Starting phenix.real_space_refine on Thu Oct 29 11:24:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdw_65908/10_2026/9wdw_65908.map" } resolution = 3.36 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= 0.004 sd= 0.504 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 34 5.49 5 S 121 5.16 5 C 19512 2.51 5 N 5592 2.21 5 O 5917 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: 31184 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1928, 15234 Classifications: {'peptide': 1928} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1818} Chain breaks: 3 Chain: "B" Number of atoms: 15275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1934, 15275 Classifications: {'peptide': 1934} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1824} Chain breaks: 2 Chain: "C" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' ZN': 4, 'ANP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8619 SG CYS A1110 33.285 64.041 85.341 1.00 49.82 S ATOM 8639 SG CYS A1113 35.196 64.560 82.032 1.00 64.38 S ATOM 8734 SG CYS A1125 35.517 67.029 84.819 1.00 81.00 S ATOM 8758 SG CYS A1128 31.879 66.915 82.426 1.00 53.97 S ATOM 5039 SG CYS A 646 39.985 62.331 72.785 1.00 62.25 S ATOM 5059 SG CYS A 649 37.552 61.050 75.251 1.00 59.94 S ATOM 5935 SG CYS A 770 36.389 63.008 72.119 1.00 66.27 S ATOM 5957 SG CYS A 773 37.692 64.813 75.013 1.00 77.66 S ATOM 14033 SG CYS A1799 43.203 35.544 54.544 1.00 76.75 S ATOM 14061 SG CYS A1803 46.083 37.485 56.539 1.00 58.82 S ATOM 14090 SG CYS A1806 47.042 35.976 53.064 1.00 62.13 S ATOM 11786 SG CYS A1509 50.113 51.217 22.112 1.00113.02 S ATOM 11804 SG CYS A1512 50.817 47.563 23.031 1.00119.36 S ATOM 11909 SG CYS A1528 52.948 49.421 20.558 1.00118.37 S ATOM 11931 SG CYS A1531 49.217 48.865 19.787 1.00133.34 S ATOM 23854 SG CYS B1110 106.675 112.070 80.835 1.00 54.63 S ATOM 23874 SG CYS B1113 104.364 111.753 77.842 1.00 59.44 S ATOM 23969 SG CYS B1125 104.261 108.939 80.020 1.00 65.24 S ATOM 23993 SG CYS B1128 107.439 110.042 78.238 1.00 63.63 S ATOM 20250 SG CYS B 646 103.860 117.410 70.079 1.00 64.65 S ATOM 20270 SG CYS B 649 106.092 118.641 72.844 1.00 60.10 S ATOM 21165 SG CYS B 770 107.543 117.510 69.450 1.00 66.34 S ATOM 21187 SG CYS B 773 106.519 115.065 71.981 1.00 64.29 S ATOM 29308 SG CYS B1799 87.720 152.374 49.919 1.00 59.49 S ATOM 29336 SG CYS B1803 84.987 150.654 51.297 1.00 77.10 S ATOM 29365 SG CYS B1806 84.903 151.075 47.520 1.00 68.42 S ATOM 27061 SG CYS B1509 94.972 128.723 21.951 1.00 72.37 S ATOM 27079 SG CYS B1512 93.849 132.488 23.502 1.00 80.35 S ATOM 27184 SG CYS B1528 92.139 130.623 20.632 1.00 75.15 S ATOM 27206 SG CYS B1531 95.621 131.939 20.322 1.00 81.77 S Time building chain proxies: 6.05, per 1000 atoms: 0.19 Number of scatterers: 31184 At special positions: 0 Unit cell: (138.24, 175.68, 128.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 121 16.00 P 34 15.00 O 5917 8.00 N 5592 7.00 C 19512 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1125 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1113 " 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 773 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 646 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A1795 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1803 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1806 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1799 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1531 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1509 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1528 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1512 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1125 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1113 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1110 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 770 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 649 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 773 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 646 " pdb=" ZN B2004 " pdb="ZN ZN B2004 " - pdb=" NE2 HIS B1795 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1803 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1799 " pdb="ZN ZN B2004 " - pdb=" SG CYS B1806 " pdb=" ZN B2005 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1531 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1528 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1509 " pdb="ZN ZN B2005 " - pdb=" SG CYS B1512 " Number of angles added : 42 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 24 sheets defined 44.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.152A pdb=" N THR A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.564A pdb=" N VAL A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 256 through 293 removed outlier: 3.702A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.943A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.776A pdb=" N LEU A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 393 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.587A pdb=" N LEU A 403 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.890A pdb=" N VAL A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.626A pdb=" N SER A 451 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 4.181A 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 Proline residue: A 575 - end of helix removed outlier: 3.848A pdb=" N ASN A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.540A pdb=" N HIS A 679 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 827 through 865 removed outlier: 3.724A pdb=" N GLU A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 848 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 865 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.698A pdb=" N LYS A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 900 removed outlier: 3.884A pdb=" N ILE A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 906 Processing helix chain 'A' and resid 911 through 915 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 984 Processing helix chain 'A' and resid 984 through 992 Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 4.225A pdb=" N ASP A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.907A pdb=" N GLU A1073 " --> pdb=" O ARG A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1095 removed outlier: 3.590A 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 removed outlier: 3.536A pdb=" N THR A1145 " --> pdb=" O ALA A1141 " (cutoff:3.500A) 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 1199 Processing helix chain 'A' and resid 1210 through 1213 removed outlier: 4.511A pdb=" N VAL A1213 " --> pdb=" O THR A1210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1210 through 1213' Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 3.520A pdb=" N TYR A1235 " --> pdb=" O GLN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.735A pdb=" N ALA A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1275 removed outlier: 3.671A pdb=" N THR A1273 " --> pdb=" O PRO A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1314 removed outlier: 3.869A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1322 removed outlier: 3.793A pdb=" N LEU A1322 " --> pdb=" O GLY A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.569A pdb=" N GLU A1351 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1368 removed outlier: 3.512A pdb=" N ASP A1361 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 3.946A 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 Processing helix chain 'A' and resid 1394 through 1397 Processing helix chain 'A' and resid 1403 through 1411 Processing helix chain 'A' and resid 1451 through 1458 removed outlier: 4.072A pdb=" N PHE A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1540 removed outlier: 3.928A 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 1691 through 1695 removed outlier: 4.325A pdb=" N PHE A1694 " --> pdb=" O LYS A1691 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A1695 " --> pdb=" O GLY A1692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1691 through 1695' 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 1755 Processing helix chain 'A' and resid 1765 through 1777 removed outlier: 3.505A 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 1816 removed outlier: 4.630A pdb=" N ARG A1814 " --> pdb=" O GLY A1811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS A1816 " --> pdb=" O ARG A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1831 removed outlier: 3.604A pdb=" N LEU A1831 " --> pdb=" O TYR A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1868 Processing helix chain 'A' and resid 1908 through 1917 Processing helix chain 'A' and resid 1918 through 1920 No H-bonds generated for 'chain 'A' and resid 1918 through 1920' Processing helix chain 'A' and resid 1929 through 1935 Processing helix chain 'A' and resid 1935 through 1945 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.593A pdb=" N GLU B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.675A pdb=" N ARG B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.578A pdb=" N VAL B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 256 through 292 removed outlier: 3.579A pdb=" N ARG B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 5.001A pdb=" N LYS B 296 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 297 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.658A pdb=" N TYR B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 306 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.525A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.816A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 374 through 393 removed outlier: 3.668A pdb=" N GLY B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.613A pdb=" N SER B 451 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 452 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 483 Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.592A pdb=" N VAL B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 535 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 560 through 574 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.659A pdb=" N HIS B 679 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 749 through 752 Processing helix chain 'B' and resid 796 through 816 Processing helix chain 'B' and resid 827 through 864 removed outlier: 3.733A pdb=" N GLU B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 864 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 883 Processing helix chain 'B' and resid 884 through 892 Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.581A pdb=" N LEU B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 933 removed outlier: 3.769A pdb=" N LEU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 removed outlier: 4.025A pdb=" N SER B 943 " --> pdb=" O HIS B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 953 Processing helix chain 'B' and resid 969 through 993 removed outlier: 3.762A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 removed outlier: 3.645A pdb=" N THR B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B1004 " --> pdb=" O LEU B1000 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 999 through 1004' Processing helix chain 'B' and resid 1016 through 1028 removed outlier: 3.544A pdb=" N ARG B1024 " --> pdb=" O ASP B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1052 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1069 through 1085 Processing helix chain 'B' and resid 1139 through 1146 removed outlier: 3.682A pdb=" N GLU B1144 " --> pdb=" O GLU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1159 removed outlier: 3.610A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1193 through 1199 Processing helix chain 'B' and resid 1209 through 1214 removed outlier: 3.775A pdb=" N VAL B1213 " --> pdb=" O THR B1210 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B1214 " --> pdb=" O MET B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1240 Processing helix chain 'B' and resid 1259 through 1268 removed outlier: 3.575A pdb=" N TYR B1264 " --> pdb=" O SER B1260 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B1265 " --> pdb=" O HIS B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1273 removed outlier: 4.366A pdb=" N ILE B1272 " --> pdb=" O HIS B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1314 removed outlier: 3.775A pdb=" N LEU B1293 " --> pdb=" O ILE B1289 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B1301 " --> pdb=" O THR B1297 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1322 removed outlier: 4.057A pdb=" N LEU B1322 " --> pdb=" O GLY B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1333 through 1339 Processing helix chain 'B' and resid 1344 through 1355 removed outlier: 3.558A pdb=" N GLN B1355 " --> pdb=" O GLU B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1368 removed outlier: 3.944A pdb=" N ARG B1360 " --> pdb=" O THR B1356 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B1368 " --> pdb=" O ILE B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1382 through 1392 Processing helix chain 'B' and resid 1393 through 1397 Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1451 through 1458 removed outlier: 3.795A pdb=" N VAL B1455 " --> pdb=" O LEU B1451 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B1456 " --> pdb=" O ASP B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1540 removed outlier: 3.697A 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: 4.260A pdb=" N PHE B1694 " --> pdb=" O LYS B1691 " (cutoff:3.500A) removed outlier: 3.978A 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 1723 No H-bonds generated for 'chain 'B' and resid 1721 through 1723' Processing helix chain 'B' and resid 1750 through 1756 Processing helix chain 'B' and resid 1765 through 1777 removed outlier: 3.539A pdb=" N ASP B1769 " --> pdb=" O PRO B1765 " (cutoff:3.500A) Processing helix chain 'B' and resid 1780 through 1787 Processing helix chain 'B' and resid 1794 through 1799 Processing helix chain 'B' and resid 1812 through 1816 removed outlier: 3.753A pdb=" N HIS B1816 " --> pdb=" O ARG B1813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1820 through 1833 removed outlier: 3.722A pdb=" N LEU B1831 " --> pdb=" O TYR B1827 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B1832 " --> pdb=" O LEU B1828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1843 through 1847 removed outlier: 4.163A pdb=" N LYS B1846 " --> pdb=" O GLY B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1868 Processing helix chain 'B' and resid 1908 through 1917 removed outlier: 3.913A pdb=" N MET B1912 " --> pdb=" O GLU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1935 Processing helix chain 'B' and resid 1935 through 1944 removed outlier: 3.648A pdb=" N LYS B1944 " --> pdb=" O LEU B1940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 7.011A pdb=" N PHE A 591 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL A1252 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 593 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR A1254 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A 595 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N CYS A1256 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 597 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A1223 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE A1255 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLN A1225 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE A 822 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A1224 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A1208 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.649A pdb=" N GLY A 236 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ASN A 331 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 195 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 365 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 408 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE A 367 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 130 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER A 409 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 132 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.708A pdb=" N PHE A 604 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 619 " --> pdb=" O PHE A 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 652 through 657 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 652 through 657 current: chain 'A' and resid 728 through 731 Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 910 Processing sheet with id=AA7, first strand: chain 'A' and resid 955 through 958 Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.710A 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: 6.978A pdb=" N SER A1445 " --> pdb=" O VAL A1428 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A1430 " --> pdb=" O GLU A1443 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU A1443 " --> pdb=" O LEU A1430 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1442 through 1450 current: chain 'A' and resid 1469 through 1476 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1469 through 1476 current: chain 'A' and resid 1515 through 1518 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1515 through 1518 current: chain 'A' and resid 1585 through 1602 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1585 through 1602 current: chain 'A' and resid 1637 through 1640 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1637 through 1640 current: chain 'A' and resid 1736 through 1743 Processing sheet with id=AB1, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AB2, first strand: chain 'A' and resid 1493 through 1494 removed outlier: 7.352A pdb=" N ILE A1493 " --> pdb=" O ASP A1634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1872 through 1876 removed outlier: 3.634A pdb=" N VAL A1899 " --> pdb=" O PRO A1883 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP A1895 " --> pdb=" O GLU A1887 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ARG A1925 " --> pdb=" O LEU A1894 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A1896 " --> pdb=" O ARG A1925 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A1927 " --> pdb=" O ARG A1896 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A1898 " --> pdb=" O LEU A1927 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.008A pdb=" N PHE B 591 " --> pdb=" O SER B1250 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL B1252 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 593 " --> pdb=" O VAL B1252 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR B1254 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 595 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS B1256 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 597 " --> pdb=" O CYS B1256 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B1223 " --> pdb=" O VAL B1253 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE B1255 " --> pdb=" O VAL B1223 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN B1225 " --> pdb=" O PHE B1255 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 822 " --> pdb=" O THR B1222 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B1224 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY B 821 " --> pdb=" O LEU B1205 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B1207 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 823 " --> pdb=" O VAL B1207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.685A pdb=" N PHE B 235 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 236 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ASN B 331 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 195 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP B 368 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 197 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 363 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 406 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 365 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER B 408 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 367 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 131 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AB8, first strand: chain 'B' and resid 604 through 608 removed outlier: 6.576A pdb=" N PHE B 604 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.131A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 668 through 671 current: chain 'B' and resid 728 through 731 Processing sheet with id=AB9, first strand: chain 'B' and resid 908 through 910 Processing sheet with id=AC1, first strand: chain 'B' and resid 955 through 958 Processing sheet with id=AC2, first strand: chain 'B' and resid 1116 through 1117 removed outlier: 3.750A pdb=" N GLY B1137 " --> pdb=" O PHE B1107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1423 through 1432 removed outlier: 6.657A pdb=" N SER B1445 " --> pdb=" O VAL B1428 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B1430 " --> pdb=" O GLU B1443 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU B1443 " --> pdb=" O LEU B1430 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1442 through 1450 current: chain 'B' and resid 1469 through 1476 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1469 through 1476 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 1743 Processing sheet with id=AC4, first strand: chain 'B' and resid 1493 through 1494 removed outlier: 7.396A pdb=" N ILE B1493 " --> pdb=" O ASP B1634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 1526 through 1527 Processing sheet with id=AC6, first strand: chain 'B' and resid 1872 through 1876 removed outlier: 4.103A pdb=" N TRP B1895 " --> pdb=" O GLU B1887 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS B1889 " --> pdb=" O GLU B1893 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU B1893 " --> pdb=" O LYS B1889 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3243 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: 7.70 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10154 1.33 - 1.46: 5380 1.46 - 1.58: 16134 1.58 - 1.70: 63 1.70 - 1.82: 186 Bond restraints: 31917 Sorted by residual: bond pdb=" O3A ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.700 1.607 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C4 ANP B2001 " pdb=" C5 ANP B2001 " ideal model delta sigma weight residual 1.387 1.470 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N3B ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.669 1.747 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 ANP B2001 " pdb=" C6 ANP B2001 " ideal model delta sigma weight residual 1.405 1.479 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C3' DT C 56 " pdb=" C2' DT C 56 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.71e+00 ... (remaining 31912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 42662 2.10 - 4.21: 630 4.21 - 6.31: 64 6.31 - 8.42: 8 8.42 - 10.52: 3 Bond angle restraints: 43367 Sorted by residual: angle pdb=" N3 DT C 43 " pdb=" C4 DT C 43 " pdb=" O4 DT C 43 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 56 " pdb=" C4 DT C 56 " pdb=" O4 DT C 56 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 50 " pdb=" C4 DT C 50 " pdb=" O4 DT C 50 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT C 47 " pdb=" C4 DT C 47 " pdb=" O4 DT C 47 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 43362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 18645 35.58 - 71.15: 619 71.15 - 106.73: 35 106.73 - 142.31: 1 142.31 - 177.89: 2 Dihedral angle restraints: 19302 sinusoidal: 8167 harmonic: 11135 Sorted by residual: dihedral pdb=" CA THR A 783 " pdb=" C THR A 783 " pdb=" N ASN A 784 " pdb=" CA ASN A 784 " ideal model delta harmonic sigma weight residual -180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" O1B ANP B2001 " pdb=" N3B ANP B2001 " pdb=" PB ANP B2001 " pdb=" PG ANP B2001 " ideal model delta sinusoidal sigma weight residual 35.15 -146.96 -177.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP B2001 " pdb=" O3A ANP B2001 " pdb=" PA ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sinusoidal sigma weight residual 83.11 -89.97 173.08 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 19299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3466 0.040 - 0.079: 905 0.079 - 0.119: 285 0.119 - 0.158: 55 0.158 - 0.198: 11 Chirality restraints: 4722 Sorted by residual: chirality pdb=" C3' DC C 57 " pdb=" C4' DC C 57 " pdb=" O3' DC C 57 " pdb=" C2' DC C 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C2' ANP B2001 " pdb=" C1' ANP B2001 " pdb=" C3' ANP B2001 " pdb=" O2' ANP B2001 " both_signs ideal model delta sigma weight residual False -2.72 -2.53 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" C3' ANP B2001 " pdb=" C2' ANP B2001 " pdb=" C4' ANP B2001 " pdb=" O3' ANP B2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 4719 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 241 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ALA B 241 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA B 241 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 242 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 71 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" CD GLU B 71 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 71 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 71 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 545 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO A 546 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 546 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 546 " 0.026 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3151 2.74 - 3.28: 29567 3.28 - 3.82: 47248 3.82 - 4.36: 55950 4.36 - 4.90: 99292 Nonbonded interactions: 235208 Sorted by model distance: nonbonded pdb=" O ASP B1761 " pdb=" OD1 ASP B1761 " model vdw 2.205 3.040 nonbonded pdb=" O ASP A 538 " pdb=" OD1 ASP A 538 " model vdw 2.256 3.040 nonbonded pdb=" O TYR A1264 " pdb=" O ALA A1267 " model vdw 2.331 3.040 nonbonded pdb=" OE1 GLN A 660 " pdb=" O SER A 661 " model vdw 2.340 3.040 nonbonded pdb=" N GLU B1792 " pdb=" OE1 GLU B1792 " model vdw 2.343 3.120 ... (remaining 235203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 940 or resid 947 through 1945 or resid 2002 thro \ ugh 2004)) selection = (chain 'B' and (resid 4 through 752 or resid 761 through 940 or resid 947 throug \ h 1434 or resid 1440 through 1945 or resid 2002 through 2004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.950 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.539 31949 Z= 0.228 Angle : 0.650 18.455 43409 Z= 0.350 Chirality : 0.041 0.198 4722 Planarity : 0.005 0.065 5607 Dihedral : 16.602 177.886 12130 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.60 % Allowed : 14.01 % Favored : 84.39 % 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: 0.42 (0.13), residues: 3848 helix: 1.50 (0.14), residues: 1459 sheet: 0.58 (0.21), residues: 554 loop : -0.82 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1362 TYR 0.014 0.001 TYR A1007 PHE 0.018 0.001 PHE B 144 TRP 0.014 0.001 TRP A1821 HIS 0.004 0.001 HIS B 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (31917) covalent geometry : angle 0.61399 / 0.35 (43367) hydrogen bonds : bond 0.15167 / 10.08 ( 1148) hydrogen bonds : angle 5.30480 / 3.96 ( 3243) metal coordination : bond 0.10234 / 4.88 ( 32) metal coordination : angle 6.89393 / 3.98 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 1.208 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 208 MET cc_start: 0.8619 (mmm) cc_final: 0.8330 (mmt) REVERT: A 294 ASP cc_start: 0.8654 (p0) cc_final: 0.8410 (p0) REVERT: A 342 GLU cc_start: 0.8817 (tp30) cc_final: 0.8543 (tp30) REVERT: A 452 LYS cc_start: 0.8873 (mttt) cc_final: 0.8292 (pttt) REVERT: A 871 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 897 LYS cc_start: 0.9032 (tptm) cc_final: 0.8622 (tppp) REVERT: A 1257 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7885 (mtt180) REVERT: A 1559 LEU cc_start: 0.9215 (mt) cc_final: 0.9003 (mt) REVERT: A 1867 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8728 (ptp) REVERT: A 1875 GLU cc_start: 0.7411 (mp0) cc_final: 0.7204 (mp0) REVERT: B 72 ASP cc_start: 0.8786 (t0) cc_final: 0.8463 (t0) REVERT: B 256 ASP cc_start: 0.8345 (t0) cc_final: 0.8107 (t0) REVERT: B 294 ASP cc_start: 0.8965 (m-30) cc_final: 0.8299 (p0) REVERT: B 300 GLU cc_start: 0.8931 (mp0) cc_final: 0.8652 (mp0) REVERT: B 782 ASP cc_start: 0.8617 (t70) cc_final: 0.8307 (t0) REVERT: B 871 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8826 (tp30) REVERT: B 1228 MET cc_start: 0.9320 (tpp) cc_final: 0.9107 (tpp) REVERT: B 1292 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8657 (mtt-85) REVERT: B 1539 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (t) REVERT: B 1560 ASP cc_start: 0.7607 (t70) cc_final: 0.7196 (t70) REVERT: B 1637 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: B 1865 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8606 (tm-30) outliers start: 52 outliers final: 33 residues processed: 359 average time/residue: 0.2404 time to fit residues: 130.0687 Evaluate side-chains 345 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1378 TYR Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1867 MET Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1292 ARG Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1718 LEU Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1893 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0040 chunk 298 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.049228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.038502 restraints weight = 87599.811| |-----------------------------------------------------------------------------| r_work (start): 0.2300 rms_B_bonded: 2.18 r_work: 0.2203 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2093 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31949 Z= 0.128 Angle : 0.580 12.087 43409 Z= 0.299 Chirality : 0.041 0.314 4722 Planarity : 0.004 0.054 5607 Dihedral : 11.247 178.100 4729 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.82 % Allowed : 14.14 % Favored : 84.05 % 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: 0.79 (0.13), residues: 3848 helix: 1.78 (0.14), residues: 1491 sheet: 0.69 (0.21), residues: 595 loop : -0.62 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 890 TYR 0.015 0.001 TYR A1007 PHE 0.021 0.001 PHE B 144 TRP 0.014 0.001 TRP A1781 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (31917) covalent geometry : angle 0.55862 / 0.30 (43367) hydrogen bonds : bond 0.05674 / 3.85 ( 1148) hydrogen bonds : angle 4.25698 / 3.17 ( 3243) metal coordination : bond 0.00780 / 0.50 ( 32) metal coordination : angle 4.99275 / 2.82 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 1.209 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 208 MET cc_start: 0.8794 (mmm) cc_final: 0.8525 (mmt) REVERT: A 345 ASP cc_start: 0.8378 (m-30) cc_final: 0.8174 (m-30) REVERT: A 452 LYS cc_start: 0.9004 (mttt) cc_final: 0.8254 (pttt) REVERT: A 538 ASP cc_start: 0.8070 (t0) cc_final: 0.7859 (t0) REVERT: A 871 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 897 LYS cc_start: 0.9045 (tptm) cc_final: 0.8706 (tppp) REVERT: A 948 GLU cc_start: 0.8759 (pm20) cc_final: 0.8521 (mp0) REVERT: A 1175 ASP cc_start: 0.8446 (m-30) cc_final: 0.8190 (m-30) REVERT: A 1257 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: A 1693 ASP cc_start: 0.8687 (p0) cc_final: 0.8445 (p0) REVERT: A 1875 GLU cc_start: 0.7517 (mp0) cc_final: 0.7233 (mp0) REVERT: B 72 ASP cc_start: 0.9127 (t0) cc_final: 0.8855 (t0) REVERT: B 256 ASP cc_start: 0.8069 (t0) cc_final: 0.7701 (t0) REVERT: B 294 ASP cc_start: 0.9070 (m-30) cc_final: 0.8359 (p0) REVERT: B 300 GLU cc_start: 0.9112 (mp0) cc_final: 0.8825 (mp0) REVERT: B 782 ASP cc_start: 0.8833 (t70) cc_final: 0.8516 (t0) REVERT: B 791 ARG cc_start: 0.9222 (mtp85) cc_final: 0.9003 (mtp85) REVERT: B 871 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8957 (tp30) REVERT: B 874 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8677 (mp0) REVERT: B 1422 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7925 (ptt90) REVERT: B 1560 ASP cc_start: 0.7798 (t70) cc_final: 0.7274 (t70) REVERT: B 1640 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 1865 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8659 (tm-30) REVERT: B 1893 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8531 (mt-10) outliers start: 59 outliers final: 31 residues processed: 362 average time/residue: 0.2335 time to fit residues: 127.5234 Evaluate side-chains 351 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1356 THR Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1893 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [265, 123, 300, 301, 268, 197, 63, 353, 91, 72, 373] chunk 265 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 373 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 676 ASN A1173 GLN A1309 GLN ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1328 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.047757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.037081 restraints weight = 86395.263| |-----------------------------------------------------------------------------| r_work (start): 0.2254 rms_B_bonded: 2.09 r_work: 0.2157 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2049 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31949 Z= 0.215 Angle : 0.641 11.645 43409 Z= 0.333 Chirality : 0.044 0.314 4722 Planarity : 0.005 0.056 5607 Dihedral : 10.788 174.087 4683 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.71 % Allowed : 15.06 % Favored : 82.23 % 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: 0.64 (0.13), residues: 3848 helix: 1.64 (0.14), residues: 1484 sheet: 0.73 (0.21), residues: 583 loop : -0.72 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B1244 TYR 0.018 0.002 TYR A1007 PHE 0.026 0.002 PHE B 144 TRP 0.016 0.002 TRP A1920 HIS 0.006 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 (31917) covalent geometry : angle 0.62279 / 0.33 (43367) hydrogen bonds : bond 0.06807 / 4.62 ( 1148) hydrogen bonds : angle 4.28727 / 3.17 ( 3243) metal coordination : bond 0.01060 / 0.68 ( 32) metal coordination : angle 4.90390 / 2.77 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 1.002 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 208 MET cc_start: 0.8840 (mmm) cc_final: 0.8597 (mmt) REVERT: A 452 LYS cc_start: 0.8962 (mttt) cc_final: 0.8263 (pttt) REVERT: A 538 ASP cc_start: 0.8224 (t0) cc_final: 0.8017 (t0) REVERT: A 871 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8417 (tm-30) REVERT: A 897 LYS cc_start: 0.9077 (tptm) cc_final: 0.8631 (tppp) REVERT: A 1175 ASP cc_start: 0.8393 (m-30) cc_final: 0.8051 (m-30) REVERT: A 1257 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8048 (mtp180) REVERT: A 1693 ASP cc_start: 0.8703 (p0) cc_final: 0.8418 (p0) REVERT: A 1875 GLU cc_start: 0.7641 (mp0) cc_final: 0.7088 (mp0) REVERT: B 72 ASP cc_start: 0.9073 (t0) cc_final: 0.8751 (t0) REVERT: B 256 ASP cc_start: 0.8123 (t0) cc_final: 0.7805 (t0) REVERT: B 294 ASP cc_start: 0.9121 (m-30) cc_final: 0.8389 (p0) REVERT: B 300 GLU cc_start: 0.9100 (mp0) cc_final: 0.8741 (mp0) REVERT: B 563 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 782 ASP cc_start: 0.8771 (t70) cc_final: 0.8447 (t0) REVERT: B 791 ARG cc_start: 0.9255 (mtp85) cc_final: 0.9023 (mtp85) REVERT: B 871 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8928 (tp30) REVERT: B 874 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8709 (mp0) REVERT: B 1129 VAL cc_start: 0.8962 (m) cc_final: 0.8745 (t) REVERT: B 1292 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8663 (mtt-85) REVERT: B 1406 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7979 (ttp80) REVERT: B 1422 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7860 (ptt90) REVERT: B 1539 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8222 (t) REVERT: B 1560 ASP cc_start: 0.7998 (t70) cc_final: 0.7508 (t70) REVERT: B 1640 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: B 1865 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8636 (tm-30) outliers start: 88 outliers final: 59 residues processed: 387 average time/residue: 0.2351 time to fit residues: 137.0834 Evaluate side-chains 370 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1378 TYR Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 716 GLN Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1292 ARG Chi-restraints excluded: chain B residue 1356 THR Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1718 LEU Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [39, 359, 172, 173, 257, 72, 218, 109, 201, 348, 153] chunk 39 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 201 optimal weight: 0.0370 chunk 348 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.047821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.037092 restraints weight = 86145.636| |-----------------------------------------------------------------------------| r_work (start): 0.2255 rms_B_bonded: 2.15 r_work: 0.2157 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2048 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31949 Z= 0.186 Angle : 0.612 11.580 43409 Z= 0.317 Chirality : 0.043 0.313 4722 Planarity : 0.005 0.054 5607 Dihedral : 10.629 175.303 4680 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 15.55 % Favored : 81.55 % 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 (0.13), residues: 3848 helix: 1.63 (0.13), residues: 1488 sheet: 0.75 (0.21), residues: 577 loop : -0.75 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 494 TYR 0.017 0.002 TYR A1007 PHE 0.025 0.002 PHE B 144 TRP 0.017 0.002 TRP A1920 HIS 0.005 0.001 HIS B1901 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (31917) covalent geometry : angle 0.59486 / 0.32 (43367) hydrogen bonds : bond 0.06407 / 4.36 ( 1148) hydrogen bonds : angle 4.20984 / 3.11 ( 3243) metal coordination : bond 0.01041 / 0.68 ( 32) metal coordination : angle 4.65988 / 2.67 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 316 time to evaluate : 1.081 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 208 MET cc_start: 0.8859 (mmm) cc_final: 0.8640 (mmt) REVERT: A 345 ASP cc_start: 0.8296 (m-30) cc_final: 0.8001 (m-30) REVERT: A 452 LYS cc_start: 0.9025 (mttt) cc_final: 0.8304 (pttt) REVERT: A 538 ASP cc_start: 0.8325 (t0) cc_final: 0.8103 (t0) REVERT: A 682 GLU cc_start: 0.8373 (tp30) cc_final: 0.8019 (tp30) REVERT: A 871 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 897 LYS cc_start: 0.9036 (tptm) cc_final: 0.8632 (tppp) REVERT: A 1175 ASP cc_start: 0.8439 (m-30) cc_final: 0.8075 (m-30) REVERT: A 1257 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8147 (mtp180) REVERT: A 1566 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 1875 GLU cc_start: 0.7942 (mp0) cc_final: 0.7687 (mp0) REVERT: B 72 ASP cc_start: 0.9078 (t0) cc_final: 0.8749 (t0) REVERT: B 256 ASP cc_start: 0.8158 (t0) cc_final: 0.7726 (t0) REVERT: B 294 ASP cc_start: 0.9133 (m-30) cc_final: 0.8370 (p0) REVERT: B 300 GLU cc_start: 0.9124 (mp0) cc_final: 0.8761 (mp0) REVERT: B 517 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 782 ASP cc_start: 0.8788 (t70) cc_final: 0.8452 (t0) REVERT: B 871 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8949 (tp30) REVERT: B 874 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8712 (mp0) REVERT: B 1406 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8022 (ttp80) REVERT: B 1422 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7868 (ptt90) REVERT: B 1560 ASP cc_start: 0.8038 (t70) cc_final: 0.7544 (t70) REVERT: B 1637 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: B 1640 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: B 1865 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8610 (tm-30) outliers start: 94 outliers final: 71 residues processed: 391 average time/residue: 0.2392 time to fit residues: 142.8050 Evaluate side-chains 382 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 304 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1378 TYR Chi-restraints excluded: chain A residue 1486 GLN Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1356 THR Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1718 LEU Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1880 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [250, 227, 105, 177, 92, 362, 381, 198, 209, 354, 88] chunk 250 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.048076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.037382 restraints weight = 85794.037| |-----------------------------------------------------------------------------| r_work (start): 0.2263 rms_B_bonded: 2.08 r_work: 0.2168 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2059 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31949 Z= 0.176 Angle : 0.606 11.073 43409 Z= 0.314 Chirality : 0.043 0.309 4722 Planarity : 0.005 0.057 5607 Dihedral : 10.552 177.308 4680 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.45 % Allowed : 15.61 % 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: 0.63 (0.13), residues: 3848 helix: 1.65 (0.14), residues: 1488 sheet: 0.69 (0.21), residues: 592 loop : -0.75 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 890 TYR 0.017 0.002 TYR A1007 PHE 0.025 0.002 PHE B 144 TRP 0.016 0.001 TRP A1821 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (31917) covalent geometry : angle 0.59005 / 0.31 (43367) hydrogen bonds : bond 0.06234 / 4.24 ( 1148) hydrogen bonds : angle 4.17915 / 3.09 ( 3243) metal coordination : bond 0.01051 / 0.70 ( 32) metal coordination : angle 4.44589 / 2.61 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 316 time to evaluate : 1.186 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 188 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8221 (ppt170) REVERT: A 208 MET cc_start: 0.8842 (mmm) cc_final: 0.8637 (mmt) REVERT: A 342 GLU cc_start: 0.8861 (tp30) cc_final: 0.8660 (tp30) REVERT: A 345 ASP cc_start: 0.8271 (m-30) cc_final: 0.7967 (m-30) REVERT: A 452 LYS cc_start: 0.8986 (mttt) cc_final: 0.8285 (pttt) REVERT: A 538 ASP cc_start: 0.8311 (t0) cc_final: 0.8096 (t0) REVERT: A 676 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.7909 (p0) REVERT: A 682 GLU cc_start: 0.8351 (tp30) cc_final: 0.8034 (tp30) REVERT: A 871 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 897 LYS cc_start: 0.9028 (tptm) cc_final: 0.8647 (tppp) REVERT: A 1175 ASP cc_start: 0.8422 (m-30) cc_final: 0.8047 (m-30) REVERT: A 1257 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8324 (mtp180) REVERT: A 1566 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8908 (t) REVERT: A 1693 ASP cc_start: 0.8678 (p0) cc_final: 0.8397 (p0) REVERT: A 1875 GLU cc_start: 0.8001 (mp0) cc_final: 0.7711 (mp0) REVERT: B 72 ASP cc_start: 0.9093 (t0) cc_final: 0.8766 (t0) REVERT: B 256 ASP cc_start: 0.8167 (t0) cc_final: 0.7743 (t0) REVERT: B 294 ASP cc_start: 0.9134 (m-30) cc_final: 0.8376 (p0) REVERT: B 300 GLU cc_start: 0.9099 (mp0) cc_final: 0.8737 (mp0) REVERT: B 517 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 563 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 782 ASP cc_start: 0.8732 (t70) cc_final: 0.8394 (t0) REVERT: B 871 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9115 (tp30) REVERT: B 1292 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8668 (mtt-85) REVERT: B 1293 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8835 (mt) REVERT: B 1406 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7980 (ttp80) REVERT: B 1422 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7836 (ptt90) REVERT: B 1539 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 1560 ASP cc_start: 0.8043 (t70) cc_final: 0.7548 (t70) REVERT: B 1597 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: B 1637 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.7378 (mm-40) REVERT: B 1640 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: B 1865 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8621 (tm-30) outliers start: 112 outliers final: 79 residues processed: 405 average time/residue: 0.2274 time to fit residues: 140.2143 Evaluate side-chains 400 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 307 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1486 GLN Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LYS Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1292 ARG Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1356 THR Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1718 LEU Chi-restraints excluded: chain B residue 1799 CYS Chi-restraints excluded: chain B residue 1872 ILE Chi-restraints excluded: chain B residue 1880 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [60, 51, 356, 33, 221, 29, 149, 120, 99, 324, 298] chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN ** A1247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.047984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.037262 restraints weight = 86354.836| |-----------------------------------------------------------------------------| r_work (start): 0.2260 rms_B_bonded: 2.15 r_work: 0.2162 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2053 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31949 Z= 0.170 Angle : 0.604 11.300 43409 Z= 0.313 Chirality : 0.042 0.237 4722 Planarity : 0.005 0.053 5607 Dihedral : 10.492 179.528 4680 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.48 % Allowed : 16.11 % Favored : 80.41 % 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: 0.66 (0.13), residues: 3848 helix: 1.68 (0.14), residues: 1489 sheet: 0.73 (0.21), residues: 601 loop : -0.75 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1362 TYR 0.017 0.002 TYR A1007 PHE 0.024 0.002 PHE B 144 TRP 0.024 0.001 TRP A1920 HIS 0.007 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (31917) covalent geometry : angle 0.58802 / 0.31 (43367) hydrogen bonds : bond 0.06088 / 4.14 ( 1148) hydrogen bonds : angle 4.15690 / 3.08 ( 3243) metal coordination : bond 0.01325 / 0.78 ( 32) metal coordination : angle 4.53956 / 2.52 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 314 time to evaluate : 1.098 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 188 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8143 (ppt170) REVERT: A 208 MET cc_start: 0.8836 (mmm) cc_final: 0.8628 (mmt) REVERT: A 342 GLU cc_start: 0.8967 (tp30) cc_final: 0.8740 (tp30) REVERT: A 345 ASP cc_start: 0.8340 (m-30) cc_final: 0.8002 (m-30) REVERT: A 452 LYS cc_start: 0.9036 (mttt) cc_final: 0.8283 (pttt) REVERT: A 538 ASP cc_start: 0.8411 (t0) cc_final: 0.8187 (t0) REVERT: A 676 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 682 GLU cc_start: 0.8356 (tp30) cc_final: 0.8054 (tp30) REVERT: A 871 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 897 LYS cc_start: 0.9026 (tptm) cc_final: 0.8651 (tppp) REVERT: A 1175 ASP cc_start: 0.8485 (m-30) cc_final: 0.8101 (m-30) REVERT: A 1257 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8306 (mtp180) REVERT: A 1362 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8134 (mmm160) REVERT: A 1566 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.8888 (t) REVERT: A 1629 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8424 (mt0) REVERT: A 1875 GLU cc_start: 0.7943 (mp0) cc_final: 0.7629 (mp0) REVERT: A 1913 ARG cc_start: 0.8902 (ttm170) cc_final: 0.8563 (ttm-80) REVERT: B 72 ASP cc_start: 0.9112 (t0) cc_final: 0.8754 (t0) REVERT: B 256 ASP cc_start: 0.8174 (t0) cc_final: 0.7732 (t0) REVERT: B 294 ASP cc_start: 0.9132 (m-30) cc_final: 0.8352 (p0) REVERT: B 300 GLU cc_start: 0.9115 (mp0) cc_final: 0.8760 (mp0) REVERT: B 563 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 782 ASP cc_start: 0.8807 (t70) cc_final: 0.8473 (t0) REVERT: B 871 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9102 (tp30) REVERT: B 1129 VAL cc_start: 0.8893 (m) cc_final: 0.8673 (t) REVERT: B 1293 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8824 (mt) REVERT: B 1406 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: B 1422 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7852 (ptt90) REVERT: B 1539 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 1560 ASP cc_start: 0.8123 (t70) cc_final: 0.7487 (t70) REVERT: B 1597 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: B 1637 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.7361 (mm-40) REVERT: B 1640 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 1865 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 113 outliers final: 86 residues processed: 406 average time/residue: 0.2308 time to fit residues: 142.7577 Evaluate side-chains 404 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 306 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1378 TYR Chi-restraints excluded: chain A residue 1486 GLN Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LYS Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1035 ASN Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1356 THR Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1880 SER Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [321, 311, 369, 21, 229, 176, 219, 245, 258, 47, 25] chunk 321 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A1054 ASN ** A1247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1486 GLN ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.049528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.038729 restraints weight = 86050.834| |-----------------------------------------------------------------------------| r_work (start): 0.2306 rms_B_bonded: 2.16 r_work: 0.2211 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2102 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31949 Z= 0.113 Angle : 0.551 11.443 43409 Z= 0.286 Chirality : 0.040 0.217 4722 Planarity : 0.004 0.052 5607 Dihedral : 10.316 179.280 4679 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.65 % Allowed : 17.12 % Favored : 80.23 % 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: 0.93 (0.14), residues: 3848 helix: 1.92 (0.14), residues: 1489 sheet: 0.75 (0.20), residues: 624 loop : -0.58 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 494 TYR 0.014 0.001 TYR B1007 PHE 0.019 0.001 PHE B 144 TRP 0.016 0.001 TRP A1781 HIS 0.004 0.001 HIS B 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (31917) covalent geometry : angle 0.53832 / 0.28 (43367) hydrogen bonds : bond 0.04878 / 3.34 ( 1148) hydrogen bonds : angle 4.01002 / 2.98 ( 3243) metal coordination : bond 0.00923 / 0.61 ( 32) metal coordination : angle 3.82733 / 2.25 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 321 time to evaluate : 0.926 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 188 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7605 (ppt170) REVERT: A 208 MET cc_start: 0.8826 (mmm) cc_final: 0.8612 (mmt) REVERT: A 342 GLU cc_start: 0.8919 (tp30) cc_final: 0.8683 (tp30) REVERT: A 345 ASP cc_start: 0.8264 (m-30) cc_final: 0.7894 (m-30) REVERT: A 452 LYS cc_start: 0.8981 (mttt) cc_final: 0.8200 (pttt) REVERT: A 538 ASP cc_start: 0.8385 (t0) cc_final: 0.8155 (t0) REVERT: A 676 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8083 (p0) REVERT: A 871 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 1175 ASP cc_start: 0.8398 (m-30) cc_final: 0.7996 (m-30) REVERT: A 1257 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8159 (mtp180) REVERT: A 1472 ARG cc_start: 0.9030 (ttt90) cc_final: 0.8734 (ttt90) REVERT: A 1629 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8429 (mt0) REVERT: A 1875 GLU cc_start: 0.7930 (mp0) cc_final: 0.7490 (mp0) REVERT: A 1913 ARG cc_start: 0.8910 (ttm170) cc_final: 0.8602 (mtm-85) REVERT: B 72 ASP cc_start: 0.9179 (t0) cc_final: 0.8841 (t0) REVERT: B 256 ASP cc_start: 0.8057 (t0) cc_final: 0.7712 (t0) REVERT: B 294 ASP cc_start: 0.9126 (m-30) cc_final: 0.8370 (p0) REVERT: B 300 GLU cc_start: 0.9099 (mp0) cc_final: 0.8750 (mp0) REVERT: B 782 ASP cc_start: 0.8770 (t70) cc_final: 0.8422 (t0) REVERT: B 1293 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8760 (mt) REVERT: B 1406 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: B 1422 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7825 (ptt90) REVERT: B 1560 ASP cc_start: 0.7942 (t70) cc_final: 0.7305 (t70) REVERT: B 1640 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: B 1865 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8642 (tm-30) outliers start: 86 outliers final: 66 residues processed: 381 average time/residue: 0.2328 time to fit residues: 134.4013 Evaluate side-chains 386 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 313 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LYS Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1177 PHE Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1640 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [286, 383, 105, 109, 371, 58, 306, 379, 325, 64, 87] chunk 286 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 306 optimal weight: 0.7980 chunk 379 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.048785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.038011 restraints weight = 85907.860| |-----------------------------------------------------------------------------| r_work (start): 0.2285 rms_B_bonded: 2.15 r_work: 0.2189 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2081 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31949 Z= 0.151 Angle : 0.581 11.716 43409 Z= 0.302 Chirality : 0.041 0.218 4722 Planarity : 0.004 0.047 5607 Dihedral : 10.270 178.145 4679 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.62 % Allowed : 17.37 % Favored : 80.01 % 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: 0.89 (0.14), residues: 3848 helix: 1.87 (0.14), residues: 1489 sheet: 0.78 (0.21), residues: 593 loop : -0.59 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 494 TYR 0.016 0.001 TYR B1007 PHE 0.024 0.001 PHE B 144 TRP 0.013 0.001 TRP A1821 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (31917) covalent geometry : angle 0.56907 / 0.30 (43367) hydrogen bonds : bond 0.05454 / 3.72 ( 1148) hydrogen bonds : angle 4.04951 / 3.00 ( 3243) metal coordination : bond 0.01043 / 0.69 ( 32) metal coordination : angle 3.86543 / 2.28 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 317 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8119 (ppt170) REVERT: A 208 MET cc_start: 0.8829 (mmm) cc_final: 0.8623 (mmt) REVERT: A 342 GLU cc_start: 0.8909 (tp30) cc_final: 0.8681 (tp30) REVERT: A 345 ASP cc_start: 0.8286 (m-30) cc_final: 0.7920 (m-30) REVERT: A 452 LYS cc_start: 0.8997 (mttt) cc_final: 0.8212 (pttt) REVERT: A 538 ASP cc_start: 0.8440 (t0) cc_final: 0.8217 (t0) REVERT: A 676 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 871 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 897 LYS cc_start: 0.9090 (tptm) cc_final: 0.8716 (tppp) REVERT: A 1175 ASP cc_start: 0.8417 (m-30) cc_final: 0.8027 (m-30) REVERT: A 1257 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8237 (mtp180) REVERT: A 1629 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8453 (mt0) REVERT: A 1693 ASP cc_start: 0.8701 (p0) cc_final: 0.8392 (p0) REVERT: A 1875 GLU cc_start: 0.7873 (mp0) cc_final: 0.7543 (mp0) REVERT: B 72 ASP cc_start: 0.9190 (t0) cc_final: 0.8804 (t0) REVERT: B 256 ASP cc_start: 0.8103 (t0) cc_final: 0.7729 (t0) REVERT: B 294 ASP cc_start: 0.9100 (m-30) cc_final: 0.8345 (p0) REVERT: B 300 GLU cc_start: 0.9085 (mp0) cc_final: 0.8731 (mp0) REVERT: B 782 ASP cc_start: 0.8786 (t70) cc_final: 0.8423 (t0) REVERT: B 896 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8111 (pttp) REVERT: B 1293 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8788 (mt) REVERT: B 1406 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7964 (ttp80) REVERT: B 1422 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7861 (ptt90) REVERT: B 1560 ASP cc_start: 0.7975 (t70) cc_final: 0.7310 (t70) REVERT: B 1597 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: B 1637 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: B 1640 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: B 1865 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8653 (tm-30) outliers start: 85 outliers final: 67 residues processed: 380 average time/residue: 0.2306 time to fit residues: 133.3319 Evaluate side-chains 381 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 304 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LYS Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [230, 232, 178, 367, 127, 253, 116, 176, 6, 284, 275] chunk 230 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 178 optimal weight: 0.0040 chunk 367 optimal weight: 0.0050 chunk 127 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 116 optimal weight: 0.0970 chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.050108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.039291 restraints weight = 85452.390| |-----------------------------------------------------------------------------| r_work (start): 0.2324 rms_B_bonded: 2.16 r_work: 0.2230 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2121 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31949 Z= 0.114 Angle : 0.564 12.285 43409 Z= 0.292 Chirality : 0.040 0.208 4722 Planarity : 0.004 0.046 5607 Dihedral : 10.138 179.138 4676 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.37 % Allowed : 17.65 % Favored : 79.98 % 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: 1.05 (0.14), residues: 3848 helix: 2.04 (0.14), residues: 1481 sheet: 0.76 (0.21), residues: 613 loop : -0.49 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1362 TYR 0.014 0.001 TYR B1007 PHE 0.020 0.001 PHE B 144 TRP 0.031 0.001 TRP A1920 HIS 0.006 0.001 HIS A1328 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (31917) covalent geometry : angle 0.55331 / 0.29 (43367) hydrogen bonds : bond 0.04592 / 3.14 ( 1148) hydrogen bonds : angle 3.96839 / 2.94 ( 3243) metal coordination : bond 0.00882 / 0.59 ( 32) metal coordination : angle 3.54043 / 2.16 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 314 time to evaluate : 1.247 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 188 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7633 (ppt170) REVERT: A 208 MET cc_start: 0.8822 (mmm) cc_final: 0.8619 (mmt) REVERT: A 345 ASP cc_start: 0.8240 (m-30) cc_final: 0.7928 (m-30) REVERT: A 452 LYS cc_start: 0.8975 (mttt) cc_final: 0.8199 (pttt) REVERT: A 538 ASP cc_start: 0.8403 (t0) cc_final: 0.8179 (t0) REVERT: A 676 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8417 (p0) REVERT: A 871 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 897 LYS cc_start: 0.9085 (tptm) cc_final: 0.8682 (tppp) REVERT: A 1175 ASP cc_start: 0.8370 (m-30) cc_final: 0.7991 (m-30) REVERT: A 1257 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8228 (mtp180) REVERT: A 1629 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8446 (mt0) REVERT: A 1693 ASP cc_start: 0.8703 (p0) cc_final: 0.8376 (p0) REVERT: A 1875 GLU cc_start: 0.7834 (mp0) cc_final: 0.7584 (mp0) REVERT: A 1913 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8669 (ttm-80) REVERT: B 72 ASP cc_start: 0.9193 (t0) cc_final: 0.8840 (t0) REVERT: B 256 ASP cc_start: 0.8032 (t0) cc_final: 0.7682 (t0) REVERT: B 294 ASP cc_start: 0.9100 (m-30) cc_final: 0.8345 (p0) REVERT: B 300 GLU cc_start: 0.9080 (mp0) cc_final: 0.8720 (mp0) REVERT: B 782 ASP cc_start: 0.8781 (t70) cc_final: 0.8425 (t0) REVERT: B 896 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8091 (pttp) REVERT: B 1293 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 1342 GLU cc_start: 0.8736 (pp20) cc_final: 0.8529 (pp20) REVERT: B 1406 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: B 1560 ASP cc_start: 0.7889 (t70) cc_final: 0.7244 (t70) REVERT: B 1597 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: B 1637 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.7385 (mm-40) REVERT: B 1640 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: B 1865 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8646 (tm-30) outliers start: 77 outliers final: 60 residues processed: 371 average time/residue: 0.2318 time to fit residues: 131.4743 Evaluate side-chains 375 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 306 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1040 LYS Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [363, 375, 37, 46, 274, 271, 277, 295, 32, 299, 221] chunk 363 optimal weight: 3.9990 chunk 375 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 277 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.048243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.037483 restraints weight = 86368.246| |-----------------------------------------------------------------------------| r_work (start): 0.2271 rms_B_bonded: 2.14 r_work: 0.2175 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2066 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31949 Z= 0.193 Angle : 0.637 14.337 43409 Z= 0.329 Chirality : 0.043 0.261 4722 Planarity : 0.005 0.057 5607 Dihedral : 10.149 175.841 4672 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.34 % Allowed : 17.71 % Favored : 79.95 % 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: 3848 helix: 1.80 (0.14), residues: 1489 sheet: 0.82 (0.21), residues: 596 loop : -0.58 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 890 TYR 0.018 0.002 TYR A1007 PHE 0.026 0.002 PHE B 144 TRP 0.023 0.002 TRP A1920 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (31917) covalent geometry : angle 0.62552 / 0.33 (43367) hydrogen bonds : bond 0.05936 / 4.05 ( 1148) hydrogen bonds : angle 4.11411 / 3.04 ( 3243) metal coordination : bond 0.01088 / 0.72 ( 32) metal coordination : angle 3.89474 / 2.29 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 1.167 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 188 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8226 (ppt170) REVERT: A 208 MET cc_start: 0.8836 (mmm) cc_final: 0.8631 (mmt) REVERT: A 345 ASP cc_start: 0.8240 (m-30) cc_final: 0.7892 (m-30) REVERT: A 452 LYS cc_start: 0.8986 (mttt) cc_final: 0.8213 (pttt) REVERT: A 660 GLN cc_start: 0.8084 (pp30) cc_final: 0.7878 (pp30) REVERT: A 682 GLU cc_start: 0.8410 (tp30) cc_final: 0.8126 (tp30) REVERT: A 871 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 897 LYS cc_start: 0.9093 (tptm) cc_final: 0.8721 (tppp) REVERT: A 1257 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: A 1629 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8477 (mt0) REVERT: A 1693 ASP cc_start: 0.8691 (p0) cc_final: 0.8411 (p0) REVERT: A 1875 GLU cc_start: 0.7864 (mp0) cc_final: 0.7536 (mp0) REVERT: A 1913 ARG cc_start: 0.8971 (ttm170) cc_final: 0.8536 (mtt-85) REVERT: B 72 ASP cc_start: 0.9216 (t0) cc_final: 0.8841 (t0) REVERT: B 256 ASP cc_start: 0.8143 (t0) cc_final: 0.7737 (t0) REVERT: B 294 ASP cc_start: 0.9098 (m-30) cc_final: 0.8313 (p0) REVERT: B 300 GLU cc_start: 0.9106 (mp0) cc_final: 0.8746 (mp0) REVERT: B 414 MET cc_start: 0.9061 (mtp) cc_final: 0.8827 (mtp) REVERT: B 782 ASP cc_start: 0.8797 (t70) cc_final: 0.8447 (t0) REVERT: B 896 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8076 (pttp) REVERT: B 1293 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8818 (mt) REVERT: B 1406 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7974 (ttp80) REVERT: B 1560 ASP cc_start: 0.8036 (t70) cc_final: 0.7368 (t70) REVERT: B 1597 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: B 1637 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.7369 (mm-40) REVERT: B 1640 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: B 1865 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8651 (tm-30) outliers start: 76 outliers final: 63 residues processed: 365 average time/residue: 0.2353 time to fit residues: 130.4743 Evaluate side-chains 370 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 299 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 940 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1268 HIS Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LYS Chi-restraints excluded: chain A residue 1628 THR Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1784 GLN Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 1015 ASP Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1406 ARG Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1512 CYS Chi-restraints excluded: chain B residue 1579 CYS Chi-restraints excluded: chain B residue 1597 GLN Chi-restraints excluded: chain B residue 1610 GLN Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1637 GLN Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1928 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [90, 383, 102, 36, 373, 236, 132, 163, 129, 74, 248] chunk 90 optimal weight: 1.9990 chunk 383 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 163 optimal weight: 0.0050 chunk 129 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 HIS ** 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 = 0.2609 r_free = 0.2609 target = 0.049336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.038542 restraints weight = 86457.259| |-----------------------------------------------------------------------------| r_work (start): 0.2302 rms_B_bonded: 2.16 r_work: 0.2207 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2098 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31949 Z= 0.129 Angle : 0.599 11.736 43409 Z= 0.311 Chirality : 0.041 0.251 4722 Planarity : 0.005 0.094 5607 Dihedral : 10.070 177.842 4672 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 18.02 % Favored : 79.64 % 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: 0.96 (0.14), residues: 3848 helix: 1.92 (0.14), residues: 1482 sheet: 0.77 (0.21), residues: 614 loop : -0.52 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 890 TYR 0.015 0.001 TYR B1007 PHE 0.021 0.001 PHE B 144 TRP 0.030 0.001 TRP A1920 HIS 0.005 0.001 HIS B 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (31917) covalent geometry : angle 0.58827 / 0.31 (43367) hydrogen bonds : bond 0.05092 / 3.48 ( 1148) hydrogen bonds : angle 4.05876 / 3.01 ( 3243) metal coordination : bond 0.00947 / 0.63 ( 32) metal coordination : angle 3.59794 / 2.18 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6695.52 seconds wall clock time: 115 minutes 10.77 seconds (6910.77 seconds total)