Starting phenix.real_space_refine on Sat Mar 7 01:29:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r03_14218/03_2026/7r03_14218.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.935 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 230 5.16 5 C 22897 2.51 5 N 6001 2.21 5 O 6493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35621 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2241, 17792 Classifications: {'peptide': 2241} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 88, 'TRANS': 2152} Chain breaks: 19 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 17829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2246, 17829 Classifications: {'peptide': 2246} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 89, 'TRANS': 2156} Chain breaks: 18 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 6.46, per 1000 atoms: 0.18 Number of scatterers: 35621 At special positions: 0 Unit cell: (141.772, 140.714, 314.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 230 16.00 O 6493 8.00 N 6001 7.00 C 22897 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8656 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 6 sheets defined 72.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.807A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.513A pdb=" N LYS A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 72 through 95 removed outlier: 4.237A pdb=" N GLU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.798A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 130 through 146 removed outlier: 4.188A pdb=" N LEU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 removed outlier: 4.683A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.704A pdb=" N LYS A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.759A pdb=" N LEU A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.613A pdb=" N PHE A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.682A pdb=" N ALA A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 Proline residue: A 268 - end of helix removed outlier: 4.299A pdb=" N ILE A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.763A pdb=" N ASP A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 removed outlier: 3.924A pdb=" N LYS A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.968A pdb=" N GLU A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.510A pdb=" N LEU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.656A pdb=" N HIS A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 452 removed outlier: 3.523A pdb=" N LEU A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 removed outlier: 3.966A pdb=" N TYR A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 539 through 553 removed outlier: 3.535A pdb=" N MET A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 547 " --> pdb=" O GLN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.861A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 588 removed outlier: 4.471A pdb=" N THR A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 615 removed outlier: 3.912A pdb=" N ILE A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 695 Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.571A pdb=" N VAL A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.713A pdb=" N LEU A 713 " --> pdb=" O CYS A 709 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 751 through 765 removed outlier: 3.849A pdb=" N LEU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.722A pdb=" N THR A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 785 " --> pdb=" O HIS A 781 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 910 through 924 removed outlier: 3.984A pdb=" N ASN A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 942 Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 954 through 974 removed outlier: 3.882A pdb=" N ALA A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 removed outlier: 3.631A pdb=" N LEU A 983 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1001 removed outlier: 4.455A pdb=" N LEU A 993 " --> pdb=" O GLU A 989 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.683A pdb=" N GLU A1020 " --> pdb=" O CYS A1016 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1050 removed outlier: 3.847A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1080 removed outlier: 3.780A pdb=" N GLN A1070 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1119 removed outlier: 3.571A pdb=" N LEU A1109 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A1110 " --> pdb=" O TYR A1106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A1119 " --> pdb=" O ASN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1156 removed outlier: 4.221A pdb=" N VAL A1146 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1147 " --> pdb=" O HIS A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 removed outlier: 4.186A pdb=" N HIS A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1170 removed outlier: 3.740A pdb=" N TYR A1169 " --> pdb=" O GLY A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1188 removed outlier: 3.706A pdb=" N ARG A1176 " --> pdb=" O ASP A1172 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1177 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1213 Processing helix chain 'A' and resid 1221 through 1231 Processing helix chain 'A' and resid 1232 through 1234 No H-bonds generated for 'chain 'A' and resid 1232 through 1234' Processing helix chain 'A' and resid 1235 through 1250 removed outlier: 3.766A pdb=" N ARG A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1246 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A1249 " --> pdb=" O THR A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1268 removed outlier: 3.672A pdb=" N LEU A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1310 removed outlier: 6.859A pdb=" N THR A1295 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A1296 " --> pdb=" O TYR A1292 " (cutoff:3.500A) Proline residue: A1303 - end of helix Processing helix chain 'A' and resid 1331 through 1353 Processing helix chain 'A' and resid 1358 through 1374 Processing helix chain 'A' and resid 1380 through 1391 removed outlier: 3.642A pdb=" N SER A1386 " --> pdb=" O GLY A1382 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A1387 " --> pdb=" O ALA A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 3.846A pdb=" N ALA A1396 " --> pdb=" O PHE A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1430 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1443 through 1449 Processing helix chain 'A' and resid 1450 through 1462 removed outlier: 3.597A pdb=" N PHE A1457 " --> pdb=" O ALA A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1492 removed outlier: 4.331A pdb=" N LEU A1489 " --> pdb=" O ALA A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 removed outlier: 3.706A pdb=" N LEU A1525 " --> pdb=" O LEU A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1571 No H-bonds generated for 'chain 'A' and resid 1568 through 1571' Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1595 through 1611 Processing helix chain 'A' and resid 1628 through 1632 removed outlier: 3.621A pdb=" N ARG A1632 " --> pdb=" O PRO A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1634 through 1641 removed outlier: 3.547A pdb=" N TRP A1641 " --> pdb=" O PHE A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.579A pdb=" N TYR A1650 " --> pdb=" O PRO A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1672 Processing helix chain 'A' and resid 1674 through 1678 removed outlier: 3.825A pdb=" N THR A1677 " --> pdb=" O ARG A1674 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A1678 " --> pdb=" O LEU A1675 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1674 through 1678' Processing helix chain 'A' and resid 1693 through 1697 Processing helix chain 'A' and resid 1699 through 1703 Processing helix chain 'A' and resid 1706 through 1712 Processing helix chain 'A' and resid 1795 through 1814 removed outlier: 3.564A pdb=" N LEU A1812 " --> pdb=" O THR A1808 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A1813 " --> pdb=" O ARG A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1842 removed outlier: 4.035A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1864 removed outlier: 3.538A pdb=" N ASN A1864 " --> pdb=" O THR A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1898 removed outlier: 3.699A pdb=" N THR A1893 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A1895 " --> pdb=" O SER A1891 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A1896 " --> pdb=" O LYS A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1901 through 1915 removed outlier: 3.543A pdb=" N PHE A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A1910 " --> pdb=" O LEU A1906 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A1911 " --> pdb=" O GLU A1907 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1929 removed outlier: 3.958A pdb=" N LEU A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS A1924 " --> pdb=" O LEU A1920 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A1925 " --> pdb=" O LYS A1921 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A1926 " --> pdb=" O HIS A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1930 through 1932 No H-bonds generated for 'chain 'A' and resid 1930 through 1932' Processing helix chain 'A' and resid 1943 through 1964 removed outlier: 3.520A pdb=" N GLU A1964 " --> pdb=" O MET A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1982 removed outlier: 3.520A pdb=" N ILE A1975 " --> pdb=" O ILE A1971 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP A1976 " --> pdb=" O GLN A1972 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1978 " --> pdb=" O LYS A1974 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A1982 " --> pdb=" O SER A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2001 removed outlier: 3.612A pdb=" N THR A1999 " --> pdb=" O LYS A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2019 removed outlier: 3.839A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A2019 " --> pdb=" O VAL A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2040 removed outlier: 3.579A pdb=" N VAL A2025 " --> pdb=" O ASN A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2068 Processing helix chain 'A' and resid 2074 through 2089 removed outlier: 3.546A pdb=" N LEU A2079 " --> pdb=" O VAL A2075 " (cutoff:3.500A) Proline residue: A2080 - end of helix Processing helix chain 'A' and resid 2094 through 2115 removed outlier: 3.547A pdb=" N HIS A2102 " --> pdb=" O ARG A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2121 through 2136 removed outlier: 3.659A pdb=" N THR A2133 " --> pdb=" O ARG A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2144 Processing helix chain 'A' and resid 2151 through 2157 removed outlier: 3.673A pdb=" N ILE A2155 " --> pdb=" O SER A2151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A2157 " --> pdb=" O ALA A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2199 removed outlier: 3.591A pdb=" N LEU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A2198 " --> pdb=" O ALA A2194 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A2199 " --> pdb=" O CYS A2195 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2217 removed outlier: 3.735A pdb=" N GLN A2207 " --> pdb=" O LYS A2203 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A2215 " --> pdb=" O LEU A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2235 removed outlier: 3.514A pdb=" N SER A2235 " --> pdb=" O PHE A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2239 through 2260 removed outlier: 3.523A pdb=" N ILE A2243 " --> pdb=" O SER A2239 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS A2244 " --> pdb=" O HIS A2240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A2255 " --> pdb=" O SER A2251 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A2256 " --> pdb=" O LYS A2252 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A2257 " --> pdb=" O ALA A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2281 removed outlier: 3.516A pdb=" N VAL A2268 " --> pdb=" O TYR A2264 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A2270 " --> pdb=" O SER A2266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A2277 " --> pdb=" O THR A2273 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A2279 " --> pdb=" O ILE A2275 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2282 through 2284 No H-bonds generated for 'chain 'A' and resid 2282 through 2284' Processing helix chain 'A' and resid 2289 through 2304 removed outlier: 4.344A pdb=" N PHE A2295 " --> pdb=" O HIS A2291 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A2296 " --> pdb=" O LYS A2292 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 removed outlier: 3.571A pdb=" N ALA A2315 " --> pdb=" O SER A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2334 through 2344 removed outlier: 3.588A pdb=" N VAL A2338 " --> pdb=" O SER A2334 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A2339 " --> pdb=" O PRO A2335 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET A2340 " --> pdb=" O GLU A2336 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A2342 " --> pdb=" O VAL A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2357 removed outlier: 3.680A pdb=" N GLN A2352 " --> pdb=" O TRP A2348 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A2353 " --> pdb=" O HIS A2349 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A2354 " --> pdb=" O CYS A2350 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A2355 " --> pdb=" O LYS A2351 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A2356 " --> pdb=" O GLN A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2364 through 2374 Processing helix chain 'A' and resid 2375 through 2379 Processing helix chain 'A' and resid 2381 through 2403 removed outlier: 4.087A pdb=" N ARG A2403 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2413 No H-bonds generated for 'chain 'A' and resid 2411 through 2413' Processing helix chain 'A' and resid 2414 through 2423 removed outlier: 4.066A pdb=" N LEU A2418 " --> pdb=" O SER A2414 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR A2423 " --> pdb=" O ALA A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2591 through 2609 removed outlier: 3.735A pdb=" N GLN A2595 " --> pdb=" O ASP A2591 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A2609 " --> pdb=" O LEU A2605 " (cutoff:3.500A) Processing helix chain 'A' and resid 2611 through 2629 removed outlier: 3.797A pdb=" N TYR A2621 " --> pdb=" O ILE A2617 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A2627 " --> pdb=" O ALA A2623 " (cutoff:3.500A) Processing helix chain 'A' and resid 2632 through 2635 Processing helix chain 'A' and resid 2636 through 2651 removed outlier: 3.905A pdb=" N LEU A2640 " --> pdb=" O VAL A2636 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A2642 " --> pdb=" O ASN A2638 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS A2643 " --> pdb=" O LEU A2639 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A2645 " --> pdb=" O ASP A2641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A2646 " --> pdb=" O SER A2642 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A2649 " --> pdb=" O ASN A2645 " (cutoff:3.500A) Processing helix chain 'A' and resid 2653 through 2671 Proline residue: A2659 - end of helix Processing helix chain 'A' and resid 2680 through 2685 removed outlier: 3.713A pdb=" N PHE A2685 " --> pdb=" O TYR A2681 " (cutoff:3.500A) Processing helix chain 'A' and resid 2689 through 2694 Processing helix chain 'A' and resid 2706 through 2722 removed outlier: 3.577A pdb=" N ILE A2718 " --> pdb=" O LEU A2714 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A2719 " --> pdb=" O ASP A2715 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.894A pdb=" N TYR B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 removed outlier: 4.118A pdb=" N VAL B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.795A pdb=" N LEU B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 129 through 146 removed outlier: 3.539A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.813A pdb=" N LEU B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 188 through 200 removed outlier: 3.988A pdb=" N ARG B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.786A pdb=" N GLN B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 239 through 257 removed outlier: 3.779A pdb=" N ALA B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.905A pdb=" N ALA B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Proline residue: B 268 - end of helix removed outlier: 3.569A pdb=" N ILE B 271 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.915A pdb=" N ILE B 281 " --> pdb=" O CYS B 277 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 309 removed outlier: 4.169A pdb=" N LYS B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 333 removed outlier: 3.814A pdb=" N GLU B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.532A pdb=" N LEU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.823A pdb=" N PHE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.546A pdb=" N TYR B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.623A pdb=" N LEU B 439 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 503 removed outlier: 3.980A pdb=" N TYR B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.673A pdb=" N ALA B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 545 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 547 " --> pdb=" O GLN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.787A pdb=" N LEU B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 588 removed outlier: 4.163A pdb=" N PHE B 570 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 615 removed outlier: 4.146A pdb=" N ILE B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 695 Processing helix chain 'B' and resid 699 through 709 Processing helix chain 'B' and resid 709 through 721 removed outlier: 4.067A pdb=" N LEU B 713 " --> pdb=" O CYS B 709 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 746 removed outlier: 3.778A pdb=" N ASN B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 766 removed outlier: 3.672A pdb=" N LEU B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 793 removed outlier: 3.501A pdb=" N THR B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 786 " --> pdb=" O ALA B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 890 through 902 Processing helix chain 'B' and resid 910 through 924 removed outlier: 3.637A pdb=" N ARG B 914 " --> pdb=" O GLY B 910 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 929 through 942 removed outlier: 3.578A pdb=" N LEU B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 954 through 974 removed outlier: 3.813A pdb=" N ALA B 966 " --> pdb=" O GLU B 962 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 974 " --> pdb=" O ASN B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.991A pdb=" N LEU B 983 " --> pdb=" O SER B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1000 removed outlier: 4.165A pdb=" N LEU B 993 " --> pdb=" O GLU B 989 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 994 " --> pdb=" O THR B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1003 No H-bonds generated for 'chain 'B' and resid 1001 through 1003' Processing helix chain 'B' and resid 1005 through 1025 removed outlier: 3.585A pdb=" N GLU B1020 " --> pdb=" O CYS B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1050 removed outlier: 3.624A pdb=" N ASP B1047 " --> pdb=" O GLU B1043 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP B1048 " --> pdb=" O TYR B1044 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1080 removed outlier: 3.805A pdb=" N GLN B1070 " --> pdb=" O ARG B1066 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B1074 " --> pdb=" O GLN B1070 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA B1075 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1119 removed outlier: 3.553A pdb=" N LEU B1109 " --> pdb=" O LYS B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1156 removed outlier: 4.375A pdb=" N VAL B1146 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B1147 " --> pdb=" O HIS B1143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B1156 " --> pdb=" O LEU B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1165 Processing helix chain 'B' and resid 1166 through 1170 removed outlier: 3.826A pdb=" N TYR B1169 " --> pdb=" O GLY B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1188 removed outlier: 3.731A pdb=" N ALA B1177 " --> pdb=" O LEU B1173 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B1178 " --> pdb=" O GLN B1174 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B1179 " --> pdb=" O THR B1175 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B1187 " --> pdb=" O LEU B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1212 Processing helix chain 'B' and resid 1221 through 1231 Processing helix chain 'B' and resid 1232 through 1234 No H-bonds generated for 'chain 'B' and resid 1232 through 1234' Processing helix chain 'B' and resid 1235 through 1251 removed outlier: 3.693A pdb=" N ARG B1241 " --> pdb=" O ASP B1237 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B1244 " --> pdb=" O ALA B1240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B1246 " --> pdb=" O VAL B1242 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B1248 " --> pdb=" O VAL B1244 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B1249 " --> pdb=" O THR B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1252 through 1268 Processing helix chain 'B' and resid 1270 through 1274 removed outlier: 3.516A pdb=" N THR B1273 " --> pdb=" O SER B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1310 removed outlier: 6.644A pdb=" N THR B1295 " --> pdb=" O VAL B1291 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR B1296 " --> pdb=" O TYR B1292 " (cutoff:3.500A) Proline residue: B1303 - end of helix Processing helix chain 'B' and resid 1331 through 1353 Processing helix chain 'B' and resid 1358 through 1376 removed outlier: 3.661A pdb=" N ARG B1375 " --> pdb=" O VAL B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1391 removed outlier: 3.688A pdb=" N ALA B1387 " --> pdb=" O ALA B1383 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B1391 " --> pdb=" O ALA B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1399 removed outlier: 3.979A pdb=" N ALA B1396 " --> pdb=" O PHE B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1430 Processing helix chain 'B' and resid 1437 through 1442 Proline residue: B1442 - end of helix Processing helix chain 'B' and resid 1443 through 1449 Processing helix chain 'B' and resid 1450 through 1462 removed outlier: 3.588A pdb=" N PHE B1457 " --> pdb=" O ALA B1453 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1492 removed outlier: 4.276A pdb=" N LEU B1489 " --> pdb=" O ALA B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1514 through 1525 removed outlier: 3.540A pdb=" N LEU B1525 " --> pdb=" O LEU B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1595 through 1611 Processing helix chain 'B' and resid 1628 through 1632 removed outlier: 3.949A pdb=" N ARG B1632 " --> pdb=" O PRO B1629 " (cutoff:3.500A) Processing helix chain 'B' and resid 1634 through 1641 removed outlier: 3.642A pdb=" N TRP B1641 " --> pdb=" O PHE B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 removed outlier: 3.564A pdb=" N TYR B1650 " --> pdb=" O PRO B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1662 through 1672 Processing helix chain 'B' and resid 1674 through 1679 removed outlier: 3.779A pdb=" N THR B1677 " --> pdb=" O ARG B1674 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY B1678 " --> pdb=" O LEU B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1697 Processing helix chain 'B' and resid 1706 through 1712 Processing helix chain 'B' and resid 1795 through 1812 Processing helix chain 'B' and resid 1829 through 1842 removed outlier: 3.534A pdb=" N LEU B1833 " --> pdb=" O VAL B1829 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B1842 " --> pdb=" O LEU B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1863 removed outlier: 3.513A pdb=" N ASN B1854 " --> pdb=" O SER B1850 " (cutoff:3.500A) Processing helix chain 'B' and resid 1883 through 1898 removed outlier: 3.810A pdb=" N THR B1893 " --> pdb=" O SER B1889 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B1895 " --> pdb=" O SER B1891 " (cutoff:3.500A) Processing helix chain 'B' and resid 1901 through 1915 removed outlier: 3.790A pdb=" N PHE B1905 " --> pdb=" O LEU B1901 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B1910 " --> pdb=" O LEU B1906 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER B1911 " --> pdb=" O GLU B1907 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1929 removed outlier: 3.650A pdb=" N LEU B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B1925 " --> pdb=" O LYS B1921 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B1926 " --> pdb=" O HIS B1922 " (cutoff:3.500A) Processing helix chain 'B' and resid 1930 through 1935 removed outlier: 3.835A pdb=" N ASN B1934 " --> pdb=" O TRP B1931 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B1935 " --> pdb=" O LEU B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1964 Processing helix chain 'B' and resid 1967 through 1982 removed outlier: 4.437A pdb=" N TRP B1976 " --> pdb=" O GLN B1972 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B1977 " --> pdb=" O ALA B1973 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B1982 " --> pdb=" O SER B1978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1985 through 2001 removed outlier: 3.777A pdb=" N THR B1999 " --> pdb=" O LYS B1995 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B2000 " --> pdb=" O THR B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2004 through 2019 removed outlier: 3.868A pdb=" N MET B2010 " --> pdb=" O LYS B2006 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2040 removed outlier: 3.834A pdb=" N VAL B2025 " --> pdb=" O ASN B2021 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B2036 " --> pdb=" O ARG B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2041 through 2043 No H-bonds generated for 'chain 'B' and resid 2041 through 2043' Processing helix chain 'B' and resid 2053 through 2068 removed outlier: 3.618A pdb=" N TYR B2063 " --> pdb=" O ILE B2059 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) Processing helix chain 'B' and resid 2074 through 2090 removed outlier: 3.698A pdb=" N LEU B2079 " --> pdb=" O VAL B2075 " (cutoff:3.500A) Proline residue: B2080 - end of helix Processing helix chain 'B' and resid 2094 through 2115 removed outlier: 3.670A pdb=" N HIS B2102 " --> pdb=" O ARG B2098 " (cutoff:3.500A) Processing helix chain 'B' and resid 2121 through 2136 removed outlier: 3.853A pdb=" N THR B2133 " --> pdb=" O ARG B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2137 through 2144 Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.804A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2199 removed outlier: 3.771A pdb=" N LEU B2181 " --> pdb=" O ALA B2177 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B2198 " --> pdb=" O ALA B2194 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B2199 " --> pdb=" O CYS B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 removed outlier: 3.913A pdb=" N GLN B2207 " --> pdb=" O LYS B2203 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B2215 " --> pdb=" O LEU B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2223 through 2235 Processing helix chain 'B' and resid 2239 through 2260 removed outlier: 4.006A pdb=" N ILE B2243 " --> pdb=" O SER B2239 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS B2244 " --> pdb=" O HIS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2264 through 2281 removed outlier: 3.790A pdb=" N ILE B2270 " --> pdb=" O SER B2266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B2277 " --> pdb=" O THR B2273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B2279 " --> pdb=" O ILE B2275 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2282 through 2284 No H-bonds generated for 'chain 'B' and resid 2282 through 2284' Processing helix chain 'B' and resid 2288 through 2303 removed outlier: 4.513A pdb=" N LYS B2292 " --> pdb=" O SER B2288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 removed outlier: 3.756A pdb=" N ALA B2315 " --> pdb=" O SER B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2328 through 2333 removed outlier: 4.238A pdb=" N ASP B2332 " --> pdb=" O ARG B2328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2334 through 2344 removed outlier: 3.671A pdb=" N VAL B2338 " --> pdb=" O SER B2334 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B2339 " --> pdb=" O PRO B2335 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B2340 " --> pdb=" O GLU B2336 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B2342 " --> pdb=" O VAL B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.602A pdb=" N CYS B2350 " --> pdb=" O LEU B2346 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN B2352 " --> pdb=" O TRP B2348 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B2353 " --> pdb=" O HIS B2349 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP B2354 " --> pdb=" O CYS B2350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B2356 " --> pdb=" O GLN B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2374 Processing helix chain 'B' and resid 2375 through 2379 Processing helix chain 'B' and resid 2381 through 2403 removed outlier: 3.622A pdb=" N VAL B2385 " --> pdb=" O SER B2381 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B2403 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2411 through 2413 No H-bonds generated for 'chain 'B' and resid 2411 through 2413' Processing helix chain 'B' and resid 2414 through 2423 removed outlier: 3.968A pdb=" N LEU B2418 " --> pdb=" O SER B2414 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B2423 " --> pdb=" O ALA B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2608 removed outlier: 3.685A pdb=" N GLN B2595 " --> pdb=" O ASP B2591 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B2608 " --> pdb=" O THR B2604 " (cutoff:3.500A) Processing helix chain 'B' and resid 2611 through 2629 removed outlier: 3.850A pdb=" N TYR B2621 " --> pdb=" O ILE B2617 " (cutoff:3.500A) Processing helix chain 'B' and resid 2632 through 2635 Processing helix chain 'B' and resid 2636 through 2651 removed outlier: 4.110A pdb=" N SER B2642 " --> pdb=" O ASN B2638 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B2645 " --> pdb=" O ASP B2641 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B2646 " --> pdb=" O SER B2642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B2649 " --> pdb=" O ASN B2645 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2671 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2680 through 2685 removed outlier: 3.739A pdb=" N PHE B2685 " --> pdb=" O TYR B2681 " (cutoff:3.500A) Processing helix chain 'B' and resid 2689 through 2694 Processing helix chain 'B' and resid 2706 through 2722 removed outlier: 3.503A pdb=" N LYS B2712 " --> pdb=" O GLU B2708 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B2719 " --> pdb=" O ASP B2715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1572 through 1577 removed outlier: 4.190A pdb=" N ILE A1584 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A1621 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A1585 " --> pdb=" O VAL A1621 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP A1623 " --> pdb=" O PHE A1585 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR A1587 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A1618 " --> pdb=" O VAL A1653 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA A1655 " --> pdb=" O TYR A1618 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A1686 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A1656 " --> pdb=" O VAL A1686 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A1688 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A1658 " --> pdb=" O ILE A1688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1759 through 1762 removed outlier: 6.278A pdb=" N ILE A1734 " --> pdb=" O HIS A1720 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS A1720 " --> pdb=" O ILE A1734 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A1736 " --> pdb=" O VAL A1718 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A1718 " --> pdb=" O VAL A1736 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR A1790 " --> pdb=" O LEU A1725 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLN A1777 " --> pdb=" O LEU A1772 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A1772 " --> pdb=" O GLN A1777 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A1779 " --> pdb=" O ILE A1770 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A1770 " --> pdb=" O THR A1779 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR A1781 " --> pdb=" O GLU A1768 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1749 through 1751 Processing sheet with id=AA4, first strand: chain 'B' and resid 1572 through 1577 removed outlier: 4.186A pdb=" N ILE B1584 " --> pdb=" O ALA B1575 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B1621 " --> pdb=" O PRO B1583 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B1585 " --> pdb=" O VAL B1621 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP B1623 " --> pdb=" O PHE B1585 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B1587 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR B1618 " --> pdb=" O VAL B1653 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B1655 " --> pdb=" O TYR B1618 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL B1686 " --> pdb=" O SER B1654 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B1656 " --> pdb=" O VAL B1686 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B1688 " --> pdb=" O VAL B1656 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B1658 " --> pdb=" O ILE B1688 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1759 through 1762 removed outlier: 6.200A pdb=" N ILE B1734 " --> pdb=" O HIS B1720 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N HIS B1720 " --> pdb=" O ILE B1734 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B1736 " --> pdb=" O VAL B1718 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL B1718 " --> pdb=" O VAL B1736 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B1790 " --> pdb=" O LEU B1725 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN B1777 " --> pdb=" O VAL B1773 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU B1769 " --> pdb=" O THR B1781 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1749 through 1751 2055 hydrogen bonds defined for protein. 6045 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: 7.02 Time building geometry restraints manager: 3.26 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: 8227 1.33 - 1.46: 7988 1.46 - 1.58: 19768 1.58 - 1.70: 0 1.70 - 1.83: 354 Bond restraints: 36337 Sorted by residual: bond pdb=" C GLN B1814 " pdb=" N PRO B1815 " ideal model delta sigma weight residual 1.331 1.418 -0.087 7.90e-03 1.60e+04 1.20e+02 bond pdb=" C GLN A1814 " pdb=" N PRO A1815 " ideal model delta sigma weight residual 1.331 1.415 -0.084 7.90e-03 1.60e+04 1.13e+02 bond pdb=" C ARG A1441 " pdb=" N PRO A1442 " ideal model delta sigma weight residual 1.336 1.391 -0.056 1.08e-02 8.57e+03 2.65e+01 bond pdb=" C ARG B1441 " pdb=" N PRO B1442 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" N SER B 368 " pdb=" CA SER B 368 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.27e-02 6.20e+03 1.20e+01 ... (remaining 36332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 48287 3.56 - 7.13: 814 7.13 - 10.69: 113 10.69 - 14.25: 27 14.25 - 17.82: 7 Bond angle restraints: 49248 Sorted by residual: angle pdb=" N VAL B 351 " pdb=" CA VAL B 351 " pdb=" C VAL B 351 " ideal model delta sigma weight residual 112.43 102.75 9.68 9.20e-01 1.18e+00 1.11e+02 angle pdb=" CA MET A 102 " pdb=" CB MET A 102 " pdb=" CG MET A 102 " ideal model delta sigma weight residual 114.10 126.41 -12.31 2.00e+00 2.50e-01 3.79e+01 angle pdb=" N GLU B 225 " pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " ideal model delta sigma weight residual 110.40 120.23 -9.83 1.63e+00 3.76e-01 3.64e+01 angle pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " ideal model delta sigma weight residual 114.10 126.10 -12.00 2.00e+00 2.50e-01 3.60e+01 angle pdb=" C CYS A 383 " pdb=" N PHE A 384 " pdb=" CA PHE A 384 " ideal model delta sigma weight residual 122.65 113.09 9.56 1.60e+00 3.91e-01 3.57e+01 ... (remaining 49243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 19706 16.93 - 33.86: 1888 33.86 - 50.78: 326 50.78 - 67.71: 58 67.71 - 84.64: 34 Dihedral angle restraints: 22012 sinusoidal: 8792 harmonic: 13220 Sorted by residual: dihedral pdb=" CA MET A 102 " pdb=" C MET A 102 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta harmonic sigma weight residual -180.00 -127.59 -52.41 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA MET B 102 " pdb=" C MET B 102 " pdb=" N ARG B 103 " pdb=" CA ARG B 103 " ideal model delta harmonic sigma weight residual -180.00 -130.32 -49.68 0 5.00e+00 4.00e-02 9.87e+01 dihedral pdb=" CA ALA A 986 " pdb=" C ALA A 986 " pdb=" N SER A 987 " pdb=" CA SER A 987 " ideal model delta harmonic sigma weight residual 180.00 -130.53 -49.47 0 5.00e+00 4.00e-02 9.79e+01 ... (remaining 22009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4691 0.069 - 0.137: 899 0.137 - 0.206: 149 0.206 - 0.274: 31 0.274 - 0.343: 8 Chirality restraints: 5778 Sorted by residual: chirality pdb=" CB ILE A 988 " pdb=" CA ILE A 988 " pdb=" CG1 ILE A 988 " pdb=" CG2 ILE A 988 " both_signs ideal model delta sigma weight residual False 2.64 2.99 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB THR B 101 " pdb=" CA THR B 101 " pdb=" OG1 THR B 101 " pdb=" CG2 THR B 101 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB ILE B 386 " pdb=" CA ILE B 386 " pdb=" CG1 ILE B 386 " pdb=" CG2 ILE B 386 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 5775 not shown) Planarity restraints: 6181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1810 " -0.024 2.00e-02 2.50e+03 3.26e-02 2.66e+01 pdb=" CG TRP B1810 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP B1810 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B1810 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B1810 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B1810 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1810 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1810 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1810 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B1810 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 267 " -0.028 2.00e-02 2.50e+03 3.19e-02 2.54e+01 pdb=" CG TRP A 267 " 0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP A 267 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 267 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 267 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 267 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 267 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 267 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 267 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 267 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 267 " 0.015 2.00e-02 2.50e+03 3.17e-02 2.51e+01 pdb=" CG TRP B 267 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 267 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP B 267 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 267 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 267 " 0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 267 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 267 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 267 " -0.007 2.00e-02 2.50e+03 ... (remaining 6178 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5166 2.76 - 3.29: 36072 3.29 - 3.83: 60560 3.83 - 4.36: 69259 4.36 - 4.90: 114448 Nonbonded interactions: 285505 Sorted by model distance: nonbonded pdb=" O LEU B1339 " pdb=" OG1 THR B1343 " model vdw 2.224 3.040 nonbonded pdb=" O LEU A1339 " pdb=" OG1 THR A1343 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 235 " pdb=" O ILE A 275 " model vdw 2.260 3.040 nonbonded pdb=" O LEU A2717 " pdb=" OG1 THR A2720 " model vdw 2.266 3.040 nonbonded pdb=" O MET A1967 " pdb=" OG SER A1970 " model vdw 2.272 3.040 ... (remaining 285500 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 5 through 2723) selection = (chain 'B' and (resid 5 through 365 or resid 372 through 2723)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.720 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.990 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 36337 Z= 0.274 Angle : 1.155 17.818 49248 Z= 0.610 Chirality : 0.058 0.343 5778 Planarity : 0.008 0.098 6181 Dihedral : 13.878 84.640 13356 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.18 (0.11), residues: 4409 helix: -1.19 (0.08), residues: 2869 sheet: -0.95 (0.46), residues: 113 loop : -1.69 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B2197 TYR 0.043 0.002 TYR A1968 PHE 0.063 0.003 PHE A1289 TRP 0.087 0.004 TRP A 267 HIS 0.010 0.001 HIS B1487 Details of bonding type rmsd covalent geometry : bond 0.00554 (36337) covalent geometry : angle 1.15484 (49248) hydrogen bonds : bond 0.16758 ( 2055) hydrogen bonds : angle 6.63153 ( 6045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.7080 (mpp) cc_final: 0.6847 (mpp) REVERT: A 376 MET cc_start: 0.8938 (mpp) cc_final: 0.7986 (mmt) REVERT: A 496 MET cc_start: 0.9636 (mtp) cc_final: 0.9420 (mtp) REVERT: A 693 MET cc_start: 0.9239 (mmp) cc_final: 0.8473 (mtp) REVERT: A 707 MET cc_start: 0.9258 (tmm) cc_final: 0.8963 (tmm) REVERT: A 739 MET cc_start: 0.8935 (mpp) cc_final: 0.8643 (mpp) REVERT: A 840 MET cc_start: 0.9050 (ttt) cc_final: 0.8810 (ttt) REVERT: A 1041 MET cc_start: 0.9541 (mpp) cc_final: 0.9331 (mpp) REVERT: A 1207 ARG cc_start: 0.6889 (mpt180) cc_final: 0.6203 (mpp-170) REVERT: A 1271 MET cc_start: 0.5417 (mmp) cc_final: 0.2934 (tpp) REVERT: A 1518 MET cc_start: 0.8894 (tmm) cc_final: 0.8464 (tmm) REVERT: A 1919 GLU cc_start: 0.8817 (pm20) cc_final: 0.8411 (pm20) REVERT: A 1928 MET cc_start: 0.8825 (ptp) cc_final: 0.8514 (ptp) REVERT: A 2196 MET cc_start: 0.8938 (ptp) cc_final: 0.8579 (ptm) REVERT: A 2353 MET cc_start: 0.9387 (mtt) cc_final: 0.9128 (mmt) REVERT: B 68 MET cc_start: 0.4512 (ppp) cc_final: 0.3713 (ppp) REVERT: B 376 MET cc_start: 0.9293 (tmm) cc_final: 0.9035 (tmm) REVERT: B 496 MET cc_start: 0.9497 (mtm) cc_final: 0.9174 (mtp) REVERT: B 739 MET cc_start: 0.9480 (mmp) cc_final: 0.9227 (mmm) REVERT: B 1041 MET cc_start: 0.9572 (mmm) cc_final: 0.9362 (mmm) REVERT: B 1134 MET cc_start: 0.8249 (ptt) cc_final: 0.7289 (pmm) REVERT: B 2010 MET cc_start: 0.7994 (tmm) cc_final: 0.7650 (ppp) REVERT: B 2340 MET cc_start: 0.8685 (mmm) cc_final: 0.8231 (mmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1948 time to fit residues: 75.1297 Evaluate side-chains 182 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A1259 ASN A1835 ASN B 64 ASN B 270 GLN B 407 HIS B 734 ASN B2402 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.090605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065381 restraints weight = 225373.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.066792 restraints weight = 124866.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.066803 restraints weight = 75507.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.067258 restraints weight = 59474.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.067296 restraints weight = 54663.473| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36337 Z= 0.150 Angle : 0.668 10.707 49248 Z= 0.345 Chirality : 0.042 0.200 5778 Planarity : 0.005 0.070 6181 Dihedral : 5.433 44.030 4737 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.58 % Allowed : 5.76 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.53 (0.12), residues: 4409 helix: 0.22 (0.09), residues: 2923 sheet: -0.37 (0.53), residues: 93 loop : -1.41 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2197 TYR 0.024 0.001 TYR A1968 PHE 0.036 0.002 PHE A 199 TRP 0.037 0.002 TRP A 267 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00320 (36337) covalent geometry : angle 0.66839 (49248) hydrogen bonds : bond 0.04441 ( 2055) hydrogen bonds : angle 4.74757 ( 6045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8797 (mpp) cc_final: 0.7835 (mmt) REVERT: A 496 MET cc_start: 0.9704 (mtp) cc_final: 0.9491 (mtp) REVERT: A 546 MET cc_start: 0.8772 (tpt) cc_final: 0.8446 (tpt) REVERT: A 693 MET cc_start: 0.9137 (mmp) cc_final: 0.8574 (mtp) REVERT: A 707 MET cc_start: 0.9187 (tmm) cc_final: 0.8875 (tmm) REVERT: A 992 MET cc_start: 0.9708 (mmp) cc_final: 0.9458 (mmm) REVERT: A 1035 MET cc_start: 0.9373 (mmm) cc_final: 0.9026 (mpp) REVERT: A 1041 MET cc_start: 0.9541 (mpp) cc_final: 0.8970 (mpp) REVERT: A 1073 MET cc_start: 0.9470 (tpt) cc_final: 0.9146 (tpp) REVERT: A 1111 MET cc_start: 0.9291 (mmp) cc_final: 0.8899 (mmm) REVERT: A 1271 MET cc_start: 0.5044 (mmp) cc_final: 0.2562 (tpp) REVERT: A 1287 PHE cc_start: 0.6016 (m-80) cc_final: 0.5678 (m-80) REVERT: A 1486 LEU cc_start: 0.8672 (mp) cc_final: 0.8353 (tp) REVERT: A 1518 MET cc_start: 0.8761 (tmm) cc_final: 0.8486 (tmm) REVERT: A 1587 TYR cc_start: 0.7017 (t80) cc_final: 0.6795 (t80) REVERT: A 1919 GLU cc_start: 0.8765 (pm20) cc_final: 0.8435 (pm20) REVERT: A 1928 MET cc_start: 0.8757 (ptp) cc_final: 0.8065 (ptp) REVERT: A 2196 MET cc_start: 0.8984 (ptp) cc_final: 0.8429 (ptm) REVERT: B 739 MET cc_start: 0.9530 (mmp) cc_final: 0.9261 (mmm) REVERT: B 760 MET cc_start: 0.8999 (mpp) cc_final: 0.8255 (mmt) REVERT: B 991 MET cc_start: 0.9228 (mmm) cc_final: 0.8835 (mmm) REVERT: B 1041 MET cc_start: 0.9527 (mmm) cc_final: 0.9200 (mmm) REVERT: B 1096 MET cc_start: 0.8777 (ppp) cc_final: 0.8296 (ppp) REVERT: B 1134 MET cc_start: 0.8213 (ptt) cc_final: 0.7261 (pmm) REVERT: B 1162 MET cc_start: 0.8748 (ptt) cc_final: 0.8487 (ptp) REVERT: B 2134 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8727 (mp0) REVERT: B 2340 MET cc_start: 0.8708 (mmm) cc_final: 0.8230 (mmm) outliers start: 23 outliers final: 10 residues processed: 210 average time/residue: 0.2041 time to fit residues: 73.5772 Evaluate side-chains 202 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1953 ILE Chi-restraints excluded: chain B residue 2134 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 9 optimal weight: 3.9990 chunk 443 optimal weight: 0.6980 chunk 417 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 255 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 407 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN A 957 ASN B 83 GLN B 957 ASN B1900 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.090505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065267 restraints weight = 218896.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.066640 restraints weight = 103171.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.067997 restraints weight = 64941.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.068697 restraints weight = 47104.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.068943 restraints weight = 38377.207| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36337 Z= 0.118 Angle : 0.614 12.497 49248 Z= 0.310 Chirality : 0.040 0.184 5778 Planarity : 0.005 0.062 6181 Dihedral : 5.026 44.021 4737 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.98 % Allowed : 8.07 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.10 (0.13), residues: 4409 helix: 0.76 (0.10), residues: 2932 sheet: -0.47 (0.52), residues: 99 loop : -1.30 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1666 TYR 0.023 0.001 TYR B1614 PHE 0.032 0.001 PHE A 358 TRP 0.027 0.002 TRP B 777 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00251 (36337) covalent geometry : angle 0.61410 (49248) hydrogen bonds : bond 0.03871 ( 2055) hydrogen bonds : angle 4.41330 ( 6045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 1.327 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 376 MET cc_start: 0.8720 (mpp) cc_final: 0.7796 (mmt) REVERT: A 496 MET cc_start: 0.9682 (mtp) cc_final: 0.9432 (mtp) REVERT: A 590 MET cc_start: 0.8279 (mpp) cc_final: 0.7143 (pmm) REVERT: A 693 MET cc_start: 0.9100 (mmp) cc_final: 0.8590 (mtp) REVERT: A 707 MET cc_start: 0.9151 (tmm) cc_final: 0.8786 (tmm) REVERT: A 895 MET cc_start: 0.8525 (mtp) cc_final: 0.8247 (mtm) REVERT: A 992 MET cc_start: 0.9678 (mmp) cc_final: 0.9369 (mmm) REVERT: A 1005 MET cc_start: 0.9408 (tpt) cc_final: 0.9200 (tpt) REVERT: A 1111 MET cc_start: 0.9326 (mmp) cc_final: 0.8946 (mmp) REVERT: A 1271 MET cc_start: 0.4795 (mmp) cc_final: 0.2281 (tpp) REVERT: A 1287 PHE cc_start: 0.6157 (m-80) cc_final: 0.5636 (m-80) REVERT: A 1486 LEU cc_start: 0.8699 (mp) cc_final: 0.8381 (tp) REVERT: A 1518 MET cc_start: 0.8793 (tmm) cc_final: 0.8447 (tmm) REVERT: A 1839 LEU cc_start: 0.9332 (tt) cc_final: 0.9107 (tp) REVERT: A 1928 MET cc_start: 0.8793 (ptp) cc_final: 0.8214 (ptp) REVERT: A 2196 MET cc_start: 0.8990 (ptp) cc_final: 0.8390 (ptm) REVERT: A 2284 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9294 (tt) REVERT: B 294 MET cc_start: 0.8961 (mpp) cc_final: 0.8435 (pmm) REVERT: B 349 MET cc_start: 0.6691 (pmm) cc_final: 0.6429 (pmm) REVERT: B 707 MET cc_start: 0.9595 (OUTLIER) cc_final: 0.9316 (ttp) REVERT: B 739 MET cc_start: 0.9460 (mmp) cc_final: 0.9191 (mmm) REVERT: B 760 MET cc_start: 0.9042 (mpp) cc_final: 0.8390 (mmt) REVERT: B 1041 MET cc_start: 0.9546 (mmm) cc_final: 0.9201 (mmm) REVERT: B 1096 MET cc_start: 0.8771 (ppp) cc_final: 0.8348 (ppp) REVERT: B 1134 MET cc_start: 0.8192 (ptt) cc_final: 0.7392 (pmm) REVERT: B 1162 MET cc_start: 0.8792 (ptt) cc_final: 0.8538 (ptp) REVERT: B 1342 MET cc_start: 0.4143 (mmt) cc_final: 0.3369 (ptm) REVERT: B 1440 MET cc_start: 0.7300 (mmm) cc_final: 0.7026 (mmm) REVERT: B 2010 MET cc_start: 0.8133 (tmm) cc_final: 0.7683 (tmm) REVERT: B 2271 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8652 (tm-30) outliers start: 39 outliers final: 19 residues processed: 223 average time/residue: 0.1960 time to fit residues: 75.6613 Evaluate side-chains 205 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1953 ILE Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 299 optimal weight: 6.9990 chunk 393 optimal weight: 0.0470 chunk 286 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 430 optimal weight: 0.0870 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS A1487 HIS A1854 ASN ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.065221 restraints weight = 217984.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.066920 restraints weight = 101884.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.068135 restraints weight = 63371.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.068537 restraints weight = 45994.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.069320 restraints weight = 39112.489| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36337 Z= 0.111 Angle : 0.587 10.916 49248 Z= 0.295 Chirality : 0.040 0.210 5778 Planarity : 0.004 0.060 6181 Dihedral : 4.729 43.962 4737 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.15 % Allowed : 9.72 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.53 (0.13), residues: 4409 helix: 1.10 (0.10), residues: 2948 sheet: -0.36 (0.53), residues: 99 loop : -1.19 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1038 TYR 0.022 0.001 TYR B1614 PHE 0.026 0.001 PHE A 199 TRP 0.024 0.001 TRP B 777 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00239 (36337) covalent geometry : angle 0.58703 (49248) hydrogen bonds : bond 0.03464 ( 2055) hydrogen bonds : angle 4.19101 ( 6045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.8561 (m-80) cc_final: 0.8182 (m-80) REVERT: A 376 MET cc_start: 0.8684 (mpp) cc_final: 0.7980 (mmt) REVERT: A 496 MET cc_start: 0.9625 (mtp) cc_final: 0.9423 (mtp) REVERT: A 546 MET cc_start: 0.8961 (tpp) cc_final: 0.8703 (mmp) REVERT: A 590 MET cc_start: 0.8275 (mpp) cc_final: 0.7369 (pmm) REVERT: A 693 MET cc_start: 0.9131 (mmp) cc_final: 0.8560 (mtp) REVERT: A 707 MET cc_start: 0.9196 (tmm) cc_final: 0.8744 (tmm) REVERT: A 840 MET cc_start: 0.9147 (ttt) cc_final: 0.8191 (ppp) REVERT: A 895 MET cc_start: 0.8528 (mtp) cc_final: 0.8318 (mtm) REVERT: A 1005 MET cc_start: 0.9467 (tpt) cc_final: 0.9204 (tpt) REVERT: A 1041 MET cc_start: 0.9565 (mpp) cc_final: 0.8879 (mpp) REVERT: A 1111 MET cc_start: 0.9306 (mmp) cc_final: 0.8980 (mmp) REVERT: A 1149 MET cc_start: 0.9201 (mmp) cc_final: 0.8795 (mmp) REVERT: A 1181 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9002 (mt-10) REVERT: A 1271 MET cc_start: 0.4873 (mmp) cc_final: 0.2292 (tpp) REVERT: A 1287 PHE cc_start: 0.6383 (m-80) cc_final: 0.5968 (m-80) REVERT: A 1486 LEU cc_start: 0.8739 (mp) cc_final: 0.8447 (tp) REVERT: A 1518 MET cc_start: 0.8813 (tmm) cc_final: 0.8461 (tmm) REVERT: A 1839 LEU cc_start: 0.9285 (tt) cc_final: 0.9080 (tp) REVERT: A 1928 MET cc_start: 0.8771 (ptp) cc_final: 0.8121 (ptp) REVERT: A 2196 MET cc_start: 0.9049 (ptp) cc_final: 0.8419 (ptm) REVERT: A 2284 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9276 (tt) REVERT: B 102 MET cc_start: 0.7995 (mmp) cc_final: 0.7393 (mpp) REVERT: B 707 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9289 (ttp) REVERT: B 739 MET cc_start: 0.9438 (mmp) cc_final: 0.9179 (mmm) REVERT: B 760 MET cc_start: 0.9068 (mpp) cc_final: 0.8551 (mmt) REVERT: B 991 MET cc_start: 0.9277 (mmm) cc_final: 0.8912 (tpt) REVERT: B 1022 MET cc_start: 0.9516 (ptp) cc_final: 0.9177 (ptm) REVERT: B 1134 MET cc_start: 0.7787 (ptt) cc_final: 0.7197 (pmm) REVERT: B 1162 MET cc_start: 0.8786 (ptt) cc_final: 0.8524 (ptp) REVERT: B 1342 MET cc_start: 0.4177 (mmt) cc_final: 0.3455 (ptm) REVERT: B 1440 MET cc_start: 0.7440 (mmm) cc_final: 0.7220 (mmm) REVERT: B 2010 MET cc_start: 0.8024 (tmm) cc_final: 0.7772 (tmm) REVERT: B 2196 MET cc_start: 0.9115 (ttm) cc_final: 0.8742 (tpp) REVERT: B 2244 LYS cc_start: 0.9376 (mttp) cc_final: 0.9100 (pptt) REVERT: B 2271 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8661 (tm-30) REVERT: B 2340 MET cc_start: 0.8728 (mmm) cc_final: 0.8250 (mmm) outliers start: 46 outliers final: 22 residues processed: 230 average time/residue: 0.1996 time to fit residues: 79.0912 Evaluate side-chains 209 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 2015 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 10 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 397 optimal weight: 0.0070 chunk 386 optimal weight: 0.0970 chunk 190 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 406 optimal weight: 0.6980 chunk 309 optimal weight: 6.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 756 GLN A 970 ASN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1366 HIS ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B2240 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.090663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067876 restraints weight = 179193.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.069485 restraints weight = 93844.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.070623 restraints weight = 62436.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.071416 restraints weight = 47691.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.071528 restraints weight = 40440.027| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 36337 Z= 0.108 Angle : 0.602 15.256 49248 Z= 0.295 Chirality : 0.040 0.208 5778 Planarity : 0.004 0.059 6181 Dihedral : 4.573 41.455 4737 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.28 % Allowed : 11.13 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4409 helix: 1.29 (0.10), residues: 2951 sheet: -0.32 (0.53), residues: 99 loop : -1.08 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1807 TYR 0.021 0.001 TYR B1614 PHE 0.038 0.001 PHE B1247 TRP 0.022 0.001 TRP B 777 HIS 0.004 0.000 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00233 (36337) covalent geometry : angle 0.60211 (49248) hydrogen bonds : bond 0.03305 ( 2055) hydrogen bonds : angle 4.07370 ( 6045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 1.289 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 333 TYR cc_start: 0.8603 (m-80) cc_final: 0.8230 (m-80) REVERT: A 376 MET cc_start: 0.8700 (mpp) cc_final: 0.8479 (mpp) REVERT: A 496 MET cc_start: 0.9637 (mtp) cc_final: 0.9429 (mtp) REVERT: A 590 MET cc_start: 0.8507 (mpp) cc_final: 0.7853 (pmm) REVERT: A 693 MET cc_start: 0.8950 (mmp) cc_final: 0.8626 (mtp) REVERT: A 707 MET cc_start: 0.9012 (tmm) cc_final: 0.8729 (tmm) REVERT: A 840 MET cc_start: 0.9094 (ttt) cc_final: 0.8332 (ppp) REVERT: A 988 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9305 (mm) REVERT: A 1005 MET cc_start: 0.9589 (tpt) cc_final: 0.9310 (tpt) REVERT: A 1111 MET cc_start: 0.9362 (mmp) cc_final: 0.9020 (mmp) REVERT: A 1149 MET cc_start: 0.9295 (mmp) cc_final: 0.8916 (mmp) REVERT: A 1181 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9022 (mt-10) REVERT: A 1252 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8962 (pp) REVERT: A 1271 MET cc_start: 0.4659 (mmp) cc_final: 0.2088 (tpp) REVERT: A 1287 PHE cc_start: 0.6433 (m-80) cc_final: 0.6013 (m-80) REVERT: A 1486 LEU cc_start: 0.8766 (mp) cc_final: 0.8486 (tp) REVERT: A 1518 MET cc_start: 0.8842 (tmm) cc_final: 0.8454 (tmm) REVERT: A 1928 MET cc_start: 0.8678 (ptp) cc_final: 0.8048 (ptp) REVERT: A 2196 MET cc_start: 0.9122 (ptp) cc_final: 0.8441 (ptm) REVERT: A 2284 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9260 (tt) REVERT: B 294 MET cc_start: 0.8938 (mpp) cc_final: 0.8680 (pmm) REVERT: B 707 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.9223 (ttm) REVERT: B 739 MET cc_start: 0.9514 (mmp) cc_final: 0.9212 (mmm) REVERT: B 760 MET cc_start: 0.8766 (mpp) cc_final: 0.8375 (mmt) REVERT: B 991 MET cc_start: 0.9313 (mmm) cc_final: 0.8977 (tpt) REVERT: B 1022 MET cc_start: 0.9613 (ptp) cc_final: 0.9301 (ptm) REVERT: B 1041 MET cc_start: 0.9684 (mmm) cc_final: 0.9444 (mmm) REVERT: B 1134 MET cc_start: 0.7973 (ptt) cc_final: 0.7308 (pmm) REVERT: B 1162 MET cc_start: 0.8812 (ptt) cc_final: 0.8568 (ptp) REVERT: B 1342 MET cc_start: 0.4186 (mmt) cc_final: 0.3538 (ptm) REVERT: B 1440 MET cc_start: 0.7427 (mmm) cc_final: 0.7217 (mmm) REVERT: B 2010 MET cc_start: 0.7963 (tmm) cc_final: 0.7673 (tmm) REVERT: B 2271 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 2301 VAL cc_start: 0.9506 (t) cc_final: 0.9229 (p) REVERT: B 2340 MET cc_start: 0.8750 (mmm) cc_final: 0.8337 (mmm) outliers start: 51 outliers final: 30 residues processed: 235 average time/residue: 0.1976 time to fit residues: 80.6977 Evaluate side-chains 212 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 380 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 275 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 351 optimal weight: 20.0000 chunk 311 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 970 ASN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1854 ASN B1966 GLN ** B2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.089353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064013 restraints weight = 228539.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065661 restraints weight = 122621.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065386 restraints weight = 68975.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065407 restraints weight = 64653.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065407 restraints weight = 64056.571| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36337 Z= 0.167 Angle : 0.646 15.280 49248 Z= 0.322 Chirality : 0.041 0.229 5778 Planarity : 0.004 0.061 6181 Dihedral : 4.539 40.260 4737 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.13 % Allowed : 11.80 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.99 (0.13), residues: 4409 helix: 1.44 (0.10), residues: 2969 sheet: -0.34 (0.53), residues: 99 loop : -1.00 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2032 TYR 0.017 0.001 TYR A2063 PHE 0.036 0.001 PHE B1287 TRP 0.021 0.002 TRP B 777 HIS 0.007 0.001 HIS A1163 Details of bonding type rmsd covalent geometry : bond 0.00363 (36337) covalent geometry : angle 0.64591 (49248) hydrogen bonds : bond 0.03432 ( 2055) hydrogen bonds : angle 4.19063 ( 6045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.8642 (m-80) cc_final: 0.8288 (m-80) REVERT: A 376 MET cc_start: 0.8813 (mpp) cc_final: 0.8595 (mpp) REVERT: A 496 MET cc_start: 0.9639 (mtp) cc_final: 0.9424 (mtp) REVERT: A 693 MET cc_start: 0.9190 (mmp) cc_final: 0.8644 (mtp) REVERT: A 707 MET cc_start: 0.9135 (tmm) cc_final: 0.8835 (tmm) REVERT: A 988 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9264 (mm) REVERT: A 992 MET cc_start: 0.9710 (mmp) cc_final: 0.9454 (mmp) REVERT: A 1005 MET cc_start: 0.9476 (tpt) cc_final: 0.9148 (tpt) REVERT: A 1111 MET cc_start: 0.9298 (mmp) cc_final: 0.8977 (mmp) REVERT: A 1252 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9033 (pp) REVERT: A 1271 MET cc_start: 0.4938 (mmp) cc_final: 0.2311 (tpp) REVERT: A 1287 PHE cc_start: 0.6382 (m-80) cc_final: 0.5977 (m-80) REVERT: A 1486 LEU cc_start: 0.8837 (mp) cc_final: 0.8528 (tp) REVERT: A 1518 MET cc_start: 0.8826 (tmm) cc_final: 0.8569 (tmm) REVERT: A 1839 LEU cc_start: 0.9364 (tt) cc_final: 0.9083 (tp) REVERT: A 1928 MET cc_start: 0.8607 (ptp) cc_final: 0.8146 (ptp) REVERT: A 2196 MET cc_start: 0.9017 (ptp) cc_final: 0.8478 (ptm) REVERT: A 2340 MET cc_start: 0.8674 (mmt) cc_final: 0.8277 (mmm) REVERT: B 102 MET cc_start: 0.8168 (mmp) cc_final: 0.7914 (mpp) REVERT: B 294 MET cc_start: 0.9067 (mpp) cc_final: 0.8765 (pmm) REVERT: B 739 MET cc_start: 0.9553 (mmp) cc_final: 0.9223 (mmm) REVERT: B 760 MET cc_start: 0.9179 (mpp) cc_final: 0.8633 (mmt) REVERT: B 991 MET cc_start: 0.9203 (mmm) cc_final: 0.8850 (tpt) REVERT: B 1041 MET cc_start: 0.9583 (mmm) cc_final: 0.9252 (mmm) REVERT: B 2010 MET cc_start: 0.7887 (tmm) cc_final: 0.7607 (tmm) REVERT: B 2196 MET cc_start: 0.9371 (tpp) cc_final: 0.8848 (tpp) outliers start: 45 outliers final: 33 residues processed: 216 average time/residue: 0.1894 time to fit residues: 72.0953 Evaluate side-chains 209 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1829 VAL Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 1975 ILE Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2222 SER Chi-restraints excluded: chain B residue 2302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 344 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 366 optimal weight: 0.0570 chunk 126 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN A 786 GLN A 994 ASN A2265 ASN ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2702 GLN B 452 GLN B 535 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 ASN B1487 HIS B1835 ASN ** B2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2349 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.088202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.062948 restraints weight = 233588.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.064070 restraints weight = 128286.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.064788 restraints weight = 74338.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064291 restraints weight = 77110.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064622 restraints weight = 61352.845| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36337 Z= 0.222 Angle : 0.703 13.393 49248 Z= 0.351 Chirality : 0.042 0.209 5778 Planarity : 0.004 0.062 6181 Dihedral : 4.658 37.729 4737 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 12.58 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.13), residues: 4409 helix: 1.38 (0.10), residues: 2981 sheet: -0.17 (0.57), residues: 93 loop : -1.01 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1137 TYR 0.016 0.001 TYR A2219 PHE 0.034 0.002 PHE B1289 TRP 0.018 0.002 TRP B2348 HIS 0.006 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00476 (36337) covalent geometry : angle 0.70319 (49248) hydrogen bonds : bond 0.03641 ( 2055) hydrogen bonds : angle 4.36098 ( 6045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9065 (pmm) cc_final: 0.8858 (pmm) REVERT: A 333 TYR cc_start: 0.8675 (m-80) cc_final: 0.8296 (m-80) REVERT: A 496 MET cc_start: 0.9651 (mtp) cc_final: 0.9439 (mtp) REVERT: A 546 MET cc_start: 0.8954 (tpp) cc_final: 0.8583 (tpt) REVERT: A 590 MET cc_start: 0.8222 (mpp) cc_final: 0.7719 (pmm) REVERT: A 693 MET cc_start: 0.9175 (mmp) cc_final: 0.8683 (mtp) REVERT: A 707 MET cc_start: 0.9109 (tmm) cc_final: 0.8775 (tmm) REVERT: A 902 MET cc_start: 0.9420 (ptp) cc_final: 0.9063 (ptp) REVERT: A 988 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9216 (mm) REVERT: A 992 MET cc_start: 0.9727 (mmp) cc_final: 0.9474 (mmm) REVERT: A 1005 MET cc_start: 0.9473 (tpt) cc_final: 0.9251 (tpt) REVERT: A 1111 MET cc_start: 0.9312 (mmp) cc_final: 0.9002 (mmp) REVERT: A 1215 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: A 1271 MET cc_start: 0.5090 (mmp) cc_final: 0.2410 (tpp) REVERT: A 1287 PHE cc_start: 0.6403 (m-80) cc_final: 0.6061 (m-80) REVERT: A 1486 LEU cc_start: 0.8961 (mp) cc_final: 0.8639 (tp) REVERT: A 1518 MET cc_start: 0.8787 (tmm) cc_final: 0.8545 (tmm) REVERT: A 1928 MET cc_start: 0.8560 (ptp) cc_final: 0.8139 (ptp) REVERT: B 577 MET cc_start: 0.9520 (ttp) cc_final: 0.8861 (ptm) REVERT: B 739 MET cc_start: 0.9512 (mmp) cc_final: 0.9187 (mmm) REVERT: B 760 MET cc_start: 0.9227 (mpp) cc_final: 0.8657 (mmt) REVERT: B 1134 MET cc_start: 0.8524 (pmm) cc_final: 0.8260 (pmm) REVERT: B 1342 MET cc_start: 0.4356 (mmp) cc_final: 0.3822 (ptm) REVERT: B 1389 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 1440 MET cc_start: 0.7306 (mmm) cc_final: 0.6991 (mmm) REVERT: B 2186 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: B 2196 MET cc_start: 0.9366 (tpp) cc_final: 0.8955 (tpp) REVERT: B 2340 MET cc_start: 0.8799 (mmm) cc_final: 0.8589 (mmm) outliers start: 57 outliers final: 34 residues processed: 226 average time/residue: 0.1851 time to fit residues: 73.1226 Evaluate side-chains 211 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1829 VAL Chi-restraints excluded: chain A residue 1936 VAL Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 1975 ILE Chi-restraints excluded: chain A residue 2015 VAL Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1389 PHE Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2222 SER Chi-restraints excluded: chain B residue 2247 ILE Chi-restraints excluded: chain B residue 2302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 349 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 387 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 447 optimal weight: 0.9980 chunk 358 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1672 HIS ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN B1360 GLN ** B2102 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 = 0.4204 r_free = 0.4204 target = 0.088938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.063423 restraints weight = 227542.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065060 restraints weight = 106367.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065060 restraints weight = 63301.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065060 restraints weight = 63301.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065060 restraints weight = 63301.823| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36337 Z= 0.124 Angle : 0.665 20.490 49248 Z= 0.321 Chirality : 0.041 0.224 5778 Planarity : 0.004 0.064 6181 Dihedral : 4.534 41.139 4737 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.10 % Allowed : 13.33 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.09 (0.13), residues: 4409 helix: 1.50 (0.10), residues: 2978 sheet: -0.20 (0.57), residues: 93 loop : -0.93 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2032 TYR 0.015 0.001 TYR A2264 PHE 0.033 0.001 PHE B1289 TRP 0.020 0.001 TRP B 777 HIS 0.005 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00276 (36337) covalent geometry : angle 0.66455 (49248) hydrogen bonds : bond 0.03336 ( 2055) hydrogen bonds : angle 4.11470 ( 6045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9155 (pmm) cc_final: 0.8947 (pmm) REVERT: A 333 TYR cc_start: 0.8695 (m-80) cc_final: 0.8325 (m-80) REVERT: A 496 MET cc_start: 0.9605 (mtp) cc_final: 0.9397 (mtp) REVERT: A 590 MET cc_start: 0.8367 (mpp) cc_final: 0.7945 (pmm) REVERT: A 693 MET cc_start: 0.9094 (mmp) cc_final: 0.8657 (mtp) REVERT: A 707 MET cc_start: 0.9115 (tmm) cc_final: 0.8568 (tmm) REVERT: A 741 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8840 (t80) REVERT: A 748 MET cc_start: 0.8504 (tmm) cc_final: 0.8265 (tmm) REVERT: A 988 ILE cc_start: 0.9633 (OUTLIER) cc_final: 0.9060 (mm) REVERT: A 992 MET cc_start: 0.9743 (mmp) cc_final: 0.9361 (mmm) REVERT: A 1005 MET cc_start: 0.9544 (tpt) cc_final: 0.9230 (tpt) REVERT: A 1111 MET cc_start: 0.9247 (mmp) cc_final: 0.9019 (mmp) REVERT: A 1149 MET cc_start: 0.8666 (mmp) cc_final: 0.8406 (mmp) REVERT: A 1180 MET cc_start: 0.9228 (tpp) cc_final: 0.8991 (tpp) REVERT: A 1215 MET cc_start: 0.7618 (pmm) cc_final: 0.7360 (pmm) REVERT: A 1271 MET cc_start: 0.5155 (mmp) cc_final: 0.2477 (tpp) REVERT: A 1287 PHE cc_start: 0.6324 (m-80) cc_final: 0.5983 (m-80) REVERT: A 1486 LEU cc_start: 0.8961 (mp) cc_final: 0.8654 (tp) REVERT: A 1518 MET cc_start: 0.8816 (tmm) cc_final: 0.8586 (tmm) REVERT: A 1928 MET cc_start: 0.8375 (ptp) cc_final: 0.7957 (ptp) REVERT: A 2192 MET cc_start: 0.8690 (ttt) cc_final: 0.8000 (tmm) REVERT: B 68 MET cc_start: 0.4412 (ptm) cc_final: 0.2994 (ppp) REVERT: B 294 MET cc_start: 0.8917 (mpp) cc_final: 0.8181 (pmm) REVERT: B 577 MET cc_start: 0.9412 (ttp) cc_final: 0.8701 (ptm) REVERT: B 739 MET cc_start: 0.9561 (mmp) cc_final: 0.9235 (mmm) REVERT: B 760 MET cc_start: 0.9239 (mpp) cc_final: 0.8679 (mmt) REVERT: B 840 MET cc_start: 0.9083 (mtp) cc_final: 0.8838 (mtm) REVERT: B 991 MET cc_start: 0.9114 (mmm) cc_final: 0.8626 (mmm) REVERT: B 1134 MET cc_start: 0.8592 (pmm) cc_final: 0.8109 (pmm) REVERT: B 1342 MET cc_start: 0.4527 (mmp) cc_final: 0.4019 (ptm) REVERT: B 1389 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8863 (t80) REVERT: B 1440 MET cc_start: 0.7449 (mmm) cc_final: 0.6552 (mmm) REVERT: B 2182 GLU cc_start: 0.8736 (pp20) cc_final: 0.8095 (pp20) REVERT: B 2196 MET cc_start: 0.9349 (tpp) cc_final: 0.8812 (tpp) REVERT: B 2301 VAL cc_start: 0.9457 (t) cc_final: 0.9228 (p) outliers start: 44 outliers final: 30 residues processed: 220 average time/residue: 0.1901 time to fit residues: 72.8214 Evaluate side-chains 210 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1829 VAL Chi-restraints excluded: chain A residue 1936 VAL Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2090 VAL Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1149 MET Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1389 PHE Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2222 SER Chi-restraints excluded: chain B residue 2302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 139 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** 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 = 0.4200 r_free = 0.4200 target = 0.088931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062781 restraints weight = 228824.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064450 restraints weight = 103946.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065635 restraints weight = 63843.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.066442 restraints weight = 45911.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.066490 restraints weight = 37101.325| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36337 Z= 0.136 Angle : 0.672 16.419 49248 Z= 0.325 Chirality : 0.041 0.213 5778 Planarity : 0.004 0.062 6181 Dihedral : 4.475 39.189 4737 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.00 % Allowed : 13.78 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.13), residues: 4409 helix: 1.54 (0.10), residues: 2985 sheet: -0.37 (0.54), residues: 99 loop : -0.95 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2032 TYR 0.015 0.001 TYR A2264 PHE 0.032 0.001 PHE B1289 TRP 0.022 0.001 TRP B 777 HIS 0.006 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00302 (36337) covalent geometry : angle 0.67181 (49248) hydrogen bonds : bond 0.03332 ( 2055) hydrogen bonds : angle 4.13870 ( 6045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9019 (pmm) cc_final: 0.8758 (pmm) REVERT: A 333 TYR cc_start: 0.8562 (m-80) cc_final: 0.8265 (m-80) REVERT: A 496 MET cc_start: 0.9596 (mtp) cc_final: 0.9376 (mtp) REVERT: A 546 MET cc_start: 0.8983 (tpp) cc_final: 0.8452 (tpt) REVERT: A 577 MET cc_start: 0.9395 (ppp) cc_final: 0.9056 (ppp) REVERT: A 590 MET cc_start: 0.8139 (mpp) cc_final: 0.7590 (pmm) REVERT: A 693 MET cc_start: 0.9146 (mmp) cc_final: 0.8519 (mtp) REVERT: A 707 MET cc_start: 0.9173 (tmm) cc_final: 0.8606 (tmm) REVERT: A 741 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8840 (t80) REVERT: A 988 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 992 MET cc_start: 0.9680 (mmp) cc_final: 0.9332 (mmm) REVERT: A 1005 MET cc_start: 0.9422 (tpt) cc_final: 0.9164 (tpt) REVERT: A 1111 MET cc_start: 0.9242 (mmp) cc_final: 0.8993 (mmp) REVERT: A 1149 MET cc_start: 0.8941 (mmp) cc_final: 0.8642 (mmp) REVERT: A 1215 MET cc_start: 0.7709 (pmm) cc_final: 0.7415 (pmm) REVERT: A 1271 MET cc_start: 0.4954 (mmp) cc_final: 0.2237 (tpp) REVERT: A 1287 PHE cc_start: 0.6460 (m-80) cc_final: 0.6134 (m-80) REVERT: A 1486 LEU cc_start: 0.8864 (mp) cc_final: 0.8597 (tp) REVERT: A 1518 MET cc_start: 0.8831 (tmm) cc_final: 0.8517 (tmm) REVERT: A 1928 MET cc_start: 0.8661 (ptp) cc_final: 0.8249 (ptp) REVERT: A 2192 MET cc_start: 0.8807 (ttt) cc_final: 0.8043 (tmm) REVERT: B 68 MET cc_start: 0.3693 (ptm) cc_final: 0.2433 (ppp) REVERT: B 294 MET cc_start: 0.8773 (mpp) cc_final: 0.7896 (pmm) REVERT: B 577 MET cc_start: 0.9488 (ttp) cc_final: 0.8845 (ptm) REVERT: B 739 MET cc_start: 0.9350 (mmp) cc_final: 0.9081 (mmm) REVERT: B 760 MET cc_start: 0.9194 (mpp) cc_final: 0.8639 (mmt) REVERT: B 840 MET cc_start: 0.9167 (mtp) cc_final: 0.8941 (mtm) REVERT: B 1134 MET cc_start: 0.8428 (pmm) cc_final: 0.7984 (pmm) REVERT: B 1342 MET cc_start: 0.4390 (mmp) cc_final: 0.3830 (ptm) REVERT: B 1389 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8793 (t80) REVERT: B 1440 MET cc_start: 0.7277 (mmm) cc_final: 0.6787 (mmm) REVERT: B 2196 MET cc_start: 0.9354 (tpp) cc_final: 0.8817 (tpp) REVERT: B 2301 VAL cc_start: 0.9574 (t) cc_final: 0.9338 (p) REVERT: B 2340 MET cc_start: 0.8816 (mmm) cc_final: 0.8122 (mmm) outliers start: 40 outliers final: 29 residues processed: 211 average time/residue: 0.1855 time to fit residues: 68.6647 Evaluate side-chains 208 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1829 VAL Chi-restraints excluded: chain A residue 1936 VAL Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1149 MET Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1389 PHE Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2222 SER Chi-restraints excluded: chain B residue 2302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 83 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 414 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.0670 chunk 214 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.089142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064772 restraints weight = 209822.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.066392 restraints weight = 100315.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.067614 restraints weight = 63410.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068359 restraints weight = 46402.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.068656 restraints weight = 38470.050| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36337 Z= 0.118 Angle : 0.671 16.891 49248 Z= 0.321 Chirality : 0.041 0.227 5778 Planarity : 0.004 0.064 6181 Dihedral : 4.396 38.714 4737 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.78 % Allowed : 14.21 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.19 (0.13), residues: 4409 helix: 1.58 (0.10), residues: 2986 sheet: -0.38 (0.53), residues: 99 loop : -0.91 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2032 TYR 0.017 0.001 TYR B1292 PHE 0.029 0.001 PHE B1289 TRP 0.023 0.001 TRP B 777 HIS 0.006 0.000 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00262 (36337) covalent geometry : angle 0.67083 (49248) hydrogen bonds : bond 0.03204 ( 2055) hydrogen bonds : angle 4.06517 ( 6045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8818 Ramachandran restraints generated. 4409 Oldfield, 0 Emsley, 4409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8952 (pmm) cc_final: 0.8735 (pmm) REVERT: A 333 TYR cc_start: 0.8612 (m-80) cc_final: 0.8288 (m-80) REVERT: A 496 MET cc_start: 0.9619 (mtp) cc_final: 0.9401 (mtp) REVERT: A 546 MET cc_start: 0.8904 (tpp) cc_final: 0.8688 (tpt) REVERT: A 577 MET cc_start: 0.9362 (ppp) cc_final: 0.9066 (ppp) REVERT: A 590 MET cc_start: 0.8410 (mpp) cc_final: 0.8047 (pmm) REVERT: A 707 MET cc_start: 0.9082 (tmm) cc_final: 0.8527 (tmm) REVERT: A 741 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8792 (t80) REVERT: A 988 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.8917 (mp) REVERT: A 992 MET cc_start: 0.9721 (mmp) cc_final: 0.9240 (mmp) REVERT: A 1005 MET cc_start: 0.9580 (tpt) cc_final: 0.9276 (tpt) REVERT: A 1111 MET cc_start: 0.9354 (mmp) cc_final: 0.9036 (mmp) REVERT: A 1215 MET cc_start: 0.7801 (pmm) cc_final: 0.7497 (pmm) REVERT: A 1271 MET cc_start: 0.4866 (mmp) cc_final: 0.2180 (tpp) REVERT: A 1287 PHE cc_start: 0.6527 (m-80) cc_final: 0.6203 (m-80) REVERT: A 1486 LEU cc_start: 0.8818 (mp) cc_final: 0.8576 (tp) REVERT: A 1518 MET cc_start: 0.8834 (tmm) cc_final: 0.8490 (tmm) REVERT: A 1928 MET cc_start: 0.8816 (ptp) cc_final: 0.8347 (ptp) REVERT: B 68 MET cc_start: 0.3845 (ptm) cc_final: 0.2565 (ppp) REVERT: B 294 MET cc_start: 0.8950 (mpp) cc_final: 0.8159 (pmm) REVERT: B 577 MET cc_start: 0.9544 (ttp) cc_final: 0.8931 (ptm) REVERT: B 739 MET cc_start: 0.9446 (mmp) cc_final: 0.9121 (mmm) REVERT: B 760 MET cc_start: 0.9035 (mpp) cc_final: 0.8570 (mmt) REVERT: B 1134 MET cc_start: 0.8650 (pmm) cc_final: 0.8072 (pmm) REVERT: B 1342 MET cc_start: 0.4401 (mmp) cc_final: 0.3866 (ptm) REVERT: B 1389 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8763 (t80) REVERT: B 1440 MET cc_start: 0.7230 (mmm) cc_final: 0.6731 (mmm) REVERT: B 2012 ASP cc_start: 0.8951 (t0) cc_final: 0.8583 (t0) REVERT: B 2196 MET cc_start: 0.9411 (tpp) cc_final: 0.8838 (tpp) REVERT: B 2271 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8988 (tm-30) REVERT: B 2301 VAL cc_start: 0.9576 (t) cc_final: 0.9324 (p) REVERT: B 2340 MET cc_start: 0.8730 (mmm) cc_final: 0.8083 (mmm) outliers start: 31 outliers final: 27 residues processed: 210 average time/residue: 0.1962 time to fit residues: 71.7192 Evaluate side-chains 210 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1792 MET Chi-restraints excluded: chain A residue 1829 VAL Chi-restraints excluded: chain A residue 1936 VAL Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2149 VAL Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1149 MET Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1389 PHE Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1929 THR Chi-restraints excluded: chain B residue 2064 MET Chi-restraints excluded: chain B residue 2134 GLU Chi-restraints excluded: chain B residue 2302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 213 optimal weight: 0.0270 chunk 366 optimal weight: 8.9990 chunk 294 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 113 optimal weight: 0.9990 chunk 442 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 219 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065849 restraints weight = 196732.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.067499 restraints weight = 97921.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.068639 restraints weight = 62843.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.069370 restraints weight = 46892.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.069534 restraints weight = 38985.435| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36337 Z= 0.113 Angle : 0.663 16.983 49248 Z= 0.317 Chirality : 0.041 0.217 5778 Planarity : 0.004 0.063 6181 Dihedral : 4.330 37.478 4737 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.85 % Allowed : 14.29 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.23 (0.13), residues: 4409 helix: 1.62 (0.10), residues: 2975 sheet: -0.37 (0.53), residues: 99 loop : -0.90 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2032 TYR 0.015 0.001 TYR A 735 PHE 0.027 0.001 PHE B1289 TRP 0.025 0.001 TRP A 777 HIS 0.004 0.000 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00253 (36337) covalent geometry : angle 0.66282 (49248) hydrogen bonds : bond 0.03171 ( 2055) hydrogen bonds : angle 4.03209 ( 6045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8629.90 seconds wall clock time: 148 minutes 45.93 seconds (8925.93 seconds total)