Starting phenix.real_space_refine on Thu Oct 29 09:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdv_65907/10_2026/9wdv_65907.map" } resolution = 3.45 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= 0.003 sd= 0.484 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 33 5.49 5 Mg 1 5.21 5 S 120 5.16 5 C 19386 2.51 5 N 5553 2.21 5 O 5864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 326 residue(s): 0.03s 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: 30965 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1918, 15167 Classifications: {'peptide': 1918} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1808} Chain breaks: 4 Chain: "B" Number of atoms: 15126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1912, 15126 Classifications: {'peptide': 1912} Link IDs: {'PCIS': 3, 'PTRANS': 106, 'TRANS': 1802} Chain breaks: 5 Chain: "C" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' MG': 1, ' ZN': 4, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8542 SG CYS A1110 60.994 109.370 63.638 1.00 72.86 S ATOM 8562 SG CYS A1113 62.289 105.955 64.473 1.00 67.02 S ATOM 8657 SG CYS A1125 60.197 107.249 66.892 1.00 68.68 S ATOM 8681 SG CYS A1128 63.423 108.410 66.152 1.00 59.22 S ATOM 5015 SG CYS A 646 68.081 96.747 62.531 1.00 71.78 S ATOM 5035 SG CYS A 649 67.615 99.840 61.549 1.00 62.55 S ATOM 5899 SG CYS A 770 70.695 98.931 63.235 1.00 76.60 S ATOM 5921 SG CYS A 773 67.596 99.745 65.214 1.00 77.98 S ATOM 13966 SG CYS A1799 83.082 83.218 36.856 1.00 94.29 S ATOM 14023 SG CYS A1806 81.722 79.559 36.727 1.00 80.78 S ATOM 11719 SG CYS A1509 105.318 60.447 53.131 1.00125.00 S ATOM 11737 SG CYS A1512 106.728 61.634 50.444 1.00133.20 S ATOM 11842 SG CYS A1528 105.262 57.373 51.878 1.00152.39 S ATOM 11864 SG CYS A1531 105.497 58.997 49.106 1.00154.90 S ATOM 23638 SG CYS B1110 22.697 46.164 111.111 1.00 56.06 S ATOM 23658 SG CYS B1113 26.345 46.449 111.079 1.00 72.77 S ATOM 23753 SG CYS B1125 24.676 47.646 108.211 1.00 78.37 S ATOM 23777 SG CYS B1128 24.311 43.866 109.395 1.00 55.87 S ATOM 20138 SG CYS B 646 32.974 42.355 117.152 1.00 80.79 S ATOM 20158 SG CYS B 649 29.507 42.381 117.817 1.00 57.82 S ATOM 21034 SG CYS B 770 31.079 39.114 116.904 1.00 70.28 S ATOM 21056 SG CYS B 773 30.005 41.291 114.586 1.00 71.36 S ATOM 29092 SG CYS B1799 57.242 44.875 154.247 1.00 84.96 S ATOM 29120 SG CYS B1803 57.969 46.936 151.989 1.00 65.70 S ATOM 29149 SG CYS B1806 60.579 46.100 151.641 1.00 79.05 S ATOM 26845 SG CYS B1509 77.053 23.547 130.647 1.00 69.28 S ATOM 26863 SG CYS B1512 75.839 25.387 134.349 1.00 82.30 S ATOM 26968 SG CYS B1528 80.004 25.165 132.649 1.00 73.54 S ATOM 26990 SG CYS B1531 78.260 22.574 133.786 1.00 75.02 S Time building chain proxies: 6.01, per 1000 atoms: 0.19 Number of scatterers: 30965 At special positions: 0 Unit cell: (127.68, 126.72, 176.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 120 16.00 P 33 15.00 Mg 1 11.99 O 5864 8.00 N 5553 7.00 C 19386 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 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 773 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 649 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 646 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1799 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1806 " pdb=" ZN A2004 " 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 ZN A2004 " - pdb=" SG CYS A1512 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1125 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1113 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1110 " pdb=" ZN B2004 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 773 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 646 " pdb="ZN ZN B2004 " - pdb=" SG CYS B 649 " pdb=" ZN B2005 " pdb="ZN ZN B2005 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1803 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1806 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1799 " pdb=" ZN B2006 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1509 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1531 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1528 " pdb="ZN ZN B2006 " - pdb=" SG CYS B1512 " Number of angles added : 39 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7114 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 25 sheets defined 43.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 removed outlier: 3.543A pdb=" N GLY A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.538A pdb=" N GLU A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.572A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.742A pdb=" N VAL A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) 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 293 removed outlier: 3.600A pdb=" N SER A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 344 through 356 removed outlier: 4.207A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 417 through 431 removed outlier: 3.675A pdb=" N GLN A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.025A pdb=" N LYS A 452 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 515 through 535 Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.802A pdb=" N ALA A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Proline residue: A 575 - end of helix removed outlier: 3.607A pdb=" N GLN A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.642A pdb=" N HIS A 679 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 680 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 680' Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 863 removed outlier: 3.517A pdb=" N ASP A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 4.183A pdb=" N THR A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 900 removed outlier: 4.531A pdb=" N LEU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 906 Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' 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: 4.617A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.615A 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: 3.789A pdb=" N ALA A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 removed outlier: 3.836A 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 1065 Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.725A pdb=" N GLU A1073 " --> pdb=" O ARG A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1090 removed outlier: 4.223A pdb=" N GLY A1089 " --> pdb=" O HIS A1086 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1090 " --> pdb=" O ARG A1087 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1086 through 1090' Processing helix chain 'A' and resid 1092 through 1095 removed outlier: 3.607A 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 1146 Processing helix chain 'A' and resid 1146 through 1159 Processing helix chain 'A' and resid 1176 through 1186 Processing helix chain 'A' and resid 1193 through 1201 Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 3.546A pdb=" N TYR A1235 " --> pdb=" O GLN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.725A pdb=" N ALA A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1275 Processing helix chain 'A' and resid 1287 through 1314 removed outlier: 3.542A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A1313 " --> pdb=" O GLN A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1321 Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.892A pdb=" N GLU A1351 " --> pdb=" O ILE A1347 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A1356 " --> pdb=" O ALA A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1368 removed outlier: 3.712A pdb=" N ASP A1361 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A1368 " --> pdb=" O ILE A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 3.552A pdb=" N GLN A1375 " --> pdb=" O GLN A1371 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.825A pdb=" N GLN A1393 " --> pdb=" O GLU A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1397 Processing helix chain 'A' and resid 1403 through 1411 Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 4.243A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1647 removed outlier: 3.878A pdb=" N SER A1646 " --> pdb=" O SER A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1718 Processing helix chain 'A' and resid 1750 through 1756 removed outlier: 3.589A pdb=" N GLY A1756 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1775 removed outlier: 3.536A pdb=" N LEU A1775 " --> pdb=" O LEU A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1787 removed outlier: 3.502A pdb=" N LEU A1787 " --> pdb=" O LEU A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1814 removed outlier: 4.637A pdb=" N ARG A1814 " --> pdb=" O GLY A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.553A pdb=" N VAL A1832 " --> pdb=" O LEU A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1866 removed outlier: 3.572A pdb=" N ALA A1866 " --> pdb=" O ASP A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1908 through 1917 Processing helix chain 'A' and resid 1929 through 1935 Processing helix chain 'A' and resid 1935 through 1944 removed outlier: 3.509A pdb=" N ARG A1939 " --> pdb=" O ARG A1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.611A pdb=" N PHE B 9 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.052A pdb=" N ARG B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.583A pdb=" N PHE B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.631A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.903A 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 291 removed outlier: 3.520A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.671A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.877A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 374 through 393 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 415 through 431 Processing helix chain 'B' and resid 446 through 451 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 561 through 574 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 676 through 680 Processing helix chain 'B' and resid 688 through 692 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 863 removed outlier: 3.672A pdb=" N GLU B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 883 removed outlier: 4.169A pdb=" N ILE B 873 " --> pdb=" O SER B 869 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 899 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.668A pdb=" N LEU B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 934 Processing helix chain 'B' and resid 950 through 953 Processing helix chain 'B' and resid 969 through 993 removed outlier: 3.724A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1016 through 1028 removed outlier: 3.715A 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 1066 Processing helix chain 'B' and resid 1069 through 1085 removed outlier: 3.525A pdb=" N GLU B1073 " --> pdb=" O ARG B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1139 through 1146 Processing helix chain 'B' and resid 1146 through 1159 removed outlier: 3.814A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1186 removed outlier: 3.720A pdb=" N ARG B1180 " --> pdb=" O ASP B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1201 Processing helix chain 'B' and resid 1209 through 1213 removed outlier: 3.874A pdb=" N VAL B1213 " --> pdb=" O THR B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1240 Processing helix chain 'B' and resid 1259 through 1268 removed outlier: 3.600A pdb=" N TYR B1264 " --> pdb=" O SER B1260 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B1265 " --> pdb=" O HIS B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1275 removed outlier: 4.376A pdb=" N ILE B1272 " --> pdb=" O HIS B1268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B1275 " --> pdb=" O ALA B1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1314 removed outlier: 3.801A pdb=" N LEU B1293 " --> pdb=" O ILE B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 removed outlier: 3.704A pdb=" N LEU B1322 " --> pdb=" O GLY B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1339 removed outlier: 3.675A pdb=" N HIS B1339 " --> pdb=" O LYS B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1344 through 1356 removed outlier: 3.660A pdb=" N ARG B1348 " --> pdb=" O ASP B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1368 removed outlier: 4.502A pdb=" N ARG B1360 " --> pdb=" O THR B1356 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B1361 " --> pdb=" O GLN B1357 " (cutoff:3.500A) removed outlier: 3.880A 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 1393 removed outlier: 3.811A pdb=" N GLN B1393 " --> pdb=" O GLU B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1397 Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1451 through 1458 removed outlier: 4.243A pdb=" N PHE B1456 " --> pdb=" O ASP B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1540 removed outlier: 3.830A pdb=" N PHE B1540 " --> pdb=" O LYS B1537 " (cutoff:3.500A) Processing helix chain 'B' and resid 1641 through 1647 Processing helix chain 'B' and resid 1696 through 1718 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 1782 through 1788 Processing helix chain 'B' and resid 1794 through 1798 Processing helix chain 'B' and resid 1820 through 1833 removed outlier: 3.614A pdb=" N LEU B1831 " --> pdb=" O TYR B1827 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B1832 " --> pdb=" O LEU B1828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1843 through 1847 removed outlier: 3.805A pdb=" N LYS B1846 " --> pdb=" O GLY B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1868 removed outlier: 3.617A pdb=" N ALA B1866 " --> pdb=" O ASP B1862 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B1867 " --> pdb=" O ASP B1863 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B1868 " --> pdb=" O VAL B1864 " (cutoff:3.500A) Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.613A pdb=" N MET B1912 " --> pdb=" O GLU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1944 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.973A pdb=" N PHE A 591 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL A1252 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 593 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR A1254 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 595 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS A1256 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 597 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A1224 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.468A 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: 6.817A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 363 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU A 406 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 131 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA5, first strand: chain 'A' and resid 604 through 608 removed outlier: 6.763A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 4.318A 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 652 through 657 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 652 through 657 current: chain 'A' and resid 728 through 731 Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA7, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.763A pdb=" N GLY A1137 " --> pdb=" O PHE A1107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1423 through 1432 removed outlier: 6.648A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.594A 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 1515 through 1518 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1515 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=AB1, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AB2, first strand: chain 'A' and resid 1493 through 1494 removed outlier: 7.588A pdb=" N ILE A1493 " --> pdb=" O ASP A1634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1872 through 1876 removed outlier: 3.743A pdb=" N VAL A1899 " --> pdb=" O PRO A1883 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A1895 " --> pdb=" O GLU A1887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.789A pdb=" N PHE B 591 " --> pdb=" O SER B1250 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL B1252 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 593 " --> pdb=" O VAL B1252 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B1254 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 595 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N CYS B1256 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 597 " --> pdb=" O CYS B1256 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 821 " --> pdb=" O LEU B1205 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B1207 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 823 " --> pdb=" O VAL B1207 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B1168 " --> pdb=" O SER B1206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.708A pdb=" N PHE B 235 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE B 363 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 406 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU B 365 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER B 408 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE B 367 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AB8, first strand: chain 'B' and resid 604 through 608 removed outlier: 6.775A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.376A 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: 3.526A pdb=" N GLN B 657 " --> pdb=" O LEU B 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 668 through 671 current: chain 'B' and resid 728 through 731 Processing sheet with id=AB9, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AC1, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AC2, first strand: chain 'B' and resid 1116 through 1117 removed outlier: 3.817A pdb=" N GLY B1137 " --> pdb=" O PHE B1107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1423 through 1431 removed outlier: 6.586A pdb=" N SER B1445 " --> pdb=" O VAL B1428 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU B1430 " --> pdb=" O GLU B1443 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU B1443 " --> pdb=" O LEU B1430 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1443 through 1450 current: chain 'B' and resid 1469 through 1477 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1469 through 1477 current: chain 'B' and resid 1515 through 1518 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1515 through 1518 current: chain 'B' and resid 1585 through 1602 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1585 through 1602 current: chain 'B' and resid 1637 through 1640 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1637 through 1640 current: chain 'B' and resid 1736 through 1743 Processing sheet with id=AC4, first strand: chain 'B' and resid 1484 through 1486 Processing sheet with id=AC5, first strand: chain 'B' and resid 1493 through 1494 removed outlier: 7.425A pdb=" N ILE B1493 " --> pdb=" O ASP B1634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 1526 through 1527 Processing sheet with id=AC7, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 6.554A pdb=" N LYS B1889 " --> pdb=" O GLU B1893 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU B1893 " --> pdb=" O LYS B1889 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N ARG B1925 " --> pdb=" O LEU B1894 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B1896 " --> pdb=" O ARG B1925 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU B1927 " --> pdb=" O ARG B1896 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B1898 " --> pdb=" O LEU B1927 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10370 1.34 - 1.46: 6251 1.46 - 1.58: 14825 1.58 - 1.70: 63 1.70 - 1.82: 183 Bond restraints: 31692 Sorted by residual: bond pdb=" C4 ADP B2002 " pdb=" C5 ADP B2002 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C5 ADP B2002 " pdb=" C6 ADP B2002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1' DT C 60 " pdb=" N1 DT C 60 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" C3' DG C 12 " pdb=" C2' DG C 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 bond pdb=" C1' DC C 57 " pdb=" N1 DC C 57 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.03e+00 ... (remaining 31687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 42538 2.48 - 4.96: 478 4.96 - 7.44: 34 7.44 - 9.92: 4 9.92 - 12.40: 3 Bond angle restraints: 43057 Sorted by residual: angle pdb=" OE1 GLN A1798 " pdb=" CD GLN A1798 " pdb=" NE2 GLN A1798 " ideal model delta sigma weight residual 122.60 117.92 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" PA ADP B2002 " pdb=" O3A ADP B2002 " pdb=" PB ADP B2002 " ideal model delta sigma weight residual 120.50 132.90 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 56 " pdb=" C4 DT C 56 " pdb=" O4 DT C 56 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 47 " pdb=" C4 DT C 47 " pdb=" O4 DT C 47 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 43052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.96: 17885 27.96 - 55.92: 1137 55.92 - 83.88: 98 83.88 - 111.84: 18 111.84 - 139.80: 3 Dihedral angle restraints: 19141 sinusoidal: 8100 harmonic: 11041 Sorted by residual: dihedral pdb=" CA CYS A1531 " pdb=" C CYS A1531 " pdb=" N GLN A1532 " pdb=" CA GLN A1532 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" O1B ADP B2002 " pdb=" O3A ADP B2002 " pdb=" PB ADP B2002 " pdb=" PA ADP B2002 " ideal model delta sinusoidal sigma weight residual -60.00 -171.35 111.35 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" C5' ADP B2002 " pdb=" O5' ADP B2002 " pdb=" PA ADP B2002 " pdb=" O2A ADP B2002 " ideal model delta sinusoidal sigma weight residual -60.00 -156.63 96.63 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 19138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4023 0.055 - 0.110: 547 0.110 - 0.165: 110 0.165 - 0.220: 6 0.220 - 0.275: 2 Chirality restraints: 4688 Sorted by residual: chirality pdb=" CA GLN A1532 " pdb=" N GLN A1532 " pdb=" C GLN A1532 " pdb=" CB GLN A1532 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA CYS A1806 " pdb=" N CYS A1806 " pdb=" C CYS A1806 " pdb=" CB CYS A1806 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' DT C 60 " pdb=" C4' DT C 60 " pdb=" O3' DT C 60 " pdb=" C2' DT C 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 4685 not shown) Planarity restraints: 5564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 398 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" CD GLU A 398 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 398 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 398 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 300 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" CD GLU A 300 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 300 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 300 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1014 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLU B1014 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU B1014 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP B1015 " 0.010 2.00e-02 2.50e+03 ... (remaining 5561 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 637 2.70 - 3.25: 30138 3.25 - 3.80: 45285 3.80 - 4.35: 57720 4.35 - 4.90: 99214 Nonbonded interactions: 232994 Sorted by model distance: nonbonded pdb=" O GLN A 292 " pdb=" NE2 GLN A 292 " model vdw 2.153 3.120 nonbonded pdb=" O TYR A1264 " pdb=" O ALA A1267 " model vdw 2.364 3.040 nonbonded pdb=" N GLU A1443 " pdb=" OE1 GLU A1443 " model vdw 2.367 3.120 nonbonded pdb=" O SER B 340 " pdb=" OE2 GLU B1330 " model vdw 2.376 3.040 nonbonded pdb=" N GLU A 300 " pdb=" OE1 GLU A 300 " model vdw 2.386 3.120 ... (remaining 232989 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 4 through 292 or resid 300 through 864 or resid 868 throug \ h 900 or resid 904 through 1945 or resid 2003 through 2004)) selection = (chain 'B' and (resid 4 through 750 or resid 761 through 1434 or resid 1439 thro \ ugh 1945 or resid 2003 through 2004)) } 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: 4.000 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: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.750 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.505 31723 Z= 0.237 Angle : 0.837 63.143 43096 Z= 0.359 Chirality : 0.042 0.275 4688 Planarity : 0.004 0.042 5564 Dihedral : 17.018 139.801 12027 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.49 % Allowed : 17.56 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.52 (0.14), residues: 3808 helix: 1.72 (0.14), residues: 1431 sheet: 0.53 (0.21), residues: 613 loop : -0.90 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 279 TYR 0.018 0.001 TYR A1804 PHE 0.015 0.001 PHE B 144 TRP 0.012 0.001 TRP B1821 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (31692) covalent geometry : angle 0.60670 / 0.34 (43057) hydrogen bonds : bond 0.14594 / 9.76 ( 1126) hydrogen bonds : angle 5.03663 / 3.59 ( 3195) metal coordination : bond 0.13407 / 9.12 ( 31) metal coordination : angle 19.17760 / 10.27 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8651 (mtt180) REVERT: A 344 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8645 (mt-10) REVERT: A 374 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8482 (ptp-170) REVERT: A 1014 GLU cc_start: 0.7766 (pm20) cc_final: 0.7428 (pm20) REVERT: A 1865 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8397 (tp30) REVERT: A 1875 GLU cc_start: 0.7562 (mp0) cc_final: 0.7308 (mp0) REVERT: B 72 ASP cc_start: 0.8708 (t0) cc_final: 0.8444 (t0) REVERT: B 285 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7544 (mtt180) REVERT: B 465 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: B 478 MET cc_start: 0.8687 (tpt) cc_final: 0.8406 (tpt) REVERT: B 513 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 537 ASN cc_start: 0.8234 (t0) cc_final: 0.7823 (t0) REVERT: B 552 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8835 (mtm-85) REVERT: B 665 MET cc_start: 0.7870 (mmm) cc_final: 0.7545 (mmm) REVERT: B 669 GLU cc_start: 0.8046 (tp30) cc_final: 0.7463 (tp30) REVERT: B 813 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8262 (t-90) REVERT: B 1211 MET cc_start: 0.8694 (mmm) cc_final: 0.8347 (tpp) REVERT: B 1804 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8110 (t80) outliers start: 48 outliers final: 38 residues processed: 373 average time/residue: 0.2420 time to fit residues: 133.4694 Evaluate side-chains 373 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain A residue 1615 ASP Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1858 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1558 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1884 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 GLN A1747 ASN B 666 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.041900 restraints weight = 87010.476| |-----------------------------------------------------------------------------| r_work (start): 0.2442 rms_B_bonded: 2.00 r_work: 0.2350 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2239 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31723 Z= 0.123 Angle : 0.670 49.613 43096 Z= 0.304 Chirality : 0.041 0.167 4688 Planarity : 0.004 0.055 5564 Dihedral : 11.012 140.216 4693 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.33 % Allowed : 16.35 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.71 (0.14), residues: 3808 helix: 1.85 (0.14), residues: 1469 sheet: 0.53 (0.21), residues: 626 loop : -0.78 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 875 TYR 0.017 0.001 TYR A1007 PHE 0.016 0.001 PHE B 144 TRP 0.013 0.001 TRP A1781 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (31692) covalent geometry : angle 0.56638 / 0.30 (43057) hydrogen bonds : bond 0.05280 / 3.55 ( 1126) hydrogen bonds : angle 4.16346 / 2.99 ( 3195) metal coordination : bond 0.00965 / 0.64 ( 31) metal coordination : angle 11.89256 / 6.82 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 LYS cc_start: 0.8728 (pptt) cc_final: 0.8498 (pttm) REVERT: A 1370 ASP cc_start: 0.7563 (t0) cc_final: 0.7344 (t0) REVERT: A 1693 ASP cc_start: 0.8151 (p0) cc_final: 0.7543 (t0) REVERT: A 1868 ARG cc_start: 0.7086 (mmt90) cc_final: 0.6879 (mmp80) REVERT: A 1869 LYS cc_start: 0.8427 (tppt) cc_final: 0.8033 (tppt) REVERT: A 1875 GLU cc_start: 0.7529 (mp0) cc_final: 0.7218 (mp0) REVERT: B 106 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7760 (mtp-110) REVERT: B 256 ASP cc_start: 0.8046 (t0) cc_final: 0.7780 (t0) REVERT: B 414 MET cc_start: 0.8369 (mmm) cc_final: 0.8043 (mmm) REVERT: B 513 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 537 ASN cc_start: 0.8398 (t0) cc_final: 0.7931 (t0) REVERT: B 552 ARG cc_start: 0.9167 (mmm-85) cc_final: 0.8912 (mtm-85) REVERT: B 665 MET cc_start: 0.8036 (mmm) cc_final: 0.7721 (mmm) REVERT: B 669 GLU cc_start: 0.8054 (tp30) cc_final: 0.7593 (tp30) REVERT: B 849 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: B 875 ARG cc_start: 0.8831 (tpm170) cc_final: 0.8538 (tpm170) REVERT: B 1211 MET cc_start: 0.8654 (mmm) cc_final: 0.8326 (tpp) REVERT: B 1637 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: B 1804 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.7999 (t80) outliers start: 75 outliers final: 39 residues processed: 399 average time/residue: 0.2387 time to fit residues: 141.8322 Evaluate side-chains 374 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 331 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1048 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1764 THR Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [53, 193, 181, 247, 120, 351, 132, 240, 32, 65, 63] chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 120 optimal weight: 0.0970 chunk 351 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN A 599 ASN B 666 ASN B 676 ASN B 679 HIS B1247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.053022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.041755 restraints weight = 87164.563| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 2.01 r_work: 0.2346 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2235 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31723 Z= 0.130 Angle : 0.649 44.414 43096 Z= 0.295 Chirality : 0.041 0.177 4688 Planarity : 0.004 0.050 5564 Dihedral : 10.533 138.931 4631 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.73 % Allowed : 17.03 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.78 (0.14), residues: 3808 helix: 1.88 (0.14), residues: 1471 sheet: 0.62 (0.21), residues: 637 loop : -0.75 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 890 TYR 0.017 0.001 TYR B1007 PHE 0.016 0.001 PHE B 144 TRP 0.010 0.001 TRP B1821 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (31692) covalent geometry : angle 0.54960 / 0.29 (43057) hydrogen bonds : bond 0.05116 / 3.44 ( 1126) hydrogen bonds : angle 4.01227 / 2.88 ( 3195) metal coordination : bond 0.00704 / 0.40 ( 31) metal coordination : angle 11.45942 / 6.37 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8652 (mt-10) REVERT: A 414 MET cc_start: 0.8151 (ttm) cc_final: 0.7924 (ttt) REVERT: A 939 LYS cc_start: 0.8737 (pptt) cc_final: 0.8371 (pttt) REVERT: A 1687 MET cc_start: 0.9037 (mmm) cc_final: 0.8346 (mmt) REVERT: A 1693 ASP cc_start: 0.8027 (p0) cc_final: 0.7668 (p0) REVERT: A 1867 MET cc_start: 0.6126 (ppp) cc_final: 0.5622 (ppp) REVERT: A 1868 ARG cc_start: 0.7042 (mmt90) cc_final: 0.6715 (mmp80) REVERT: B 66 ASP cc_start: 0.8659 (t70) cc_final: 0.8441 (t0) REVERT: B 72 ASP cc_start: 0.8583 (t0) cc_final: 0.8374 (t0) REVERT: B 106 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7746 (mtp-110) REVERT: B 256 ASP cc_start: 0.8159 (t0) cc_final: 0.7829 (t0) REVERT: B 513 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 537 ASN cc_start: 0.8375 (t0) cc_final: 0.7983 (t0) REVERT: B 552 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8913 (mtm-85) REVERT: B 665 MET cc_start: 0.8070 (mmm) cc_final: 0.7752 (mmm) REVERT: B 669 GLU cc_start: 0.8049 (tp30) cc_final: 0.7623 (tp30) REVERT: B 813 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8322 (t-90) REVERT: B 849 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: B 875 ARG cc_start: 0.8744 (tpm170) cc_final: 0.8391 (tpm170) REVERT: B 1211 MET cc_start: 0.8669 (mmm) cc_final: 0.8326 (tpp) REVERT: B 1637 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: B 1804 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8127 (t80) outliers start: 88 outliers final: 58 residues processed: 413 average time/residue: 0.2422 time to fit residues: 148.1392 Evaluate side-chains 391 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 327 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1696 HIS Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1048 LYS Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [347, 150, 208, 356, 271, 14, 282, 138, 113, 239, 383] chunk 347 optimal weight: 4.9990 chunk 150 optimal weight: 0.0370 chunk 208 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 282 optimal weight: 0.0060 chunk 138 optimal weight: 0.6980 chunk 113 optimal weight: 0.4980 chunk 239 optimal weight: 3.9990 chunk 383 optimal weight: 10.0000 overall best weight: 0.6476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN A 594 HIS A1479 ASN B 627 HIS B 666 ASN B 679 HIS B1247 GLN B1637 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.053495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.042296 restraints weight = 86845.630| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 2.01 r_work: 0.2363 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2253 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31723 Z= 0.116 Angle : 0.641 43.420 43096 Z= 0.290 Chirality : 0.041 0.174 4688 Planarity : 0.004 0.052 5564 Dihedral : 10.457 139.611 4627 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.85 % Allowed : 17.16 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.85 (0.14), residues: 3808 helix: 1.91 (0.14), residues: 1473 sheet: 0.76 (0.21), residues: 614 loop : -0.71 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 875 TYR 0.016 0.001 TYR B1007 PHE 0.015 0.001 PHE B 144 TRP 0.010 0.001 TRP B1821 HIS 0.004 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (31692) covalent geometry : angle 0.54350 / 0.28 (43057) hydrogen bonds : bond 0.04648 / 3.12 ( 1126) hydrogen bonds : angle 3.93223 / 2.82 ( 3195) metal coordination : bond 0.00544 / 0.31 ( 31) metal coordination : angle 11.28574 / 6.21 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 341 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 LYS cc_start: 0.8775 (pptt) cc_final: 0.8419 (pttm) REVERT: A 1015 ASP cc_start: 0.8707 (p0) cc_final: 0.8500 (p0) REVERT: A 1531 CYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5683 (p) REVERT: A 1687 MET cc_start: 0.9027 (mmm) cc_final: 0.8357 (mmt) REVERT: A 1693 ASP cc_start: 0.7983 (p0) cc_final: 0.7598 (p0) REVERT: B 66 ASP cc_start: 0.8635 (t70) cc_final: 0.8418 (t0) REVERT: B 72 ASP cc_start: 0.8558 (t0) cc_final: 0.8354 (t0) REVERT: B 256 ASP cc_start: 0.8119 (t0) cc_final: 0.7859 (t0) REVERT: B 513 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 537 ASN cc_start: 0.8408 (t0) cc_final: 0.8021 (t0) REVERT: B 552 ARG cc_start: 0.9164 (mmm-85) cc_final: 0.8936 (mtm-85) REVERT: B 669 GLU cc_start: 0.8015 (tp30) cc_final: 0.7642 (tp30) REVERT: B 813 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: B 849 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: B 875 ARG cc_start: 0.8841 (tpm170) cc_final: 0.8511 (tpm170) REVERT: B 1637 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: B 1804 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8138 (t80) outliers start: 92 outliers final: 61 residues processed: 415 average time/residue: 0.2427 time to fit residues: 149.1628 Evaluate side-chains 400 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1696 HIS Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1446 MET Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [361, 198, 266, 325, 338, 324, 276, 220, 178, 225, 181] chunk 361 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 178 optimal weight: 0.2980 chunk 225 optimal weight: 0.9990 chunk 181 optimal weight: 0.0970 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 ASN B 13 GLN B 666 ASN B 679 HIS ** B1247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.053621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.042378 restraints weight = 87135.640| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 2.02 r_work: 0.2366 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2256 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31723 Z= 0.119 Angle : 0.645 46.687 43096 Z= 0.291 Chirality : 0.040 0.163 4688 Planarity : 0.004 0.048 5564 Dihedral : 10.416 140.265 4625 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.76 % Allowed : 17.81 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.90 (0.14), residues: 3808 helix: 1.92 (0.14), residues: 1480 sheet: 0.75 (0.21), residues: 637 loop : -0.66 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 875 TYR 0.016 0.001 TYR B1007 PHE 0.016 0.001 PHE B 144 TRP 0.010 0.001 TRP A1895 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (31692) covalent geometry : angle 0.54864 / 0.28 (43057) hydrogen bonds : bond 0.04523 / 3.04 ( 1126) hydrogen bonds : angle 3.89072 / 2.79 ( 3195) metal coordination : bond 0.00555 / 0.32 ( 31) metal coordination : angle 11.31327 / 6.32 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 337 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8661 (tp30) cc_final: 0.8442 (tp30) REVERT: A 344 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: A 939 LYS cc_start: 0.8755 (pptt) cc_final: 0.8374 (pttm) REVERT: A 1531 CYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5739 (p) REVERT: A 1687 MET cc_start: 0.9030 (mmm) cc_final: 0.8373 (mmt) REVERT: A 1693 ASP cc_start: 0.7975 (p0) cc_final: 0.7602 (p0) REVERT: A 1695 MET cc_start: 0.7894 (mtp) cc_final: 0.7509 (mtp) REVERT: A 1871 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 66 ASP cc_start: 0.8645 (t70) cc_final: 0.8432 (t0) REVERT: B 72 ASP cc_start: 0.8549 (t0) cc_final: 0.8330 (t0) REVERT: B 256 ASP cc_start: 0.8112 (t0) cc_final: 0.7873 (t0) REVERT: B 513 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 537 ASN cc_start: 0.8407 (t0) cc_final: 0.8031 (t0) REVERT: B 552 ARG cc_start: 0.9164 (mmm-85) cc_final: 0.8947 (mtm-85) REVERT: B 669 GLU cc_start: 0.8014 (tp30) cc_final: 0.7677 (tp30) REVERT: B 813 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8397 (t-90) REVERT: B 849 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: B 1017 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: B 1637 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: B 1804 TYR cc_start: 0.9375 (OUTLIER) cc_final: 0.8161 (t80) outliers start: 89 outliers final: 67 residues processed: 407 average time/residue: 0.2476 time to fit residues: 150.0168 Evaluate side-chains 404 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1696 HIS Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1871 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1231 GLN Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [150, 46, 127, 161, 373, 70, 112, 166, 308, 253, 118] chunk 150 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 161 optimal weight: 0.0570 chunk 373 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 166 optimal weight: 0.0970 chunk 308 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 292 GLN B 666 ASN B 679 HIS B1247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.051067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.039930 restraints weight = 88319.398| |-----------------------------------------------------------------------------| r_work (start): 0.2369 rms_B_bonded: 2.03 r_work: 0.2278 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2168 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31723 Z= 0.166 Angle : 0.675 45.524 43096 Z= 0.310 Chirality : 0.042 0.217 4688 Planarity : 0.004 0.080 5564 Dihedral : 10.476 141.361 4625 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.16 % Allowed : 17.81 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.79 (0.14), residues: 3808 helix: 1.82 (0.14), residues: 1475 sheet: 0.79 (0.21), residues: 612 loop : -0.72 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 494 TYR 0.018 0.001 TYR A1007 PHE 0.020 0.002 PHE B 144 TRP 0.011 0.001 TRP B1821 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (31692) covalent geometry : angle 0.58372 / 0.30 (43057) hydrogen bonds : bond 0.05337 / 3.57 ( 1126) hydrogen bonds : angle 3.94424 / 2.84 ( 3195) metal coordination : bond 0.00784 / 0.47 ( 31) metal coordination : angle 11.31013 / 6.30 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 335 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8514 (p0) cc_final: 0.8313 (p0) REVERT: A 187 LYS cc_start: 0.8827 (mppt) cc_final: 0.8525 (mppt) REVERT: A 344 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8687 (mt-10) REVERT: A 939 LYS cc_start: 0.8824 (pptt) cc_final: 0.8460 (pttt) REVERT: A 1531 CYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5545 (p) REVERT: A 1871 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8326 (m) REVERT: A 1875 GLU cc_start: 0.7584 (mp0) cc_final: 0.7360 (mp0) REVERT: B 66 ASP cc_start: 0.8727 (t70) cc_final: 0.8500 (t0) REVERT: B 72 ASP cc_start: 0.8660 (t0) cc_final: 0.8393 (t0) REVERT: B 256 ASP cc_start: 0.8234 (t0) cc_final: 0.7938 (t0) REVERT: B 513 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 537 ASN cc_start: 0.8420 (t0) cc_final: 0.8043 (t0) REVERT: B 552 ARG cc_start: 0.9178 (mmm-85) cc_final: 0.8958 (mtm-85) REVERT: B 665 MET cc_start: 0.8048 (mmm) cc_final: 0.7737 (mmm) REVERT: B 669 GLU cc_start: 0.8138 (tp30) cc_final: 0.7764 (tp30) REVERT: B 813 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8315 (t-90) REVERT: B 849 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: B 1017 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: B 1231 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: B 1597 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: B 1637 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: B 1804 TYR cc_start: 0.9398 (OUTLIER) cc_final: 0.8353 (t80) outliers start: 102 outliers final: 74 residues processed: 415 average time/residue: 0.2419 time to fit residues: 150.2407 Evaluate side-chains 416 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 332 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1858 SER Chi-restraints excluded: chain A residue 1871 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain A residue 1944 LYS Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1048 LYS Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1231 GLN Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Chi-restraints excluded: chain B residue 1935 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [48, 171, 64, 168, 79, 265, 378, 62, 31, 349, 370] chunk 48 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 378 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 349 optimal weight: 0.4980 chunk 370 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 666 ASN B 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.053367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.042009 restraints weight = 86542.203| |-----------------------------------------------------------------------------| r_work (start): 0.2449 rms_B_bonded: 2.04 r_work: 0.2358 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2247 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31723 Z= 0.120 Angle : 0.667 44.654 43096 Z= 0.304 Chirality : 0.041 0.279 4688 Planarity : 0.004 0.070 5564 Dihedral : 10.415 141.390 4625 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 18.80 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.88 (0.14), residues: 3808 helix: 1.84 (0.14), residues: 1490 sheet: 0.80 (0.21), residues: 637 loop : -0.65 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1873 TYR 0.016 0.001 TYR B1007 PHE 0.015 0.001 PHE B 144 TRP 0.012 0.001 TRP B1821 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (31692) covalent geometry : angle 0.57592 / 0.30 (43057) hydrogen bonds : bond 0.04644 / 3.12 ( 1126) hydrogen bonds : angle 3.87677 / 2.79 ( 3195) metal coordination : bond 0.00544 / 0.31 ( 31) metal coordination : angle 11.19870 / 6.21 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 339 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8685 (tp30) cc_final: 0.8431 (tp30) REVERT: A 344 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: A 939 LYS cc_start: 0.8760 (pptt) cc_final: 0.8404 (pttt) REVERT: A 1531 CYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5663 (p) REVERT: A 1871 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8212 (m) REVERT: B 66 ASP cc_start: 0.8722 (t70) cc_final: 0.8454 (t0) REVERT: B 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8311 (t0) REVERT: B 256 ASP cc_start: 0.8150 (t0) cc_final: 0.7834 (t0) REVERT: B 513 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 537 ASN cc_start: 0.8390 (t0) cc_final: 0.8019 (t0) REVERT: B 552 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8949 (mtm-85) REVERT: B 665 MET cc_start: 0.8081 (mmm) cc_final: 0.7790 (mmm) REVERT: B 669 GLU cc_start: 0.8011 (tp30) cc_final: 0.7652 (tp30) REVERT: B 813 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.8305 (t-90) REVERT: B 849 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: B 1017 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7731 (mm-40) REVERT: B 1597 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: B 1637 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: B 1804 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8229 (t80) outliers start: 88 outliers final: 74 residues processed: 408 average time/residue: 0.2336 time to fit residues: 142.8796 Evaluate side-chains 413 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1696 HIS Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1871 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain A residue 1944 LYS Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 533 HIS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1563 GLU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Chi-restraints excluded: chain B residue 1935 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [31, 102, 279, 169, 81, 372, 240, 255, 116, 234, 206] chunk 31 optimal weight: 0.3980 chunk 102 optimal weight: 0.2980 chunk 279 optimal weight: 0.3980 chunk 169 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 372 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 666 ASN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.053829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.042631 restraints weight = 86588.342| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 2.01 r_work: 0.2360 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31723 Z= 0.117 Angle : 0.666 44.550 43096 Z= 0.303 Chirality : 0.040 0.192 4688 Planarity : 0.004 0.052 5564 Dihedral : 10.367 141.947 4625 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.70 % Allowed : 19.05 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 3808 helix: 1.92 (0.14), residues: 1481 sheet: 0.84 (0.22), residues: 609 loop : -0.64 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 875 TYR 0.015 0.001 TYR B1007 PHE 0.015 0.001 PHE B 144 TRP 0.010 0.001 TRP B1821 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31692) covalent geometry : angle 0.57593 / 0.30 (43057) hydrogen bonds : bond 0.04358 / 2.93 ( 1126) hydrogen bonds : angle 3.82982 / 2.75 ( 3195) metal coordination : bond 0.00507 / 0.29 ( 31) metal coordination : angle 11.16521 / 6.18 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 336 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8680 (tp30) cc_final: 0.8422 (tp30) REVERT: A 161 LYS cc_start: 0.8775 (tppt) cc_final: 0.8569 (tppt) REVERT: A 187 LYS cc_start: 0.8820 (mppt) cc_final: 0.8559 (mppt) REVERT: A 338 MET cc_start: 0.9130 (mtp) cc_final: 0.8890 (mtp) REVERT: A 344 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: A 939 LYS cc_start: 0.8752 (pptt) cc_final: 0.8390 (pttm) REVERT: A 1531 CYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5643 (p) REVERT: A 1871 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.7939 (m) REVERT: B 66 ASP cc_start: 0.8626 (t70) cc_final: 0.8413 (t0) REVERT: B 72 ASP cc_start: 0.8519 (t0) cc_final: 0.8283 (t0) REVERT: B 256 ASP cc_start: 0.8129 (t0) cc_final: 0.7801 (t0) REVERT: B 513 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 537 ASN cc_start: 0.8371 (t0) cc_final: 0.7989 (t0) REVERT: B 665 MET cc_start: 0.8068 (mmm) cc_final: 0.7774 (mmm) REVERT: B 669 GLU cc_start: 0.8006 (tp30) cc_final: 0.7675 (tp30) REVERT: B 813 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8391 (t-90) REVERT: B 849 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: B 875 ARG cc_start: 0.8732 (tpm170) cc_final: 0.8499 (tpm170) REVERT: B 1017 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7665 (mm-40) REVERT: B 1597 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.7951 (mt0) REVERT: B 1637 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: B 1771 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8771 (tt) REVERT: B 1804 TYR cc_start: 0.9392 (OUTLIER) cc_final: 0.8242 (t80) outliers start: 87 outliers final: 68 residues processed: 407 average time/residue: 0.2420 time to fit residues: 147.2866 Evaluate side-chains 411 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 333 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1696 HIS Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1858 SER Chi-restraints excluded: chain A residue 1871 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Chi-restraints excluded: chain B residue 1935 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [53, 49, 36, 145, 322, 120, 378, 164, 35, 31, 202] chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 666 ASN B 679 HIS B1357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.051742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.040563 restraints weight = 87217.659| |-----------------------------------------------------------------------------| r_work (start): 0.2402 rms_B_bonded: 2.00 r_work: 0.2310 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31723 Z= 0.200 Angle : 0.733 44.910 43096 Z= 0.344 Chirality : 0.044 0.182 4688 Planarity : 0.005 0.051 5564 Dihedral : 10.497 142.264 4622 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.85 % Allowed : 19.02 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3808 helix: 1.69 (0.14), residues: 1473 sheet: 0.77 (0.21), residues: 609 loop : -0.75 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1868 TYR 0.021 0.002 TYR A1007 PHE 0.023 0.002 PHE B 144 TRP 0.008 0.001 TRP B1895 HIS 0.010 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (31692) covalent geometry : angle 0.65060 / 0.34 (43057) hydrogen bonds : bond 0.05824 / 3.90 ( 1126) hydrogen bonds : angle 4.01139 / 2.88 ( 3195) metal coordination : bond 0.00857 / 0.52 ( 31) metal coordination : angle 11.27657 / 6.28 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8755 (tp30) cc_final: 0.8491 (tp30) REVERT: A 187 LYS cc_start: 0.8880 (mppt) cc_final: 0.8631 (mppt) REVERT: A 317 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7629 (mtm180) REVERT: A 344 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8640 (mt-10) REVERT: A 414 MET cc_start: 0.8052 (ttm) cc_final: 0.7758 (ttt) REVERT: A 493 ASP cc_start: 0.8112 (p0) cc_final: 0.7853 (p0) REVERT: A 939 LYS cc_start: 0.8827 (pptt) cc_final: 0.8455 (pttt) REVERT: A 1012 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7300 (tmm) REVERT: A 1531 CYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5669 (p) REVERT: A 1606 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8639 (mmmt) REVERT: A 1693 ASP cc_start: 0.8034 (p0) cc_final: 0.7372 (t0) REVERT: A 1871 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8317 (m) REVERT: B 66 ASP cc_start: 0.8671 (t70) cc_final: 0.8466 (t0) REVERT: B 256 ASP cc_start: 0.8257 (t0) cc_final: 0.8034 (t0) REVERT: B 513 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 537 ASN cc_start: 0.8414 (t0) cc_final: 0.8030 (t0) REVERT: B 665 MET cc_start: 0.7958 (mmm) cc_final: 0.7693 (mmm) REVERT: B 669 GLU cc_start: 0.8054 (tp30) cc_final: 0.7703 (tp30) REVERT: B 813 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8256 (t-90) REVERT: B 849 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: B 875 ARG cc_start: 0.8784 (tpm170) cc_final: 0.8540 (tpm170) REVERT: B 1017 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: B 1457 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 1597 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: B 1637 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: B 1804 TYR cc_start: 0.9430 (OUTLIER) cc_final: 0.8535 (t80) outliers start: 92 outliers final: 65 residues processed: 409 average time/residue: 0.2419 time to fit residues: 147.8986 Evaluate side-chains 404 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 328 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1858 SER Chi-restraints excluded: chain A residue 1871 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain A residue 1944 LYS Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Chi-restraints excluded: chain B residue 1935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [127, 65, 92, 309, 299, 13, 121, 356, 103, 211, 146] chunk 127 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 309 optimal weight: 0.1980 chunk 299 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 121 optimal weight: 0.7980 chunk 356 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1629 GLN B 666 ASN B 679 HIS B1637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.053730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.042493 restraints weight = 86216.550| |-----------------------------------------------------------------------------| r_work (start): 0.2456 rms_B_bonded: 2.02 r_work: 0.2369 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31723 Z= 0.121 Angle : 0.699 44.614 43096 Z= 0.323 Chirality : 0.041 0.209 4688 Planarity : 0.004 0.052 5564 Dihedral : 10.388 141.595 4622 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 20.07 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3808 helix: 1.89 (0.14), residues: 1485 sheet: 0.82 (0.21), residues: 613 loop : -0.64 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 875 TYR 0.015 0.001 TYR B1007 PHE 0.013 0.001 PHE B1930 TRP 0.013 0.001 TRP A1781 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (31692) covalent geometry : angle 0.61421 / 0.32 (43057) hydrogen bonds : bond 0.04448 / 3.00 ( 1126) hydrogen bonds : angle 3.85691 / 2.77 ( 3195) metal coordination : bond 0.00482 / 0.27 ( 31) metal coordination : angle 11.14238 / 6.18 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8709 (tp30) cc_final: 0.8444 (tp30) REVERT: A 344 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: A 414 MET cc_start: 0.7974 (ttm) cc_final: 0.7666 (ttt) REVERT: A 939 LYS cc_start: 0.8752 (pptt) cc_final: 0.8412 (pttm) REVERT: A 1012 MET cc_start: 0.7306 (tmm) cc_final: 0.7038 (tmm) REVERT: A 1531 CYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5607 (p) REVERT: A 1687 MET cc_start: 0.9017 (mmm) cc_final: 0.8387 (mmt) REVERT: A 1693 ASP cc_start: 0.8033 (p0) cc_final: 0.7089 (t0) REVERT: B 66 ASP cc_start: 0.8629 (t70) cc_final: 0.8423 (t0) REVERT: B 256 ASP cc_start: 0.8171 (t0) cc_final: 0.7858 (t0) REVERT: B 513 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 514 THR cc_start: 0.9003 (t) cc_final: 0.8797 (t) REVERT: B 537 ASN cc_start: 0.8347 (t0) cc_final: 0.7963 (t0) REVERT: B 665 MET cc_start: 0.7999 (mmm) cc_final: 0.7717 (mmm) REVERT: B 669 GLU cc_start: 0.7982 (tp30) cc_final: 0.7642 (tp30) REVERT: B 813 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: B 828 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7055 (mtp180) REVERT: B 849 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: B 875 ARG cc_start: 0.8825 (tpm170) cc_final: 0.8602 (tpm170) REVERT: B 1017 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7677 (mm-40) REVERT: B 1597 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: B 1637 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: B 1804 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8466 (t80) outliers start: 66 outliers final: 56 residues processed: 387 average time/residue: 0.2480 time to fit residues: 143.0447 Evaluate side-chains 395 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1531 CYS Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1680 ASP Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1921 SER Chi-restraints excluded: chain A residue 1944 LYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain B residue 1054 ASN Chi-restraints excluded: chain B residue 1093 ILE Chi-restraints excluded: chain B residue 1106 ASP Chi-restraints excluded: chain B residue 1119 HIS Chi-restraints excluded: chain B residue 1286 HIS Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1628 THR Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1653 SER Chi-restraints excluded: chain B residue 1788 ARG Chi-restraints excluded: chain B residue 1804 TYR Chi-restraints excluded: chain B residue 1849 GLU Chi-restraints excluded: chain B residue 1858 SER Chi-restraints excluded: chain B residue 1869 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: [294, 161, 353, 325, 202, 28, 319, 75, 321, 282, 324] chunk 294 optimal weight: 0.4980 chunk 161 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 325 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 321 optimal weight: 0.8980 chunk 282 optimal weight: 0.0270 chunk 324 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN A1629 GLN B 666 ASN B 679 HIS B1637 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.042680 restraints weight = 86566.219| |-----------------------------------------------------------------------------| r_work (start): 0.2462 rms_B_bonded: 2.03 r_work: 0.2375 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31723 Z= 0.120 Angle : 0.691 44.633 43096 Z= 0.317 Chirality : 0.041 0.225 4688 Planarity : 0.004 0.051 5564 Dihedral : 10.340 142.332 4622 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 20.01 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3808 helix: 1.94 (0.14), residues: 1480 sheet: 0.90 (0.22), residues: 590 loop : -0.63 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1873 TYR 0.017 0.001 TYR A1338 PHE 0.015 0.001 PHE B 144 TRP 0.012 0.001 TRP B1895 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (31692) covalent geometry : angle 0.60462 / 0.31 (43057) hydrogen bonds : bond 0.04284 / 2.88 ( 1126) hydrogen bonds : angle 3.82830 / 2.74 ( 3195) metal coordination : bond 0.00502 / 0.29 ( 31) metal coordination : angle 11.14457 / 6.18 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6870.69 seconds wall clock time: 118 minutes 2.62 seconds (7082.62 seconds total)