: 129 loop : -1.69 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 596 TYR 0.015 0.001 TYR A1672 PHE 0.022 0.001 PHE A 473 TRP 0.011 0.001 TRP A1041 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (15171) covalent geometry : angle 0.58538 / 0.29 (20508) hydrogen bonds : bond 0.03163 / 2.07 ( 616) hydrogen bonds : angle 3.98465 / 2.92 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6302 (ppp) REVERT: A 163 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: A 167 MET cc_start: 0.8122 (tpp) cc_final: 0.7779 (tpp) REVERT: A 501 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7952 (pttp) REVERT: A 565 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6810 (p90) REVERT: A 578 PHE cc_start: 0.8004 (t80) cc_final: 0.7551 (t80) REVERT: A 1369 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: A 1781 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5617 (tt) REVERT: A 1855 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6914 (t0) REVERT: A 1962 GLN cc_start: 0.8898 (mp10) cc_final: 0.8271 (mm-40) REVERT: A 2085 TYR cc_start: 0.8448 (t80) cc_final: 0.8071 (t80) REVERT: A 2086 LYS cc_start: 0.7146 (ttpp) cc_final: 0.5432 (mmtt) REVERT: A 2090 ARG cc_start: 0.6654 (ttm170) cc_final: 0.6252 (mpt180) outliers start: 47 outliers final: 37 residues processed: 289 average time/residue: 0.1087 time to fit residues: 48.9676 Evaluate side-chains 292 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1486 ILE Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 VAL Chi-restraints excluded: chain A residue 1826 TRP Chi-restraints excluded: chain A residue 1855 ASN Chi-restraints excluded: chain A residue 1881 ASN Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1889 GLU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1999 SER Chi-restraints excluded: chain A residue 2073 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 182 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 GLN ** A1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119148 restraints weight = 18877.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123316 restraints weight = 10183.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125865 restraints weight = 7061.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127371 restraints weight = 5709.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128194 restraints weight = 5089.933| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 15171 Z= 0.109 Angle : 0.586 12.754 20508 Z= 0.287 Chirality : 0.041 0.155 2340 Planarity : 0.003 0.042 2583 Dihedral : 3.873 22.185 1974 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.78 % Rotamer: Outliers : 2.57 % Allowed : 31.38 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1801 helix: 0.85 (0.18), residues: 870 sheet: -0.60 (0.47), residues: 129 loop : -1.70 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 596 TYR 0.016 0.001 TYR A1551 PHE 0.020 0.001 PHE A 530 TRP 0.019 0.001 TRP A 786 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15171) covalent geometry : angle 0.58586 / 0.29 (20508) hydrogen bonds : bond 0.03053 / 2.00 ( 616) hydrogen bonds : angle 3.92073 / 2.87 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.93 seconds wall clock time: 46 minutes 22.68 seconds (2782.68 seconds total)