Starting phenix.real_space_refine on Thu Oct 29 06:59:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wae_65815/10_2026/9wae_65815.map" } resolution = 3.49 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= 0.472 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 122 5.16 5 C 19165 2.51 5 N 5462 2.21 5 O 5702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 328 residue(s): 0.02s 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: 30459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1928, 15240 Classifications: {'peptide': 1928} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1818} Chain breaks: 2 Chain: "B" Number of atoms: 15211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1923, 15211 Classifications: {'peptide': 1923} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1813} Chain breaks: 3 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8585 SG CYS A1110 61.033 115.678 63.103 1.00 77.69 S ATOM 8605 SG CYS A1113 62.416 112.702 63.936 1.00 74.65 S ATOM 8700 SG CYS A1125 60.029 113.998 65.932 1.00 83.44 S ATOM 8724 SG CYS A1128 63.882 116.098 66.482 1.00 84.95 S ATOM 5039 SG CYS A 646 68.182 103.317 62.171 1.00 74.49 S ATOM 5059 SG CYS A 649 67.352 106.720 61.104 1.00 78.99 S ATOM 5923 SG CYS A 770 70.567 105.758 62.608 1.00100.68 S ATOM 5945 SG CYS A 773 67.482 106.359 64.453 1.00 85.31 S ATOM 14039 SG CYS A1799 82.723 89.890 35.517 1.00107.18 S ATOM 14067 SG CYS A1803 80.535 88.561 37.455 1.00 61.14 S ATOM 14096 SG CYS A1806 82.142 85.503 35.090 1.00107.34 S ATOM 11792 SG CYS A1509 106.094 67.579 53.039 1.00119.15 S ATOM 11810 SG CYS A1512 106.029 67.227 49.433 1.00110.95 S ATOM 11915 SG CYS A1528 105.717 63.842 51.528 1.00138.48 S ATOM 11937 SG CYS A1531 108.522 66.183 50.290 1.00153.76 S ATOM 23796 SG CYS B1110 20.779 54.536 111.557 1.00 91.62 S ATOM 23816 SG CYS B1113 24.272 54.947 111.172 1.00 97.52 S ATOM 23911 SG CYS B1125 22.251 55.831 108.724 1.00122.81 S ATOM 23935 SG CYS B1128 22.098 52.002 109.621 1.00104.13 S ATOM 20255 SG CYS B 646 33.746 52.775 114.378 1.00 88.12 S ATOM 20275 SG CYS B 649 30.805 52.167 115.325 1.00 93.16 S ATOM 21134 SG CYS B 770 32.615 49.444 113.331 1.00109.28 S ATOM 21156 SG CYS B 773 31.624 51.938 111.294 1.00117.34 S ATOM 29250 SG CYS B1799 49.186 47.143 141.984 1.00 83.26 S ATOM 29278 SG CYS B1803 49.552 49.983 140.625 1.00 81.23 S ATOM 29307 SG CYS B1806 52.623 48.971 141.993 1.00100.13 S ATOM 27003 SG CYS B1509 79.317 30.742 130.532 1.00127.70 S ATOM 27021 SG CYS B1512 79.349 30.565 134.142 1.00122.81 S ATOM 27126 SG CYS B1528 82.149 32.758 132.288 1.00138.08 S ATOM 27148 SG CYS B1531 81.890 29.478 133.596 1.00166.99 S Time building chain proxies: 6.29, per 1000 atoms: 0.21 Number of scatterers: 30459 At special positions: 0 Unit cell: (127.68, 134.4, 173.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 122 16.00 O 5702 8.00 N 5462 7.00 C 19165 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 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1113 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1125 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1128 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 770 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 649 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 773 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1803 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1799 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1806 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1512 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1528 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1509 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1531 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1113 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1125 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 649 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 646 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2002 " - pdb=" SG CYS B 773 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1799 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1806 " pdb="ZN ZN B2003 " - pdb=" SG CYS B1803 " pdb=" ZN B2004 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1512 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1528 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1509 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1531 " Number of angles added : 42 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 22 sheets defined 44.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.668A pdb=" N ILE A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.046A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.949A pdb=" N ARG A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.967A pdb=" N SER A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.627A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.014A pdb=" N TYR A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.796A pdb=" N SER A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 removed outlier: 4.167A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 393 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 416 through 430 Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.673A pdb=" N SER A 451 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 452 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 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 578 removed outlier: 3.698A pdb=" N ALA A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Proline residue: A 575 - end of helix removed outlier: 3.619A pdb=" N ASN A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.531A pdb=" N ASP A 691 " --> pdb=" O TYR A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 865 removed outlier: 3.708A pdb=" N GLU A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 865 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 4.243A pdb=" N THR A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 900 removed outlier: 4.997A pdb=" N SER A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 894 " --> pdb=" O ARG A 890 " (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: 3.705A pdb=" N TYR A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.825A 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: 3.637A pdb=" N ALA A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1069 through 1085 Processing helix chain 'A' and resid 1086 through 1090 removed outlier: 3.923A pdb=" N GLY A1089 " --> pdb=" O HIS A1086 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.628A 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 1210 through 1215 removed outlier: 5.049A pdb=" N VAL A1213 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A1215 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1241 removed outlier: 3.729A pdb=" N ARG A1241 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.856A pdb=" N ALA A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1274 Processing helix chain 'A' and resid 1287 through 1314 removed outlier: 3.659A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1301 " --> pdb=" O THR A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1322 removed outlier: 3.620A pdb=" N LEU A1322 " --> pdb=" O GLY A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1340 removed outlier: 3.856A pdb=" N SER A1340 " --> pdb=" O ASP A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.702A pdb=" N ARG A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1368 removed outlier: 3.879A pdb=" N GLU A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A1368 " --> pdb=" O ILE A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.737A 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 1412 Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 4.283A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1540 removed outlier: 3.789A pdb=" N PHE A1540 " --> pdb=" O LYS A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1647 Processing helix chain 'A' and resid 1696 through 1719 Processing helix chain 'A' and resid 1721 through 1723 No H-bonds generated for 'chain 'A' and resid 1721 through 1723' Processing helix chain 'A' and resid 1750 through 1757 Processing helix chain 'A' and resid 1765 through 1777 removed outlier: 3.543A pdb=" N LEU A1775 " --> pdb=" O LEU A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1787 Processing helix chain 'A' and resid 1810 through 1815 removed outlier: 4.455A pdb=" N ARG A1814 " --> pdb=" O GLY A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.591A pdb=" N VAL A1832 " --> pdb=" O LEU A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1847 removed outlier: 3.658A pdb=" N LYS A1846 " --> pdb=" O GLY A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1868 Processing helix chain 'A' and resid 1908 through 1917 removed outlier: 3.597A pdb=" N MET A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A1914 " --> pdb=" O GLY A1910 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1915 " --> pdb=" O VAL A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1935 Processing helix chain 'A' and resid 1935 through 1945 Processing helix chain 'B' and resid 4 through 24 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 93 Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.542A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Proline residue: B 147 - end of helix removed outlier: 3.808A pdb=" N VAL B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 256 through 294 removed outlier: 4.133A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.910A pdb=" N TYR B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.991A 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 430 removed outlier: 4.096A pdb=" N VAL B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.911A pdb=" N LYS B 452 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 482 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 515 through 535 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 561 through 578 removed outlier: 3.693A pdb=" N ARG B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 796 through 815 Processing helix chain 'B' and resid 827 through 865 removed outlier: 3.579A pdb=" N GLU B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 865 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 883 removed outlier: 3.846A pdb=" N ILE B 877 " --> pdb=" O ILE B 873 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 879 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 890 through 898 removed outlier: 3.848A pdb=" N GLN B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 906 Processing helix chain 'B' and resid 911 through 916 Processing helix chain 'B' and resid 918 through 922 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 994 removed outlier: 3.757A pdb=" N ASP B 979 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 987 " --> pdb=" O GLY B 983 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 994 " --> pdb=" O ASP B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1017 through 1029 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1069 through 1084 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: 3.624A pdb=" N GLY B1159 " --> pdb=" O GLY B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1193 through 1201 Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'B' and resid 1216 through 1220 removed outlier: 4.057A pdb=" N ALA B1219 " --> pdb=" O ASP B1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1241 removed outlier: 3.919A pdb=" N ARG B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 3.924A pdb=" N ALA B1267 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1269 through 1275 removed outlier: 3.585A pdb=" N THR B1273 " --> pdb=" O PRO B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1312 removed outlier: 3.852A pdb=" N LEU B1293 " --> pdb=" O ILE B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 removed outlier: 4.295A pdb=" N LEU B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B1322 " --> pdb=" O PRO B1318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1317 through 1322' Processing helix chain 'B' and resid 1333 through 1338 Processing helix chain 'B' and resid 1344 through 1357 removed outlier: 3.698A pdb=" N GLN B1355 " --> pdb=" O GLU B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1368 removed outlier: 4.032A pdb=" N ASP B1361 " --> pdb=" O GLN B1357 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B1362 " --> pdb=" O SER B1358 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B1368 " --> pdb=" O ILE B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 removed outlier: 3.762A pdb=" N ARG B1374 " --> pdb=" O ASP B1370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B1375 " --> pdb=" O GLN B1371 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B1376 " --> pdb=" O GLU B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1393 removed outlier: 4.007A pdb=" N GLN B1393 " --> pdb=" O GLU B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1451 through 1458 removed outlier: 3.852A pdb=" N PHE B1456 " --> pdb=" O ASP B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1540 removed outlier: 3.674A 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 1691 through 1695 removed outlier: 4.344A pdb=" N PHE B1694 " --> pdb=" O LYS B1691 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET B1695 " --> pdb=" O GLY B1692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1691 through 1695' Processing helix chain 'B' and resid 1696 through 1718 Processing helix chain 'B' and resid 1721 through 1725 Processing helix chain 'B' and resid 1750 through 1757 Processing helix chain 'B' and resid 1765 through 1777 Processing helix chain 'B' and resid 1780 through 1787 Processing helix chain 'B' and resid 1794 through 1799 Processing helix chain 'B' and resid 1820 through 1833 removed outlier: 3.674A pdb=" N VAL B1832 " --> pdb=" O LEU B1828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1843 through 1847 removed outlier: 4.220A pdb=" N LYS B1846 " --> pdb=" O GLY B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1868 removed outlier: 3.668A pdb=" N ARG B1856 " --> pdb=" O GLY B1852 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1868 " --> pdb=" O VAL B1864 " (cutoff:3.500A) Processing helix chain 'B' and resid 1889 through 1892 Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.620A pdb=" N ASP B1914 " --> pdb=" O GLY B1910 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1915 " --> pdb=" O VAL B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1920 No H-bonds generated for 'chain 'B' and resid 1918 through 1920' Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1945 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 54 removed outlier: 6.420A pdb=" N ALA A 46 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG A 598 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU A 48 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 596 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A 591 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL A1252 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 593 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR A1254 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 595 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N CYS A1256 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 597 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A1224 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU A1168 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR A1208 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU A1170 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.773A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 194 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR A 330 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL A 196 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 363 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 406 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.693A 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: 6.793A 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 658 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 667 through 671 current: chain 'A' and resid 728 through 731 Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA7, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.593A 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: 6.786A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.603A 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 1526 through 1527 Processing sheet with id=AB2, first strand: chain 'A' and resid 1872 through 1876 removed outlier: 4.244A pdb=" N TRP A1895 " --> pdb=" O GLU A1887 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 46 through 54 removed outlier: 6.001A pdb=" N GLU B 48 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 596 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE B 591 " --> pdb=" O SER B1250 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B1252 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 593 " --> pdb=" O VAL B1252 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR B1254 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 595 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B1224 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B1168 " --> pdb=" O SER B1206 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B1208 " --> pdb=" O GLU B1168 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU B1170 " --> pdb=" O THR B1208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 237 removed outlier: 6.297A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE B 363 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 406 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 365 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N SER B 408 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE B 367 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY B 130 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AB6, first strand: chain 'B' and resid 604 through 608 removed outlier: 6.776A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.372A 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: 3.520A 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 667 through 671 current: chain 'B' and resid 728 through 731 Processing sheet with id=AB7, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AB8, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AB9, first strand: chain 'B' and resid 1116 through 1117 removed outlier: 4.015A pdb=" N GLY B1137 " --> pdb=" O PHE B1107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1423 through 1431 removed outlier: 5.668A pdb=" N ASN B1425 " --> pdb=" O ARG B1449 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG B1449 " --> pdb=" O ASN B1425 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B1427 " --> pdb=" O MET B1447 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET B1447 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B1429 " --> pdb=" O SER B1445 " (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 1599 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1585 through 1599 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 1742 Processing sheet with id=AC2, first strand: chain 'B' and resid 1480 through 1481 removed outlier: 4.104A pdb=" N ARG B1494 " --> pdb=" O THR B1481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1526 through 1527 removed outlier: 3.877A pdb=" N LEU B1526 " --> pdb=" O ILE B1535 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 3.786A pdb=" N VAL B1899 " --> pdb=" O PRO B1883 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B1895 " --> pdb=" O GLU B1887 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3246 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: 7.07 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10387 1.34 - 1.46: 5525 1.46 - 1.58: 15018 1.58 - 1.70: 0 1.70 - 1.81: 186 Bond restraints: 31116 Sorted by residual: bond pdb=" CA ASP B 690 " pdb=" C ASP B 690 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.21e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" CA PHE A1188 " pdb=" C PHE A1188 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 3.07e+00 bond pdb=" N PRO A1131 " pdb=" CD PRO A1131 " ideal model delta sigma weight residual 1.473 1.449 0.024 1.40e-02 5.10e+03 2.91e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 ... (remaining 31111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 41418 1.87 - 3.74: 651 3.74 - 5.61: 72 5.61 - 7.48: 4 7.48 - 9.35: 2 Bond angle restraints: 42147 Sorted by residual: angle pdb=" N ARG A1127 " pdb=" CA ARG A1127 " pdb=" C ARG A1127 " ideal model delta sigma weight residual 109.59 102.18 7.41 1.61e+00 3.86e-01 2.12e+01 angle pdb=" N PHE A1188 " pdb=" CA PHE A1188 " pdb=" C PHE A1188 " ideal model delta sigma weight residual 110.80 101.92 8.88 2.13e+00 2.20e-01 1.74e+01 angle pdb=" N PRO A 199 " pdb=" CA PRO A 199 " pdb=" C PRO A 199 " ideal model delta sigma weight residual 112.47 118.93 -6.46 2.06e+00 2.36e-01 9.82e+00 angle pdb=" CB MET B 200 " pdb=" CG MET B 200 " pdb=" SD MET B 200 " ideal model delta sigma weight residual 112.70 122.05 -9.35 3.00e+00 1.11e-01 9.72e+00 angle pdb=" C GLY A1186 " pdb=" N ILE A1187 " pdb=" CA ILE A1187 " ideal model delta sigma weight residual 123.19 119.37 3.82 1.24e+00 6.50e-01 9.49e+00 ... (remaining 42142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16669 17.93 - 35.87: 1732 35.87 - 53.80: 395 53.80 - 71.73: 68 71.73 - 89.66: 31 Dihedral angle restraints: 18895 sinusoidal: 7791 harmonic: 11104 Sorted by residual: dihedral pdb=" CA ASN A 676 " pdb=" C ASN A 676 " pdb=" N LEU A 677 " pdb=" CA LEU A 677 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 242 " pdb=" C THR A 242 " pdb=" N PRO A 243 " pdb=" CA PRO A 243 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE B 992 " pdb=" C ILE B 992 " pdb=" N PHE B 993 " pdb=" CA PHE B 993 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 18892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2726 0.030 - 0.061: 1297 0.061 - 0.091: 323 0.091 - 0.121: 201 0.121 - 0.151: 37 Chirality restraints: 4584 Sorted by residual: chirality pdb=" CA PHE A1188 " pdb=" N PHE A1188 " pdb=" C PHE A1188 " pdb=" CB PHE A1188 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE A 461 " pdb=" N ILE A 461 " pdb=" C ILE A 461 " pdb=" CB ILE A 461 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE A 962 " pdb=" N ILE A 962 " pdb=" C ILE A 962 " pdb=" CB ILE A 962 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 4581 not shown) Planarity restraints: 5566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1887 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C GLU B1887 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU B1887 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B1888 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 219 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" CD GLU B 219 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 219 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 219 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 494 " -0.179 9.50e-02 1.11e+02 8.07e-02 4.66e+00 pdb=" NE ARG B 494 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 494 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 494 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 494 " -0.002 2.00e-02 2.50e+03 ... (remaining 5563 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3679 2.74 - 3.28: 29565 3.28 - 3.82: 45837 3.82 - 4.36: 53534 4.36 - 4.90: 94615 Nonbonded interactions: 227230 Sorted by model distance: nonbonded pdb=" O GLN B1859 " pdb=" OD1 ASP B1863 " model vdw 2.203 3.040 nonbonded pdb=" O GLN A 292 " pdb=" NE2 GLN A 292 " model vdw 2.231 3.120 nonbonded pdb=" O ASP A 72 " pdb=" OD1 ASP A 72 " model vdw 2.271 3.040 nonbonded pdb=" O SER B1760 " pdb=" OD1 ASP B1761 " model vdw 2.302 3.040 nonbonded pdb=" O ASP B1467 " pdb=" OD1 ASP B1467 " model vdw 2.332 3.040 ... (remaining 227225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 294 or resid 299 through 749 or resid 761 throug \ h 2004)) selection = chain 'B' } 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 31.270 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 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 0.530 31148 Z= 0.259 Angle : 0.749 33.879 42189 Z= 0.336 Chirality : 0.041 0.151 4584 Planarity : 0.005 0.081 5566 Dihedral : 15.513 89.665 11743 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.30 % Allowed : 13.73 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.41 (0.14), residues: 3837 helix: 1.58 (0.14), residues: 1428 sheet: 0.60 (0.22), residues: 541 loop : -0.87 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 494 TYR 0.022 0.002 TYR A1070 PHE 0.019 0.002 PHE A 144 TRP 0.010 0.001 TRP B1895 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (31116) covalent geometry : angle 0.59490 / 0.32 (42147) hydrogen bonds : bond 0.15968 / 10.87 ( 1137) hydrogen bonds : angle 5.37755 / 3.94 ( 3246) metal coordination : bond 0.11852 / 5.58 ( 32) metal coordination : angle 14.43302 / 10.63 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 1.000 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 161 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9078 (ttmm) REVERT: A 749 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8858 (tptp) REVERT: A 890 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8444 (ptt90) REVERT: A 1490 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 809 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8739 (t80) REVERT: B 1431 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8498 (ppt90) REVERT: B 1526 LEU cc_start: 0.8963 (mm) cc_final: 0.8656 (mm) REVERT: B 1564 ARG cc_start: 0.8723 (mpp80) cc_final: 0.8335 (mtm-85) REVERT: B 1628 THR cc_start: 0.9199 (p) cc_final: 0.8866 (t) REVERT: B 1733 ARG cc_start: 0.8380 (tmm-80) cc_final: 0.8029 (tmm160) REVERT: B 1912 MET cc_start: 0.9108 (mmm) cc_final: 0.8568 (tpp) outliers start: 42 outliers final: 23 residues processed: 327 average time/residue: 0.2461 time to fit residues: 120.0828 Evaluate side-chains 318 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1431 ARG Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1538 GLU Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1431 ARG Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 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: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 GLN B 898 GLN B1086 HIS B1425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.048714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.040200 restraints weight = 98258.485| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.40 r_work: 0.2344 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31148 Z= 0.156 Angle : 0.618 20.271 42189 Z= 0.307 Chirality : 0.042 0.164 4584 Planarity : 0.005 0.050 5566 Dihedral : 5.406 58.682 4335 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.76 % Allowed : 13.76 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3837 helix: 1.76 (0.14), residues: 1460 sheet: 0.73 (0.23), residues: 531 loop : -0.78 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.015 0.001 TYR A1007 PHE 0.022 0.001 PHE B 144 TRP 0.041 0.001 TRP B1895 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (31116) covalent geometry : angle 0.57770 / 0.30 (42147) hydrogen bonds : bond 0.06181 / 4.21 ( 1137) hydrogen bonds : angle 4.35836 / 3.20 ( 3246) metal coordination : bond 0.01265 / 0.81 ( 32) metal coordination : angle 6.97464 / 5.39 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 1.064 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 72 ASP cc_start: 0.8832 (t0) cc_final: 0.8589 (t0) REVERT: A 140 LYS cc_start: 0.8039 (mppt) cc_final: 0.7803 (mmtm) REVERT: A 161 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9035 (ttmm) REVERT: A 749 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8835 (tptp) REVERT: A 1039 ASP cc_start: 0.8648 (t0) cc_final: 0.8207 (p0) REVERT: A 1908 GLU cc_start: 0.8480 (tp30) cc_final: 0.8226 (tm-30) REVERT: B 679 HIS cc_start: 0.8246 (m170) cc_final: 0.8025 (m170) REVERT: B 809 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8813 (t80) REVERT: B 830 ASP cc_start: 0.8782 (t70) cc_final: 0.8433 (t70) REVERT: B 1191 ASP cc_start: 0.8522 (m-30) cc_final: 0.8177 (m-30) REVERT: B 1309 GLN cc_start: 0.9328 (mm-40) cc_final: 0.9114 (mm-40) REVERT: B 1438 ASP cc_start: 0.8783 (p0) cc_final: 0.8531 (p0) REVERT: B 1526 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (mm) REVERT: B 1564 ARG cc_start: 0.8728 (mpp80) cc_final: 0.8342 (mtm180) REVERT: B 1606 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8888 (mmtm) REVERT: B 1628 THR cc_start: 0.9193 (p) cc_final: 0.8871 (t) REVERT: B 1733 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.8064 (tmm160) outliers start: 57 outliers final: 28 residues processed: 357 average time/residue: 0.2387 time to fit residues: 128.2946 Evaluate side-chains 325 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [263, 127, 239, 172, 180, 374, 95, 160, 192, 64, 63] chunk 263 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 374 optimal weight: 0.0670 chunk 95 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1436 GLN B 966 HIS B1439 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.048528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.039989 restraints weight = 99240.168| |-----------------------------------------------------------------------------| r_work (start): 0.2439 rms_B_bonded: 2.41 r_work: 0.2339 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2221 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31148 Z= 0.161 Angle : 0.594 16.469 42189 Z= 0.300 Chirality : 0.042 0.161 4584 Planarity : 0.005 0.055 5566 Dihedral : 4.858 57.908 4294 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.22 % Allowed : 14.62 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.67 (0.14), residues: 3837 helix: 1.81 (0.14), residues: 1455 sheet: 0.80 (0.23), residues: 527 loop : -0.79 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 269 TYR 0.016 0.001 TYR A1070 PHE 0.020 0.001 PHE B 144 TRP 0.053 0.001 TRP B1895 HIS 0.007 0.001 HIS B1439 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (31116) covalent geometry : angle 0.56385 / 0.30 (42147) hydrogen bonds : bond 0.05876 / 4.01 ( 1137) hydrogen bonds : angle 4.23307 / 3.11 ( 3246) metal coordination : bond 0.00994 / 0.62 ( 32) metal coordination : angle 5.92920 / 4.53 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.8944 (mtt) cc_final: 0.8617 (mtt) REVERT: A 334 MET cc_start: 0.9211 (mmm) cc_final: 0.8898 (mmm) REVERT: A 749 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8820 (tptp) REVERT: A 1039 ASP cc_start: 0.8622 (t0) cc_final: 0.8180 (p0) REVERT: A 1654 GLN cc_start: 0.9138 (mp10) cc_final: 0.8808 (mp10) REVERT: B 809 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8822 (t80) REVERT: B 830 ASP cc_start: 0.8789 (t70) cc_final: 0.8329 (t0) REVERT: B 995 ASN cc_start: 0.9594 (OUTLIER) cc_final: 0.9281 (m-40) REVERT: B 1069 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8524 (mtp85) REVERT: B 1191 ASP cc_start: 0.8512 (m-30) cc_final: 0.8149 (m-30) REVERT: B 1438 ASP cc_start: 0.8754 (p0) cc_final: 0.8515 (p0) REVERT: B 1494 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7815 (ttp80) REVERT: B 1526 LEU cc_start: 0.8946 (mm) cc_final: 0.8637 (mm) REVERT: B 1564 ARG cc_start: 0.8760 (mpp80) cc_final: 0.8404 (mtm110) REVERT: B 1606 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8843 (mmtm) REVERT: B 1628 THR cc_start: 0.9188 (p) cc_final: 0.8861 (t) REVERT: B 1733 ARG cc_start: 0.8388 (tmm-80) cc_final: 0.8134 (tmm160) outliers start: 72 outliers final: 40 residues processed: 359 average time/residue: 0.2350 time to fit residues: 127.5473 Evaluate side-chains 332 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1431 ARG Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 995 ASN Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1439 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1657 SER Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [70, 247, 209, 200, 14, 286, 338, 267, 300, 92, 310] chunk 70 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 286 optimal weight: 0.9990 chunk 338 optimal weight: 0.2980 chunk 267 optimal weight: 0.3980 chunk 300 optimal weight: 2.9990 chunk 92 optimal weight: 0.0070 chunk 310 optimal weight: 2.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 HIS B1620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.050381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.041769 restraints weight = 97188.367| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 2.42 r_work: 0.2396 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31148 Z= 0.107 Angle : 0.540 13.242 42189 Z= 0.272 Chirality : 0.040 0.187 4584 Planarity : 0.004 0.052 5566 Dihedral : 4.541 58.243 4290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.88 % Allowed : 15.18 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3837 helix: 2.06 (0.14), residues: 1446 sheet: 0.83 (0.23), residues: 518 loop : -0.72 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 890 TYR 0.012 0.001 TYR A1007 PHE 0.022 0.001 PHE B 144 TRP 0.053 0.001 TRP B1895 HIS 0.011 0.001 HIS B1439 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (31116) covalent geometry : angle 0.51760 / 0.27 (42147) hydrogen bonds : bond 0.04559 / 3.14 ( 1137) hydrogen bonds : angle 3.96740 / 2.91 ( 3246) metal coordination : bond 0.00682 / 0.44 ( 32) metal coordination : angle 4.89690 / 3.68 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 1.293 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 320 MET cc_start: 0.8900 (mtt) cc_final: 0.8582 (mtt) REVERT: A 749 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8789 (tptp) REVERT: A 896 LYS cc_start: 0.9246 (mttt) cc_final: 0.8977 (tptp) REVERT: A 900 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.7952 (p) REVERT: A 1129 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8964 (t) REVERT: A 1216 ASP cc_start: 0.6477 (p0) cc_final: 0.6218 (p0) REVERT: A 1654 GLN cc_start: 0.9135 (mp10) cc_final: 0.8732 (mp10) REVERT: A 1908 GLU cc_start: 0.8474 (tp30) cc_final: 0.8262 (tm-30) REVERT: B 21 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: B 292 GLN cc_start: 0.8838 (tp40) cc_final: 0.7854 (pp30) REVERT: B 673 SER cc_start: 0.8317 (m) cc_final: 0.7983 (t) REVERT: B 809 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8912 (t80) REVERT: B 830 ASP cc_start: 0.8760 (t70) cc_final: 0.8445 (t70) REVERT: B 995 ASN cc_start: 0.9557 (OUTLIER) cc_final: 0.9249 (m-40) REVERT: B 1191 ASP cc_start: 0.8534 (m-30) cc_final: 0.8171 (m-30) REVERT: B 1526 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 1564 ARG cc_start: 0.8785 (mpp80) cc_final: 0.8416 (mtm110) REVERT: B 1606 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8827 (mmtm) REVERT: B 1608 ASP cc_start: 0.8365 (t0) cc_final: 0.8132 (t0) REVERT: B 1628 THR cc_start: 0.9153 (p) cc_final: 0.8823 (t) REVERT: B 1733 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.8117 (tmm160) outliers start: 61 outliers final: 37 residues processed: 356 average time/residue: 0.2401 time to fit residues: 127.8801 Evaluate side-chains 335 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 995 ASN Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [366, 176, 7, 248, 64, 169, 115, 319, 237, 307, 350] chunk 366 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 307 optimal weight: 0.0020 chunk 350 optimal weight: 8.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 898 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.042009 restraints weight = 97686.411| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.43 r_work: 0.2401 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31148 Z= 0.107 Angle : 0.531 10.928 42189 Z= 0.268 Chirality : 0.040 0.182 4584 Planarity : 0.004 0.055 5566 Dihedral : 4.393 58.240 4289 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.00 % Allowed : 15.61 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.95 (0.14), residues: 3837 helix: 2.12 (0.14), residues: 1449 sheet: 0.78 (0.23), residues: 520 loop : -0.63 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 178 TYR 0.012 0.001 TYR A1007 PHE 0.020 0.001 PHE B 144 TRP 0.037 0.001 TRP B1895 HIS 0.007 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (31116) covalent geometry : angle 0.51339 / 0.27 (42147) hydrogen bonds : bond 0.04368 / 3.00 ( 1137) hydrogen bonds : angle 3.88016 / 2.85 ( 3246) metal coordination : bond 0.00615 / 0.39 ( 32) metal coordination : angle 4.32215 / 3.20 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.907 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 161 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9065 (ttmm) REVERT: A 320 MET cc_start: 0.8900 (mtt) cc_final: 0.8601 (mtt) REVERT: A 749 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8790 (tptp) REVERT: A 890 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8770 (ptt90) REVERT: A 1129 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8955 (t) REVERT: A 1216 ASP cc_start: 0.6348 (p0) cc_final: 0.6028 (p0) REVERT: A 1654 GLN cc_start: 0.9083 (mp10) cc_final: 0.8710 (mp10) REVERT: A 1908 GLU cc_start: 0.8488 (tp30) cc_final: 0.8243 (tm-30) REVERT: B 21 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: B 292 GLN cc_start: 0.8818 (tp40) cc_final: 0.7814 (pp30) REVERT: B 673 SER cc_start: 0.8332 (m) cc_final: 0.8012 (t) REVERT: B 809 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8926 (t80) REVERT: B 830 ASP cc_start: 0.8743 (t70) cc_final: 0.8306 (t0) REVERT: B 1191 ASP cc_start: 0.8516 (m-30) cc_final: 0.8157 (m-30) REVERT: B 1344 ASP cc_start: 0.6530 (t70) cc_final: 0.6026 (t70) REVERT: B 1526 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8591 (mm) REVERT: B 1564 ARG cc_start: 0.8723 (mpp80) cc_final: 0.8404 (mtm180) REVERT: B 1606 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8812 (mmtm) REVERT: B 1608 ASP cc_start: 0.8418 (t0) cc_final: 0.8162 (t0) REVERT: B 1628 THR cc_start: 0.9134 (p) cc_final: 0.8802 (t) REVERT: B 1733 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.8139 (tmm160) outliers start: 65 outliers final: 38 residues processed: 353 average time/residue: 0.2413 time to fit residues: 127.9952 Evaluate side-chains 342 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 299 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [2, 342, 58, 328, 94, 7, 308, 238, 3, 288, 76] chunk 2 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 308 optimal weight: 0.3980 chunk 238 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 898 GLN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.050516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.041864 restraints weight = 97407.333| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 2.42 r_work: 0.2397 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2281 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31148 Z= 0.113 Angle : 0.544 10.613 42189 Z= 0.274 Chirality : 0.040 0.181 4584 Planarity : 0.004 0.050 5566 Dihedral : 4.302 57.859 4286 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.22 % Allowed : 15.76 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.97 (0.14), residues: 3837 helix: 2.11 (0.14), residues: 1454 sheet: 0.81 (0.23), residues: 529 loop : -0.61 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 635 TYR 0.012 0.001 TYR B1338 PHE 0.020 0.001 PHE B 144 TRP 0.026 0.001 TRP B1895 HIS 0.007 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (31116) covalent geometry : angle 0.52800 / 0.27 (42147) hydrogen bonds : bond 0.04408 / 3.03 ( 1137) hydrogen bonds : angle 3.87120 / 2.83 ( 3246) metal coordination : bond 0.00617 / 0.39 ( 32) metal coordination : angle 4.16941 / 3.10 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 1.227 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 72 ASP cc_start: 0.9075 (t0) cc_final: 0.8796 (t0) REVERT: A 161 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9073 (ttmm) REVERT: A 320 MET cc_start: 0.8899 (mtt) cc_final: 0.8619 (mtt) REVERT: A 749 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8807 (tptp) REVERT: A 1129 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8953 (t) REVERT: A 1216 ASP cc_start: 0.6391 (p0) cc_final: 0.6071 (p0) REVERT: A 1654 GLN cc_start: 0.9094 (mp10) cc_final: 0.8714 (mp10) REVERT: B 21 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: B 292 GLN cc_start: 0.8807 (tp40) cc_final: 0.7806 (pp30) REVERT: B 673 SER cc_start: 0.8325 (m) cc_final: 0.8029 (t) REVERT: B 809 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8920 (t80) REVERT: B 830 ASP cc_start: 0.8739 (t70) cc_final: 0.8286 (t0) REVERT: B 1069 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (mtp85) REVERT: B 1191 ASP cc_start: 0.8528 (m-30) cc_final: 0.8178 (m-30) REVERT: B 1244 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8370 (ttt180) REVERT: B 1526 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 1564 ARG cc_start: 0.8762 (mpp80) cc_final: 0.8444 (mtm110) REVERT: B 1606 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8867 (mmtm) REVERT: B 1608 ASP cc_start: 0.8476 (t0) cc_final: 0.8188 (t0) REVERT: B 1628 THR cc_start: 0.9132 (p) cc_final: 0.8801 (t) REVERT: B 1733 ARG cc_start: 0.8388 (tmm-80) cc_final: 0.8150 (tmm160) outliers start: 72 outliers final: 44 residues processed: 358 average time/residue: 0.2364 time to fit residues: 127.7520 Evaluate side-chains 344 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [217, 296, 13, 307, 257, 323, 190, 322, 330, 68, 31] chunk 217 optimal weight: 3.9990 chunk 296 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 307 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 323 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.050056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.041409 restraints weight = 97740.680| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 2.42 r_work: 0.2384 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31148 Z= 0.131 Angle : 0.564 11.474 42189 Z= 0.283 Chirality : 0.040 0.171 4584 Planarity : 0.004 0.050 5566 Dihedral : 4.347 57.625 4286 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.07 % Allowed : 16.53 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.97 (0.14), residues: 3837 helix: 2.09 (0.14), residues: 1455 sheet: 0.82 (0.23), residues: 518 loop : -0.59 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 875 TYR 0.013 0.001 TYR A1007 PHE 0.020 0.001 PHE B 144 TRP 0.047 0.001 TRP B1895 HIS 0.005 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (31116) covalent geometry : angle 0.54875 / 0.28 (42147) hydrogen bonds : bond 0.04670 / 3.20 ( 1137) hydrogen bonds : angle 3.89744 / 2.85 ( 3246) metal coordination : bond 0.00665 / 0.42 ( 32) metal coordination : angle 4.15381 / 3.09 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 295 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9095 (t0) cc_final: 0.8802 (t0) REVERT: A 161 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9059 (ttmm) REVERT: A 749 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8802 (tptp) REVERT: A 1216 ASP cc_start: 0.6382 (p0) cc_final: 0.6107 (p0) REVERT: A 1654 GLN cc_start: 0.9102 (mp10) cc_final: 0.8699 (mp10) REVERT: A 1908 GLU cc_start: 0.8520 (tp30) cc_final: 0.8189 (tm-30) REVERT: B 21 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: B 292 GLN cc_start: 0.8790 (tp40) cc_final: 0.7795 (pp30) REVERT: B 809 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8859 (t80) REVERT: B 830 ASP cc_start: 0.8758 (t70) cc_final: 0.8306 (t0) REVERT: B 1069 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8408 (mtp85) REVERT: B 1191 ASP cc_start: 0.8516 (m-30) cc_final: 0.8154 (m-30) REVERT: B 1244 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8428 (ttt180) REVERT: B 1526 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 1564 ARG cc_start: 0.8775 (mpp80) cc_final: 0.8460 (mtm110) REVERT: B 1628 THR cc_start: 0.9138 (p) cc_final: 0.8812 (t) REVERT: B 1733 ARG cc_start: 0.8391 (tmm-80) cc_final: 0.8164 (tmm160) outliers start: 67 outliers final: 50 residues processed: 343 average time/residue: 0.2357 time to fit residues: 121.5865 Evaluate side-chains 349 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1746 ILE Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [25, 99, 352, 201, 164, 348, 349, 35, 29, 82, 127] chunk 25 optimal weight: 0.0770 chunk 99 optimal weight: 0.9990 chunk 352 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 349 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.041509 restraints weight = 97748.023| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.43 r_work: 0.2385 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31148 Z= 0.125 Angle : 0.564 11.134 42189 Z= 0.284 Chirality : 0.040 0.170 4584 Planarity : 0.004 0.050 5566 Dihedral : 4.334 57.670 4286 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 16.84 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3837 helix: 2.07 (0.14), residues: 1460 sheet: 0.84 (0.23), residues: 512 loop : -0.62 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 178 TYR 0.013 0.001 TYR A1007 PHE 0.020 0.001 PHE B 144 TRP 0.078 0.001 TRP B1895 HIS 0.005 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (31116) covalent geometry : angle 0.54926 / 0.28 (42147) hydrogen bonds : bond 0.04599 / 3.15 ( 1137) hydrogen bonds : angle 3.89052 / 2.84 ( 3246) metal coordination : bond 0.00636 / 0.40 ( 32) metal coordination : angle 4.04774 / 3.04 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 301 time to evaluate : 1.060 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: A 72 ASP cc_start: 0.9103 (t0) cc_final: 0.8801 (t0) REVERT: A 161 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (ttmm) REVERT: A 749 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8801 (tptp) REVERT: A 1216 ASP cc_start: 0.6299 (p0) cc_final: 0.6000 (p0) REVERT: A 1908 GLU cc_start: 0.8486 (tp30) cc_final: 0.8133 (tm-30) REVERT: B 21 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8516 (mt-10) REVERT: B 292 GLN cc_start: 0.8783 (tp40) cc_final: 0.7766 (pp30) REVERT: B 809 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8851 (t80) REVERT: B 830 ASP cc_start: 0.8756 (t70) cc_final: 0.8306 (t0) REVERT: B 1069 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: B 1191 ASP cc_start: 0.8522 (m-30) cc_final: 0.8163 (m-30) REVERT: B 1244 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8432 (ttt180) REVERT: B 1526 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8653 (mm) REVERT: B 1553 PHE cc_start: 0.7933 (m-10) cc_final: 0.7665 (m-80) REVERT: B 1564 ARG cc_start: 0.8838 (mpp80) cc_final: 0.8535 (mtm110) REVERT: B 1565 MET cc_start: 0.8589 (mmm) cc_final: 0.8160 (mmm) REVERT: B 1628 THR cc_start: 0.9137 (p) cc_final: 0.8812 (t) REVERT: B 1733 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.8171 (tmm160) outliers start: 67 outliers final: 54 residues processed: 347 average time/residue: 0.2275 time to fit residues: 119.0624 Evaluate side-chains 353 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 294 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1484 GLN Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1562 PHE Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1746 ILE Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1846 LYS Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1657 SER Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Chi-restraints excluded: chain B residue 1943 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [20, 316, 375, 327, 150, 147, 61, 133, 117, 60, 193] chunk 20 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 327 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.050865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.042194 restraints weight = 97447.112| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.42 r_work: 0.2407 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31148 Z= 0.113 Angle : 0.570 12.148 42189 Z= 0.286 Chirality : 0.040 0.181 4584 Planarity : 0.004 0.050 5566 Dihedral : 4.239 57.849 4284 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.04 % Allowed : 17.03 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3837 helix: 2.15 (0.14), residues: 1453 sheet: 0.87 (0.23), residues: 512 loop : -0.58 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 178 TYR 0.012 0.001 TYR B1338 PHE 0.020 0.001 PHE B 144 TRP 0.057 0.001 TRP B1895 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (31116) covalent geometry : angle 0.55638 / 0.29 (42147) hydrogen bonds : bond 0.04223 / 2.91 ( 1137) hydrogen bonds : angle 3.83635 / 2.79 ( 3246) metal coordination : bond 0.00547 / 0.35 ( 32) metal coordination : angle 3.90393 / 3.00 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 1.051 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: A 72 ASP cc_start: 0.9114 (t0) cc_final: 0.8790 (t0) REVERT: A 161 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9054 (ttmm) REVERT: A 749 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8785 (tptp) REVERT: A 1216 ASP cc_start: 0.6198 (p0) cc_final: 0.5647 (p0) REVERT: A 1908 GLU cc_start: 0.8475 (tp30) cc_final: 0.8149 (tm-30) REVERT: B 21 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: B 292 GLN cc_start: 0.8765 (tp40) cc_final: 0.7756 (pp30) REVERT: B 809 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8910 (t80) REVERT: B 830 ASP cc_start: 0.8725 (t70) cc_final: 0.8286 (t0) REVERT: B 875 ARG cc_start: 0.8914 (ttp80) cc_final: 0.8594 (tpt90) REVERT: B 1069 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (mtp85) REVERT: B 1191 ASP cc_start: 0.8506 (m-30) cc_final: 0.8156 (m-30) REVERT: B 1244 ARG cc_start: 0.8934 (mmm-85) cc_final: 0.8399 (ttt180) REVERT: B 1526 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8649 (mm) REVERT: B 1564 ARG cc_start: 0.8803 (mpp80) cc_final: 0.8524 (mtm110) REVERT: B 1628 THR cc_start: 0.9104 (p) cc_final: 0.8766 (t) REVERT: B 1733 ARG cc_start: 0.8400 (tmm-80) cc_final: 0.8183 (tmm160) outliers start: 66 outliers final: 48 residues processed: 353 average time/residue: 0.2412 time to fit residues: 127.6850 Evaluate side-chains 349 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1484 GLN Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1746 ILE Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1657 SER Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1771 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [37, 208, 94, 161, 18, 263, 107, 142, 157, 91, 247] chunk 37 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 247 optimal weight: 0.0670 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B1054 ASN B1808 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.049234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.040607 restraints weight = 97675.984| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 2.41 r_work: 0.2360 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2243 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31148 Z= 0.160 Angle : 0.608 12.322 42189 Z= 0.308 Chirality : 0.042 0.211 4584 Planarity : 0.004 0.051 5566 Dihedral : 4.445 57.326 4284 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.91 % Allowed : 17.27 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 0.87 (0.14), residues: 3837 helix: 1.98 (0.14), residues: 1459 sheet: 0.78 (0.23), residues: 530 loop : -0.65 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 890 TYR 0.016 0.001 TYR A1070 PHE 0.020 0.001 PHE A 144 TRP 0.053 0.001 TRP B1895 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (31116) covalent geometry : angle 0.59358 / 0.31 (42147) hydrogen bonds : bond 0.05260 / 3.60 ( 1137) hydrogen bonds : angle 3.97989 / 2.89 ( 3246) metal coordination : bond 0.00766 / 0.48 ( 32) metal coordination : angle 4.26832 / 3.26 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 1.116 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: A 72 ASP cc_start: 0.9138 (t0) cc_final: 0.8836 (t0) REVERT: A 161 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9044 (ttmm) REVERT: A 749 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8811 (tptp) REVERT: A 1908 GLU cc_start: 0.8490 (tp30) cc_final: 0.8124 (tm-30) REVERT: B 21 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: B 809 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8829 (t80) REVERT: B 830 ASP cc_start: 0.8795 (t70) cc_final: 0.8325 (t0) REVERT: B 1069 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8468 (mtp85) REVERT: B 1191 ASP cc_start: 0.8544 (m-30) cc_final: 0.8188 (m-30) REVERT: B 1244 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8459 (ttt180) REVERT: B 1526 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8644 (mm) REVERT: B 1564 ARG cc_start: 0.8807 (mpp80) cc_final: 0.8533 (mtm110) REVERT: B 1565 MET cc_start: 0.8644 (mmm) cc_final: 0.8222 (mmm) REVERT: B 1628 THR cc_start: 0.9133 (p) cc_final: 0.8801 (t) REVERT: B 1912 MET cc_start: 0.9112 (tpt) cc_final: 0.8855 (tpt) outliers start: 62 outliers final: 46 residues processed: 348 average time/residue: 0.2410 time to fit residues: 125.4419 Evaluate side-chains 343 residues out of total 3242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 1286 HIS Chi-restraints excluded: chain A residue 1484 GLN Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1745 LEU Chi-restraints excluded: chain A residue 1746 ILE Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1886 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1069 ARG Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1250 SER Chi-restraints excluded: chain B residue 1268 HIS Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1528 CYS Chi-restraints excluded: chain B residue 1607 ASN Chi-restraints excluded: chain B residue 1615 ASP Chi-restraints excluded: chain B residue 1657 SER Chi-restraints excluded: chain B residue 1738 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: [252, 37, 288, 45, 95, 247, 232, 181, 210, 335, 313] chunk 252 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 247 optimal weight: 0.0470 chunk 232 optimal weight: 6.9990 chunk 181 optimal weight: 0.5980 chunk 210 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 313 optimal weight: 0.1980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.042424 restraints weight = 97230.952| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 2.42 r_work: 0.2414 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31148 Z= 0.109 Angle : 0.577 12.390 42189 Z= 0.290 Chirality : 0.040 0.205 4584 Planarity : 0.004 0.052 5566 Dihedral : 4.239 58.074 4284 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.60 % Allowed : 17.58 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3837 helix: 2.22 (0.14), residues: 1440 sheet: 0.82 (0.23), residues: 515 loop : -0.56 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 875 TYR 0.011 0.001 TYR A1007 PHE 0.020 0.001 PHE B 144 TRP 0.047 0.001 TRP B1895 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (31116) covalent geometry : angle 0.56517 / 0.29 (42147) hydrogen bonds : bond 0.04103 / 2.83 ( 1137) hydrogen bonds : angle 3.83075 / 2.79 ( 3246) metal coordination : bond 0.00510 / 0.34 ( 32) metal coordination : angle 3.72170 / 2.86 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6718.15 seconds wall clock time: 115 minutes 36.79 seconds (6936.79 seconds total)