Starting phenix.real_space_refine on Wed Oct 28 20:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.map" model { file = "/net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdu_65906/10_2026/9wdu_65906.cif" } resolution = 3.28 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= -0.008 sd= 0.496 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 9 5.49 5 S 113 5.16 5 C 18100 2.51 5 N 5157 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 309 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28790 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1931, 15257 Classifications: {'peptide': 1931} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1821} Chain breaks: 2 Chain: "B" Number of atoms: 13344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 13344 Classifications: {'peptide': 1687} Link IDs: {'PCIS': 1, 'PTRANS': 91, 'TRANS': 1594} Chain breaks: 6 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8589 SG CYS A1110 34.545 62.702 85.635 1.00 49.69 S ATOM 8609 SG CYS A1113 36.456 63.440 82.347 1.00 53.94 S ATOM 8704 SG CYS A1125 36.601 65.818 85.098 1.00 65.31 S ATOM 8728 SG CYS A1128 33.144 65.232 83.453 1.00 55.27 S ATOM 5039 SG CYS A 646 41.003 61.255 72.940 1.00 59.07 S ATOM 5059 SG CYS A 649 38.581 59.961 75.486 1.00 61.70 S ATOM 5923 SG CYS A 770 37.395 61.809 72.315 1.00 57.67 S ATOM 5945 SG CYS A 773 38.648 63.682 75.180 1.00 60.19 S ATOM 14043 SG CYS A1799 44.179 35.257 54.160 1.00 62.42 S ATOM 14071 SG CYS A1803 47.040 36.116 56.521 1.00 50.58 S ATOM 14100 SG CYS A1806 47.910 35.161 52.993 1.00 59.98 S ATOM 11796 SG CYS A1509 49.342 49.679 22.558 1.00 89.96 S ATOM 11814 SG CYS A1512 50.970 46.404 22.892 1.00 96.98 S ATOM 11919 SG CYS A1528 52.176 48.804 20.115 1.00107.92 S ATOM 11941 SG CYS A1531 48.532 46.940 20.249 1.00127.90 S ATOM 23788 SG CYS B1110 107.175 112.089 81.674 1.00 54.08 S ATOM 23808 SG CYS B1113 105.491 111.546 78.203 1.00 51.40 S ATOM 23903 SG CYS B1125 104.964 108.983 80.816 1.00 60.03 S ATOM 23927 SG CYS B1128 108.467 109.611 79.277 1.00 62.99 S ATOM 20272 SG CYS B 646 104.669 117.090 71.040 1.00 64.13 S ATOM 20292 SG CYS B 649 106.759 118.022 73.966 1.00 57.34 S ATOM 21174 SG CYS B 770 108.434 117.130 70.615 1.00 77.80 S ATOM 21196 SG CYS B 773 106.955 114.442 72.697 1.00 72.00 S ATOM 27400 SG CYS B1799 99.355 145.299 56.208 1.00 75.38 S ATOM 27428 SG CYS B1803 96.674 143.304 58.044 1.00 59.72 S ATOM 27457 SG CYS B1806 95.773 144.873 54.720 1.00 71.10 S Time building chain proxies: 6.17, per 1000 atoms: 0.21 Number of scatterers: 28790 At special positions: 0 Unit cell: (146.88, 175.68, 128.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 113 16.00 P 9 15.00 O 5404 8.00 N 5157 7.00 C 18100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1125 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1113 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1128 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 770 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 649 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 773 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 646 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1803 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1799 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1806 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1512 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1509 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1531 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1528 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1113 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1125 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1110 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 649 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 773 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 646 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1803 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1799 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1806 " Number of angles added : 36 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6714 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 20 sheets defined 44.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.897A pdb=" N ILE A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.614A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 157 removed outlier: 3.523A pdb=" N PHE A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 256 through 294 removed outlier: 3.553A pdb=" N ALA A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.852A pdb=" N TYR A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 344 through 358 removed outlier: 4.255A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 358 " --> pdb=" O TRP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 393 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 417 through 431 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.503A pdb=" N LEU A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.695A pdb=" N ARG A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 Proline residue: A 575 - end of helix removed outlier: 3.514A pdb=" N ASN A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.506A pdb=" N MET A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 861 removed outlier: 3.756A pdb=" N GLU A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.668A pdb=" N LYS A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 900 Processing helix chain 'A' and resid 903 through 906 Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 950 through 953 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.793A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1017 through 1029 removed outlier: 3.679A pdb=" N ALA A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 removed outlier: 3.812A pdb=" N VAL A1043 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1054 through 1084 removed outlier: 7.576A pdb=" N GLU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N THR A1068 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG A1069 " --> pdb=" O TYR A1065 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP A1072 " --> pdb=" O THR A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1095 removed outlier: 3.715A pdb=" N LYS A1095 " --> pdb=" O ASN A1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1092 through 1095' Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1146 through 1159 Processing helix chain 'A' and resid 1173 through 1186 removed outlier: 4.380A pdb=" N SER A1178 " --> pdb=" O THR A1174 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1201 Processing helix chain 'A' and resid 1216 through 1220 removed outlier: 3.614A pdb=" N ALA A1219 " --> pdb=" O ASP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1241 removed outlier: 3.849A pdb=" N ARG A1241 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.516A pdb=" N ALA A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1314 removed outlier: 3.811A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1322 removed outlier: 4.043A pdb=" N LEU A1322 " --> pdb=" O GLY A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.787A pdb=" N ARG A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1368 removed outlier: 3.985A pdb=" N ARG A1360 " --> pdb=" O THR A1356 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A1368 " --> pdb=" O ILE A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1381 removed outlier: 3.630A pdb=" N ARG A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.973A pdb=" N GLN A1393 " --> pdb=" O GLU A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1411 Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 4.227A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1540 removed outlier: 3.541A pdb=" N PHE A1540 " --> pdb=" O LYS A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1647 Processing helix chain 'A' and resid 1696 through 1719 Processing helix chain 'A' and resid 1721 through 1723 No H-bonds generated for 'chain 'A' and resid 1721 through 1723' Processing helix chain 'A' and resid 1750 through 1756 Processing helix chain 'A' and resid 1765 through 1777 removed outlier: 3.563A pdb=" N ASP A1769 " --> pdb=" O PRO A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1787 Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.717A pdb=" N LEU A1831 " --> pdb=" O TYR A1827 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1832 " --> pdb=" O LEU A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1847 removed outlier: 3.810A pdb=" N LYS A1846 " --> pdb=" O GLY A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1867 Processing helix chain 'A' and resid 1908 through 1917 removed outlier: 3.536A pdb=" N MET A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1935 Processing helix chain 'A' and resid 1935 through 1945 removed outlier: 3.524A pdb=" N ARG A1939 " --> pdb=" O ARG A1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.519A pdb=" N THR B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.908A pdb=" N ARG B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 Proline residue: B 147 - end of helix removed outlier: 3.898A pdb=" N VAL B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 removed outlier: 3.623A pdb=" N ARG B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 256 through 294 removed outlier: 3.618A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.695A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 344 through 356 removed outlier: 4.212A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.656A pdb=" N LEU B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 393 removed outlier: 3.778A pdb=" N GLY B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.744A pdb=" N LYS B 452 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 482 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 515 through 535 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 560 through 578 Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.533A pdb=" N ASP B 691 " --> pdb=" O TYR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 752 Processing helix chain 'B' and resid 796 through 816 Processing helix chain 'B' and resid 827 through 865 removed outlier: 3.774A pdb=" N MET B 836 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 865 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.936A pdb=" N ARG B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 882 removed outlier: 4.042A pdb=" N GLU B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 898 removed outlier: 3.620A pdb=" N ILE B 889 " --> pdb=" O LYS B 885 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.551A pdb=" N LEU B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 934 removed outlier: 3.712A pdb=" N LEU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 953 Processing helix chain 'B' and resid 969 through 993 removed outlier: 3.625A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1029 removed outlier: 3.546A pdb=" N ASP B1020 " --> pdb=" O ASP B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1052 Processing helix chain 'B' and resid 1054 through 1085 removed outlier: 7.945A pdb=" N GLU B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N THR B1068 " --> pdb=" O LEU B1064 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B1069 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B1070 " --> pdb=" O GLY B1066 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP B1072 " --> pdb=" O THR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1138 through 1146 Processing helix chain 'B' and resid 1146 through 1159 removed outlier: 3.589A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1186 Processing helix chain 'B' and resid 1193 through 1199 Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'B' and resid 1231 through 1240 Processing helix chain 'B' and resid 1261 through 1268 removed outlier: 3.572A pdb=" N ALA B1267 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1275 removed outlier: 3.955A pdb=" N ILE B1272 " --> pdb=" O HIS B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1314 removed outlier: 3.713A pdb=" N LEU B1293 " --> pdb=" O ILE B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 Processing helix chain 'B' and resid 1333 through 1339 Processing helix chain 'B' and resid 1344 through 1368 removed outlier: 3.798A pdb=" N ARG B1348 " --> pdb=" O ASP B1344 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B1354 " --> pdb=" O SER B1350 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B1355 " --> pdb=" O GLU B1351 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER B1358 " --> pdb=" O LYS B1354 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B1359 " --> pdb=" O GLN B1355 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B1360 " --> pdb=" O THR B1356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B1365 " --> pdb=" O ASP B1361 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B1368 " --> pdb=" O ILE B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1382 through 1392 Processing helix chain 'B' and resid 1403 through 1412 Processing helix chain 'B' and resid 1696 through 1717 Processing helix chain 'B' and resid 1721 through 1723 No H-bonds generated for 'chain 'B' and resid 1721 through 1723' Processing helix chain 'B' and resid 1750 through 1756 Processing helix chain 'B' and resid 1765 through 1777 Processing helix chain 'B' and resid 1780 through 1785 Processing helix chain 'B' and resid 1810 through 1816 removed outlier: 4.597A pdb=" N ARG B1814 " --> pdb=" O GLY B1811 " (cutoff:3.500A) Processing helix chain 'B' and resid 1820 through 1830 Processing helix chain 'B' and resid 1843 through 1847 removed outlier: 3.621A pdb=" N LYS B1846 " --> pdb=" O GLY B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1868 Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.608A pdb=" N MET B1912 " --> pdb=" O GLU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1920 No H-bonds generated for 'chain 'B' and resid 1918 through 1920' Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1945 removed outlier: 3.501A pdb=" N ARG B1939 " --> pdb=" O ARG B1935 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 54 removed outlier: 6.216A pdb=" N ALA A 46 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG A 598 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A 48 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 596 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A1224 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A1168 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.773A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY A 130 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 131 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 604 through 608 removed outlier: 6.664A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 619 " --> pdb=" O PHE A 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 653 through 658 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 667 through 671 current: chain 'A' and resid 728 through 731 Processing sheet with id=AA5, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA6, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AA7, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.801A pdb=" N GLY A1137 " --> pdb=" O PHE A1107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1423 through 1432 removed outlier: 6.482A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A1443 " --> pdb=" O LEU A1430 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1442 through 1450 current: chain 'A' and resid 1469 through 1476 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1469 through 1476 current: chain 'A' and resid 1514 through 1518 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1514 through 1518 current: chain 'A' and resid 1585 through 1602 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1585 through 1602 current: chain 'A' and resid 1637 through 1640 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1637 through 1640 current: chain 'A' and resid 1736 through 1743 Processing sheet with id=AA9, first strand: chain 'A' and resid 1872 through 1876 removed outlier: 4.159A pdb=" N TRP A1895 " --> pdb=" O GLU A1887 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.031A pdb=" N PHE B 591 " --> pdb=" O SER B1250 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL B1252 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 593 " --> pdb=" O VAL B1252 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR B1254 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 595 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N CYS B1256 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 597 " --> pdb=" O CYS B1256 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B1224 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B1208 " --> pdb=" O LEU B1170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'B' and resid 235 through 237 removed outlier: 6.800A pdb=" N GLY B 236 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASN B 331 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 363 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 406 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 365 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N SER B 408 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE B 367 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY B 130 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER B 409 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 132 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AB5, first strand: chain 'B' and resid 604 through 608 removed outlier: 6.706A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE B 619 " --> pdb=" O PHE B 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 615 through 620 current: chain 'B' and resid 652 through 658 removed outlier: 3.737A pdb=" N LEU B 671 " --> pdb=" O GLN B 657 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 667 through 671 current: chain 'B' and resid 728 through 731 Processing sheet with id=AB6, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AB7, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AB8, first strand: chain 'B' and resid 1108 through 1109 Processing sheet with id=AB9, first strand: chain 'B' and resid 1580 through 1581 removed outlier: 6.575A pdb=" N MET B1738 " --> pdb=" O PRO B1730 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN B1740 " --> pdb=" O LEU B1728 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1789 through 1790 removed outlier: 4.097A pdb=" N GLY B1790 " --> pdb=" O GLY B1793 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 4.002A pdb=" N TRP B1895 " --> pdb=" O GLU B1887 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS B1889 " --> pdb=" O GLU B1893 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU B1893 " --> pdb=" O LYS B1889 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ARG B1925 " --> pdb=" O LEU B1894 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B1896 " --> pdb=" O ARG B1925 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU B1927 " --> pdb=" O ARG B1896 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B1898 " --> pdb=" O LEU B1927 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9665 1.34 - 1.46: 4424 1.46 - 1.58: 15141 1.58 - 1.70: 16 1.70 - 1.82: 173 Bond restraints: 29419 Sorted by residual: bond pdb=" C1' DT C 51 " pdb=" N1 DT C 51 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.42e+00 bond pdb=" C3' DC C 54 " pdb=" O3' DC C 54 " ideal model delta sigma weight residual 1.435 1.413 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C4' DT C 50 " pdb=" O4' DT C 50 " ideal model delta sigma weight residual 1.446 1.462 -0.016 1.00e-02 1.00e+04 2.71e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 29414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 38506 1.33 - 2.67: 1085 2.67 - 4.00: 249 4.00 - 5.34: 24 5.34 - 6.67: 7 Bond angle restraints: 39871 Sorted by residual: angle pdb=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT C 50 " pdb=" C4 DT C 50 " pdb=" O4 DT C 50 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 52 " pdb=" C4 DT C 52 " pdb=" O4 DT C 52 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT C 53 " pdb=" C4 DT C 53 " pdb=" O4 DT C 53 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.59e+01 angle pdb=" O5' DT C 51 " pdb=" C5' DT C 51 " pdb=" C4' DT C 51 " ideal model delta sigma weight residual 109.40 112.50 -3.10 8.00e-01 1.56e+00 1.50e+01 ... (remaining 39866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15458 17.92 - 35.84: 1732 35.84 - 53.76: 513 53.76 - 71.68: 86 71.68 - 89.60: 36 Dihedral angle restraints: 17825 sinusoidal: 7400 harmonic: 10425 Sorted by residual: dihedral pdb=" CA CYS A1806 " pdb=" C CYS A1806 " pdb=" N ILE A1807 " pdb=" CA ILE A1807 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA B1717 " pdb=" C ALA B1717 " pdb=" N LEU B1718 " pdb=" CA LEU B1718 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR A 242 " pdb=" C THR A 242 " pdb=" N PRO A 243 " pdb=" CA PRO A 243 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 17822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3027 0.036 - 0.072: 978 0.072 - 0.109: 247 0.109 - 0.145: 84 0.145 - 0.181: 9 Chirality restraints: 4345 Sorted by residual: chirality pdb=" C3' DC C 54 " pdb=" C4' DC C 54 " pdb=" O3' DC C 54 " pdb=" C2' DC C 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" C3' DG C 63 " pdb=" C4' DG C 63 " pdb=" O3' DG C 63 " pdb=" C2' DG C 63 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C3' DA C 62 " pdb=" C4' DA C 62 " pdb=" O3' DA C 62 " pdb=" C2' DA C 62 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 4342 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1882 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO A1883 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A1883 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1883 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 178 " -0.205 9.50e-02 1.11e+02 9.23e-02 5.75e+00 pdb=" NE ARG A 178 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 178 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 178 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 178 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 71 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" CD GLU B 71 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU B 71 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 71 " 0.013 2.00e-02 2.50e+03 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7592 2.81 - 3.33: 25703 3.33 - 3.85: 42911 3.85 - 4.38: 50779 4.38 - 4.90: 89405 Nonbonded interactions: 216390 Sorted by model distance: nonbonded pdb=" O ASP B 920 " pdb=" OD1 ASP B 920 " model vdw 2.287 3.040 nonbonded pdb=" O ASP A 538 " pdb=" OD1 ASP A 538 " model vdw 2.305 3.040 nonbonded pdb=" O ASP B1344 " pdb=" OD1 ASP B1344 " model vdw 2.313 3.040 nonbonded pdb=" O TYR A1264 " pdb=" O ALA A1267 " model vdw 2.319 3.040 nonbonded pdb=" O LEU B 841 " pdb=" OD1 ASP B 845 " model vdw 2.345 3.040 ... (remaining 216385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 294 or resid 299 through 899 or resid 906 throug \ h 939 or resid 948 through 1418 or resid 1579 through 1594 or resid 1668 through \ 1945 or resid 2002 through 2004)) selection = (chain 'B' and (resid 1 through 750 or resid 761 through 2003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.480 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29447 Z= 0.189 Angle : 0.584 12.432 39907 Z= 0.316 Chirality : 0.040 0.181 4345 Planarity : 0.005 0.092 5228 Dihedral : 16.741 89.603 11111 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 16.01 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3598 helix: 1.58 (0.14), residues: 1417 sheet: 0.52 (0.23), residues: 504 loop : -1.12 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 178 TYR 0.021 0.002 TYR B1070 PHE 0.018 0.002 PHE B1580 TRP 0.015 0.001 TRP A1821 HIS 0.008 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (29419) covalent geometry : angle 0.56663 / 0.32 (39871) hydrogen bonds : bond 0.15336 / 10.41 ( 1130) hydrogen bonds : angle 5.46939 / 4.01 ( 3216) metal coordination : bond 0.00899 / 0.63 ( 28) metal coordination : angle 4.71110 / 3.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 296 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.8990 (p0) cc_final: 0.8783 (p0) REVERT: A 356 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8691 (mmt) REVERT: A 722 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8962 (tp) REVERT: A 734 ILE cc_start: 0.9308 (mm) cc_final: 0.9105 (mm) REVERT: A 818 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 875 ARG cc_start: 0.8947 (mtt90) cc_final: 0.8539 (mmt90) REVERT: B 250 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8407 (t-90) REVERT: B 671 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 772 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7376 (tmmt) REVERT: B 802 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: B 1190 ASP cc_start: 0.9013 (m-30) cc_final: 0.8797 (m-30) REVERT: B 1292 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8045 (mtt-85) REVERT: B 1388 LYS cc_start: 0.9204 (tptp) cc_final: 0.8910 (tptp) outliers start: 67 outliers final: 52 residues processed: 353 average time/residue: 0.2189 time to fit residues: 117.3296 Evaluate side-chains 350 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1579 CYS Chi-restraints excluded: chain A residue 1653 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1851 GLN Chi-restraints excluded: chain A residue 1880 SER Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1292 ARG Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.045719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.035884 restraints weight = 81660.272| |-----------------------------------------------------------------------------| r_work (start): 0.2222 rms_B_bonded: 1.84 r_work: 0.2136 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2038 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29447 Z= 0.136 Angle : 0.563 11.365 39907 Z= 0.293 Chirality : 0.041 0.178 4345 Planarity : 0.005 0.059 5228 Dihedral : 8.234 58.862 4232 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 16.04 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3598 helix: 1.88 (0.14), residues: 1427 sheet: 0.73 (0.23), residues: 491 loop : -0.98 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 265 TYR 0.017 0.001 TYR B1070 PHE 0.015 0.001 PHE B1147 TRP 0.015 0.001 TRP B1781 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (29419) covalent geometry : angle 0.55112 / 0.29 (39871) hydrogen bonds : bond 0.06093 / 4.08 ( 1130) hydrogen bonds : angle 4.31699 / 3.16 ( 3216) metal coordination : bond 0.00578 / 0.39 ( 28) metal coordination : angle 3.90978 / 2.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 318 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9071 (tp) REVERT: A 867 LEU cc_start: 0.9172 (mp) cc_final: 0.8951 (mp) REVERT: A 875 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8536 (mmt90) REVERT: A 1687 MET cc_start: 0.9236 (mmm) cc_final: 0.8810 (mtp) REVERT: A 1945 GLN cc_start: 0.8941 (tp40) cc_final: 0.8541 (tm-30) REVERT: B 250 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8425 (t-90) REVERT: B 671 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8640 (pp) REVERT: B 687 GLU cc_start: 0.8131 (tp30) cc_final: 0.7924 (mm-30) REVERT: B 749 LYS cc_start: 0.9254 (tppt) cc_final: 0.8929 (tppt) REVERT: B 772 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7624 (tmmt) REVERT: B 802 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: B 1388 LYS cc_start: 0.9202 (tptp) cc_final: 0.8838 (tptp) REVERT: B 1582 TYR cc_start: 0.8172 (t80) cc_final: 0.7848 (t80) REVERT: B 1583 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8099 (mtm110) outliers start: 75 outliers final: 40 residues processed: 383 average time/residue: 0.2154 time to fit residues: 124.0352 Evaluate side-chains 345 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1320 ASP Chi-restraints excluded: chain B residue 1362 ARG Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [252, 65, 101, 242, 202, 204, 198, 291, 116, 54, 338] chunk 252 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 291 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.045762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2228 r_free = 0.2228 target = 0.035921 restraints weight = 81819.401| |-----------------------------------------------------------------------------| r_work (start): 0.2224 rms_B_bonded: 1.84 r_work: 0.2138 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2038 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29447 Z= 0.140 Angle : 0.552 11.026 39907 Z= 0.286 Chirality : 0.041 0.176 4345 Planarity : 0.004 0.058 5228 Dihedral : 7.341 59.617 4152 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.80 % Allowed : 16.34 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3598 helix: 1.91 (0.14), residues: 1434 sheet: 0.78 (0.23), residues: 490 loop : -0.91 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1645 TYR 0.018 0.001 TYR B1070 PHE 0.014 0.001 PHE B1147 TRP 0.013 0.001 TRP A1821 HIS 0.006 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (29419) covalent geometry : angle 0.53863 / 0.29 (39871) hydrogen bonds : bond 0.05872 / 3.92 ( 1130) hydrogen bonds : angle 4.17435 / 3.04 ( 3216) metal coordination : bond 0.00566 / 0.38 ( 28) metal coordination : angle 4.02506 / 2.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 313 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8377 (ttt-90) REVERT: A 722 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9237 (tt) REVERT: A 875 ARG cc_start: 0.8889 (mtt90) cc_final: 0.8598 (mmt90) REVERT: A 1687 MET cc_start: 0.9236 (mmm) cc_final: 0.8838 (mtp) REVERT: A 1945 GLN cc_start: 0.8955 (tp40) cc_final: 0.8546 (tm-30) REVERT: B 250 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8466 (t-90) REVERT: B 494 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8566 (mmt-90) REVERT: B 671 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8677 (pp) REVERT: B 749 LYS cc_start: 0.9181 (tppt) cc_final: 0.8847 (tppt) REVERT: B 772 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7609 (tmmt) REVERT: B 802 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: B 1238 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.9175 (ttm170) REVERT: B 1388 LYS cc_start: 0.9211 (tptp) cc_final: 0.8851 (tptp) REVERT: B 1406 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8641 (tpp80) REVERT: B 1582 TYR cc_start: 0.8181 (t80) cc_final: 0.7912 (t80) REVERT: B 1583 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8154 (mtm110) outliers start: 85 outliers final: 56 residues processed: 381 average time/residue: 0.2168 time to fit residues: 124.7321 Evaluate side-chains 365 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1238 ARG Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1911 VAL Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [39, 110, 344, 24, 30, 45, 162, 12, 138, 67, 108] chunk 39 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.0070 chunk 162 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.4980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1119 HIS B1808 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.047176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.037218 restraints weight = 80899.539| |-----------------------------------------------------------------------------| r_work (start): 0.2264 rms_B_bonded: 1.85 r_work: 0.2179 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2081 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29447 Z= 0.108 Angle : 0.517 14.916 39907 Z= 0.267 Chirality : 0.039 0.173 4345 Planarity : 0.004 0.053 5228 Dihedral : 7.077 59.678 4145 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 16.86 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3598 helix: 2.08 (0.14), residues: 1437 sheet: 0.81 (0.23), residues: 493 loop : -0.83 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1406 TYR 0.013 0.001 TYR A1007 PHE 0.011 0.001 PHE B1147 TRP 0.012 0.001 TRP A1821 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (29419) covalent geometry : angle 0.50769 / 0.27 (39871) hydrogen bonds : bond 0.04792 / 3.19 ( 1130) hydrogen bonds : angle 3.98337 / 2.89 ( 3216) metal coordination : bond 0.00460 / 0.32 ( 28) metal coordination : angle 3.33127 / 2.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 313 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 867 LEU cc_start: 0.9167 (mp) cc_final: 0.8805 (pt) REVERT: A 875 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8539 (mmt90) REVERT: A 919 ASN cc_start: 0.8400 (t0) cc_final: 0.7892 (t0) REVERT: A 1687 MET cc_start: 0.9193 (mmm) cc_final: 0.8900 (mtp) REVERT: B 250 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8375 (t-90) REVERT: B 671 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 749 LYS cc_start: 0.9121 (tppt) cc_final: 0.8816 (tppt) REVERT: B 772 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7618 (tmmt) REVERT: B 1375 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8568 (mm-40) REVERT: B 1388 LYS cc_start: 0.9201 (tptp) cc_final: 0.8834 (tptp) REVERT: B 1733 ARG cc_start: 0.9016 (tmm-80) cc_final: 0.8791 (tmm-80) REVERT: B 1913 ARG cc_start: 0.9023 (ttp-110) cc_final: 0.8589 (ttp-110) outliers start: 78 outliers final: 50 residues processed: 372 average time/residue: 0.2201 time to fit residues: 124.0825 Evaluate side-chains 358 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1911 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [298, 22, 243, 167, 345, 7, 140, 252, 37, 66, 2] chunk 298 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 243 optimal weight: 0.0370 chunk 167 optimal weight: 0.7980 chunk 345 optimal weight: 0.5980 chunk 7 optimal weight: 0.0570 chunk 140 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.046923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.037042 restraints weight = 81347.064| |-----------------------------------------------------------------------------| r_work (start): 0.2255 rms_B_bonded: 1.86 r_work: 0.2170 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2072 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29447 Z= 0.117 Angle : 0.520 12.458 39907 Z= 0.269 Chirality : 0.040 0.235 4345 Planarity : 0.004 0.050 5228 Dihedral : 6.898 59.655 4138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.64 % Allowed : 17.06 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3598 helix: 2.07 (0.14), residues: 1440 sheet: 0.92 (0.23), residues: 490 loop : -0.81 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 178 TYR 0.022 0.001 TYR B1007 PHE 0.013 0.001 PHE A 15 TRP 0.011 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (29419) covalent geometry : angle 0.51089 / 0.27 (39871) hydrogen bonds : bond 0.04947 / 3.27 ( 1130) hydrogen bonds : angle 3.97492 / 2.88 ( 3216) metal coordination : bond 0.00497 / 0.35 ( 28) metal coordination : angle 3.28282 / 2.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 309 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8341 (ttt-90) REVERT: A 582 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 875 ARG cc_start: 0.8903 (mtt90) cc_final: 0.8547 (mmt90) REVERT: A 919 ASN cc_start: 0.8412 (t0) cc_final: 0.7908 (t0) REVERT: A 1563 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 1597 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: A 1687 MET cc_start: 0.9192 (mmm) cc_final: 0.8931 (mtp) REVERT: A 1945 GLN cc_start: 0.8922 (tp40) cc_final: 0.8575 (tm-30) REVERT: B 250 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.8380 (t-90) REVERT: B 256 ASP cc_start: 0.6940 (t70) cc_final: 0.6593 (t70) REVERT: B 671 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8573 (pp) REVERT: B 749 LYS cc_start: 0.9111 (tppt) cc_final: 0.8806 (tppt) REVERT: B 772 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7614 (tmmt) REVERT: B 802 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: B 1162 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8424 (mtt-85) REVERT: B 1388 LYS cc_start: 0.9185 (tptp) cc_final: 0.8821 (tptp) REVERT: B 1406 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8669 (tpp80) REVERT: B 1913 ARG cc_start: 0.9021 (ttp-110) cc_final: 0.8559 (ttp-110) outliers start: 80 outliers final: 61 residues processed: 374 average time/residue: 0.2231 time to fit residues: 126.0284 Evaluate side-chains 370 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [11, 220, 292, 113, 247, 316, 9, 81, 218, 311, 281] chunk 11 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 316 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 218 optimal weight: 0.0060 chunk 311 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.047012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.037147 restraints weight = 81087.842| |-----------------------------------------------------------------------------| r_work (start): 0.2258 rms_B_bonded: 1.84 r_work: 0.2174 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29447 Z= 0.118 Angle : 0.526 11.580 39907 Z= 0.271 Chirality : 0.040 0.174 4345 Planarity : 0.004 0.050 5228 Dihedral : 6.818 59.318 4136 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.03 % Allowed : 17.36 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3598 helix: 2.06 (0.14), residues: 1446 sheet: 0.91 (0.24), residues: 492 loop : -0.79 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 210 TYR 0.021 0.001 TYR B1582 PHE 0.013 0.001 PHE B1147 TRP 0.012 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (29419) covalent geometry : angle 0.51759 / 0.27 (39871) hydrogen bonds : bond 0.04907 / 3.24 ( 1130) hydrogen bonds : angle 3.96246 / 2.86 ( 3216) metal coordination : bond 0.00491 / 0.34 ( 28) metal coordination : angle 3.20870 / 2.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 303 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8333 (ttt-90) REVERT: A 582 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 875 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8452 (mmt90) REVERT: A 919 ASN cc_start: 0.8400 (t0) cc_final: 0.7895 (t0) REVERT: A 1563 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8193 (mm-30) REVERT: A 1597 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.7906 (mm-40) REVERT: A 1687 MET cc_start: 0.9194 (mmm) cc_final: 0.8939 (mtp) REVERT: A 1945 GLN cc_start: 0.8922 (tp40) cc_final: 0.8526 (tm-30) REVERT: B 250 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8368 (t-90) REVERT: B 671 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8567 (pp) REVERT: B 749 LYS cc_start: 0.9125 (tppt) cc_final: 0.8792 (tppt) REVERT: B 772 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7623 (tmmt) REVERT: B 802 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: B 1162 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8427 (mtt-85) REVERT: B 1388 LYS cc_start: 0.9176 (tptp) cc_final: 0.8795 (tptp) REVERT: B 1913 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8535 (ttp-110) outliers start: 92 outliers final: 70 residues processed: 378 average time/residue: 0.2176 time to fit residues: 124.8944 Evaluate side-chains 377 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 299 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [36, 292, 70, 155, 115, 311, 307, 347, 93, 302, 122] chunk 36 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 311 optimal weight: 5.9990 chunk 307 optimal weight: 0.7980 chunk 347 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.045723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.035869 restraints weight = 81590.634| |-----------------------------------------------------------------------------| r_work (start): 0.2222 rms_B_bonded: 1.84 r_work: 0.2136 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2037 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29447 Z= 0.162 Angle : 0.569 10.999 39907 Z= 0.294 Chirality : 0.041 0.182 4345 Planarity : 0.004 0.055 5228 Dihedral : 6.931 59.923 4136 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 17.56 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3598 helix: 1.97 (0.14), residues: 1436 sheet: 0.86 (0.23), residues: 495 loop : -0.79 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 210 TYR 0.021 0.002 TYR B1582 PHE 0.017 0.002 PHE A1930 TRP 0.013 0.001 TRP A1821 HIS 0.007 0.001 HIS A1901 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (29419) covalent geometry : angle 0.55678 / 0.29 (39871) hydrogen bonds : bond 0.05807 / 3.83 ( 1130) hydrogen bonds : angle 4.05683 / 2.93 ( 3216) metal coordination : bond 0.00652 / 0.44 ( 28) metal coordination : angle 3.95879 / 2.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 300 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8393 (ttt-90) REVERT: A 582 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 867 LEU cc_start: 0.9151 (mp) cc_final: 0.8720 (pt) REVERT: A 875 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8463 (mmt90) REVERT: A 919 ASN cc_start: 0.8536 (t0) cc_final: 0.8009 (t0) REVERT: A 1561 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6763 (mt-10) REVERT: A 1563 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 1597 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: A 1687 MET cc_start: 0.9230 (mmm) cc_final: 0.8916 (mtp) REVERT: A 1945 GLN cc_start: 0.8977 (tp40) cc_final: 0.8581 (tm-30) REVERT: B 208 MET cc_start: 0.9296 (mmm) cc_final: 0.8844 (mmt) REVERT: B 250 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8373 (t-90) REVERT: B 256 ASP cc_start: 0.7246 (t0) cc_final: 0.6715 (t70) REVERT: B 671 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8619 (pp) REVERT: B 749 LYS cc_start: 0.9142 (tppt) cc_final: 0.8814 (tppt) REVERT: B 772 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7645 (tmmt) REVERT: B 802 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: B 895 LEU cc_start: 0.8737 (pp) cc_final: 0.8450 (mm) REVERT: B 1913 ARG cc_start: 0.9024 (ttp-110) cc_final: 0.8583 (ttp-110) outliers start: 94 outliers final: 71 residues processed: 379 average time/residue: 0.2165 time to fit residues: 124.8205 Evaluate side-chains 374 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1383 ILE Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [297, 241, 298, 324, 268, 84, 296, 235, 25, 318, 80] chunk 297 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 318 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.046820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.036923 restraints weight = 81035.954| |-----------------------------------------------------------------------------| r_work (start): 0.2257 rms_B_bonded: 1.84 r_work: 0.2172 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2074 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29447 Z= 0.116 Angle : 0.535 10.827 39907 Z= 0.277 Chirality : 0.040 0.175 4345 Planarity : 0.004 0.053 5228 Dihedral : 6.830 59.715 4136 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 18.38 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3598 helix: 2.08 (0.14), residues: 1436 sheet: 0.96 (0.24), residues: 487 loop : -0.77 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 210 TYR 0.022 0.001 TYR B1582 PHE 0.012 0.001 PHE B1147 TRP 0.014 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (29419) covalent geometry : angle 0.52447 / 0.28 (39871) hydrogen bonds : bond 0.04938 / 3.27 ( 1130) hydrogen bonds : angle 3.96606 / 2.86 ( 3216) metal coordination : bond 0.00516 / 0.36 ( 28) metal coordination : angle 3.54226 / 2.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8349 (ttt-90) REVERT: A 582 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8527 (p) REVERT: A 867 LEU cc_start: 0.9191 (mp) cc_final: 0.8749 (pt) REVERT: A 875 ARG cc_start: 0.8882 (mtt90) cc_final: 0.8471 (mmt90) REVERT: A 919 ASN cc_start: 0.8492 (t0) cc_final: 0.7967 (t0) REVERT: A 1561 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6762 (mt-10) REVERT: A 1563 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 1597 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.7922 (mm-40) REVERT: A 1687 MET cc_start: 0.9206 (mmm) cc_final: 0.8939 (mtp) REVERT: A 1945 GLN cc_start: 0.8963 (tp40) cc_final: 0.8586 (tm-30) REVERT: B 208 MET cc_start: 0.9284 (mmm) cc_final: 0.8880 (mmt) REVERT: B 250 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8391 (t-90) REVERT: B 494 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8648 (mmt-90) REVERT: B 671 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8560 (pp) REVERT: B 749 LYS cc_start: 0.9110 (tppt) cc_final: 0.8784 (tppt) REVERT: B 772 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7694 (tmmt) REVERT: B 802 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 895 LEU cc_start: 0.8798 (pp) cc_final: 0.8541 (mm) REVERT: B 1388 LYS cc_start: 0.9149 (tptp) cc_final: 0.8857 (tptp) REVERT: B 1757 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8453 (mp0) REVERT: B 1913 ARG cc_start: 0.9029 (ttp-110) cc_final: 0.8584 (ttp-110) outliers start: 82 outliers final: 65 residues processed: 370 average time/residue: 0.2165 time to fit residues: 121.7814 Evaluate side-chains 369 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1383 ILE Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [154, 342, 335, 359, 336, 205, 273, 306, 133, 188, 316] chunk 154 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 336 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 316 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 579 GLN B1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.046763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.036898 restraints weight = 81277.390| |-----------------------------------------------------------------------------| r_work (start): 0.2256 rms_B_bonded: 1.84 r_work: 0.2172 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2073 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29447 Z= 0.121 Angle : 0.541 10.420 39907 Z= 0.281 Chirality : 0.040 0.176 4345 Planarity : 0.004 0.052 5228 Dihedral : 6.793 59.620 4136 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.83 % Allowed : 18.35 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3598 helix: 2.07 (0.14), residues: 1438 sheet: 1.00 (0.24), residues: 481 loop : -0.75 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1645 TYR 0.020 0.001 TYR B1582 PHE 0.012 0.001 PHE B1147 TRP 0.012 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (29419) covalent geometry : angle 0.53187 / 0.28 (39871) hydrogen bonds : bond 0.04933 / 3.26 ( 1130) hydrogen bonds : angle 3.95895 / 2.85 ( 3216) metal coordination : bond 0.00524 / 0.36 ( 28) metal coordination : angle 3.41636 / 2.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 302 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8348 (ttt-90) REVERT: A 582 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 867 LEU cc_start: 0.9166 (mp) cc_final: 0.8740 (pt) REVERT: A 875 ARG cc_start: 0.8881 (mtt90) cc_final: 0.8462 (mmt90) REVERT: A 919 ASN cc_start: 0.8502 (t0) cc_final: 0.7981 (t0) REVERT: A 958 ASN cc_start: 0.8382 (p0) cc_final: 0.8132 (p0) REVERT: A 1561 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 1563 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 1597 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: A 1687 MET cc_start: 0.9207 (mmm) cc_final: 0.8955 (mtp) REVERT: A 1945 GLN cc_start: 0.8973 (tp40) cc_final: 0.8596 (tm-30) REVERT: B 208 MET cc_start: 0.9284 (mmm) cc_final: 0.8884 (mmt) REVERT: B 250 HIS cc_start: 0.8829 (OUTLIER) cc_final: 0.8431 (t-90) REVERT: B 494 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8687 (mmt-90) REVERT: B 671 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 749 LYS cc_start: 0.9114 (tppt) cc_final: 0.8783 (tppt) REVERT: B 772 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7630 (tmmt) REVERT: B 802 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: B 895 LEU cc_start: 0.8805 (pp) cc_final: 0.8544 (mm) REVERT: B 1162 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8429 (mtt-85) REVERT: B 1388 LYS cc_start: 0.9150 (tptp) cc_final: 0.8842 (tptp) REVERT: B 1913 ARG cc_start: 0.9022 (ttp-110) cc_final: 0.8565 (ttp-110) outliers start: 86 outliers final: 71 residues processed: 374 average time/residue: 0.2185 time to fit residues: 123.8429 Evaluate side-chains 375 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 296 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1383 ILE Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [350, 81, 27, 232, 249, 316, 327, 223, 209, 158, 203] chunk 350 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1607 ASN B1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.045535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.035698 restraints weight = 81367.642| |-----------------------------------------------------------------------------| r_work (start): 0.2217 rms_B_bonded: 1.83 r_work: 0.2130 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2031 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29447 Z= 0.169 Angle : 0.595 10.142 39907 Z= 0.309 Chirality : 0.042 0.182 4345 Planarity : 0.005 0.054 5228 Dihedral : 6.906 59.865 4136 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.64 % Allowed : 18.68 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3598 helix: 1.94 (0.14), residues: 1435 sheet: 0.96 (0.24), residues: 475 loop : -0.81 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 178 TYR 0.021 0.002 TYR B1070 PHE 0.020 0.002 PHE A1930 TRP 0.012 0.001 TRP A1821 HIS 0.007 0.001 HIS A1901 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (29419) covalent geometry : angle 0.58433 / 0.31 (39871) hydrogen bonds : bond 0.05969 / 3.93 ( 1130) hydrogen bonds : angle 4.08053 / 2.95 ( 3216) metal coordination : bond 0.00715 / 0.49 ( 28) metal coordination : angle 3.85794 / 2.55 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8406 (ttt-90) REVERT: A 582 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 867 LEU cc_start: 0.9155 (mp) cc_final: 0.8725 (pt) REVERT: A 875 ARG cc_start: 0.8862 (mtt90) cc_final: 0.8424 (mmt90) REVERT: A 919 ASN cc_start: 0.8561 (t0) cc_final: 0.8055 (t0) REVERT: A 1597 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.7977 (mm-40) REVERT: A 1687 MET cc_start: 0.9239 (mmm) cc_final: 0.8931 (mtp) REVERT: A 1945 GLN cc_start: 0.9004 (tp40) cc_final: 0.8600 (tm-30) REVERT: B 208 MET cc_start: 0.9275 (mmm) cc_final: 0.8813 (mmt) REVERT: B 250 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8439 (t-90) REVERT: B 345 ASP cc_start: 0.7972 (m-30) cc_final: 0.7548 (m-30) REVERT: B 494 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8676 (mmt-90) REVERT: B 671 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8660 (pp) REVERT: B 749 LYS cc_start: 0.9151 (tppt) cc_final: 0.8800 (tppt) REVERT: B 772 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7673 (tmmt) REVERT: B 802 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: B 895 LEU cc_start: 0.8838 (pp) cc_final: 0.8610 (mm) REVERT: B 1388 LYS cc_start: 0.9164 (tptp) cc_final: 0.8865 (tptp) REVERT: B 1913 ARG cc_start: 0.9036 (ttp-110) cc_final: 0.8570 (ttp-110) outliers start: 80 outliers final: 70 residues processed: 358 average time/residue: 0.2177 time to fit residues: 118.7251 Evaluate side-chains 368 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 291 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 GLN Chi-restraints excluded: chain A residue 1365 GLU Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1597 GLN Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1881 ASP Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1919 ASP Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1110 CYS Chi-restraints excluded: chain B residue 1298 TRP Chi-restraints excluded: chain B residue 1378 TYR Chi-restraints excluded: chain B residue 1383 ILE Chi-restraints excluded: chain B residue 1696 HIS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [268, 174, 170, 58, 317, 137, 250, 331, 62, 238, 38] chunk 268 optimal weight: 2.9990 chunk 174 optimal weight: 0.0010 chunk 170 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 317 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 579 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.046305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.036447 restraints weight = 81959.520| |-----------------------------------------------------------------------------| r_work (start): 0.2241 rms_B_bonded: 1.85 r_work: 0.2155 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2056 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29447 Z= 0.130 Angle : 0.559 10.227 39907 Z= 0.290 Chirality : 0.040 0.177 4345 Planarity : 0.004 0.054 5228 Dihedral : 6.817 59.878 4135 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.60 % Allowed : 18.81 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3598 helix: 2.03 (0.14), residues: 1437 sheet: 0.91 (0.24), residues: 487 loop : -0.77 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 178 TYR 0.021 0.001 TYR B1582 PHE 0.013 0.001 PHE B1147 TRP 0.014 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (29419) covalent geometry : angle 0.54928 / 0.29 (39871) hydrogen bonds : bond 0.05248 / 3.47 ( 1130) hydrogen bonds : angle 4.01623 / 2.90 ( 3216) metal coordination : bond 0.00553 / 0.38 ( 28) metal coordination : angle 3.55700 / 2.39 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6067.06 seconds wall clock time: 104 minutes 28.62 seconds (6268.62 seconds total)