Starting phenix.real_space_refine on Sat Mar 7 05:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219.map" model { file = "/net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r04_14219/03_2026/7r04_14219_trim.cif" } resolution = 3.7 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= 0.998 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2176 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 236 5.16 5 C 23263 2.51 5 N 6109 2.21 5 O 6639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s 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: 36250 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2326, 18523 Classifications: {'peptide': 2326} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 91, 'TRANS': 2234} Chain breaks: 13 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 17695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2229, 17695 Classifications: {'peptide': 2229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 86, 'TRANS': 2142} Chain breaks: 16 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.93, per 1000 atoms: 0.22 Number of scatterers: 36250 At special positions: 0 Unit cell: (141.772, 173.512, 329.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 3 15.00 O 6639 8.00 N 6109 7.00 C 23263 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8794 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 7 sheets defined 74.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.570A pdb=" N TRP A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.731A pdb=" N ILE A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.866A pdb=" N TYR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 72 through 96 Processing helix chain 'A' and resid 106 through 120 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 127 through 164 removed outlier: 7.021A pdb=" N GLU A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.854A pdb=" N HIS A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.836A pdb=" N ALA A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 227 " --> pdb=" O TRP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 239 through 258 removed outlier: 3.976A pdb=" N ALA A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 276 removed outlier: 4.014A pdb=" N ALA A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.555A pdb=" N ILE A 281 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.724A pdb=" N LYS A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 332 Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.934A pdb=" N MET A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 4.616A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 391 through 399 removed outlier: 4.002A pdb=" N CYS A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) 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 429 through 434 removed outlier: 4.402A pdb=" N CYS A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.555A pdb=" N GLY A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.895A pdb=" N LEU A 507 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.532A pdb=" N HIS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 removed outlier: 3.773A pdb=" N ASN A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 588 removed outlier: 3.989A pdb=" N THR A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 615 removed outlier: 3.752A pdb=" N GLU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 695 removed outlier: 3.545A pdb=" N GLU A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 721 removed outlier: 3.679A pdb=" N VAL A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 747 Processing helix chain 'A' and resid 751 through 765 removed outlier: 3.759A pdb=" N LEU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 890 through 903 removed outlier: 4.360A pdb=" N VAL A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 924 removed outlier: 3.522A pdb=" N GLY A 922 " --> pdb=" O LYS A 918 " (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 944 removed outlier: 3.797A pdb=" N LEU A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 934 " --> pdb=" O TYR A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 974 removed outlier: 3.756A pdb=" N ALA A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 988 through 1001 removed outlier: 3.915A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 Processing helix chain 'A' and resid 1033 through 1046 Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.833A pdb=" N GLU A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1119 removed outlier: 4.028A pdb=" N GLU A1119 " --> pdb=" O ASN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1156 removed outlier: 3.706A pdb=" N ASN A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 3.705A pdb=" N HIS A1163 " --> pdb=" O GLY A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1188 removed outlier: 4.437A pdb=" N THR A1184 " --> pdb=" O MET A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1214 Processing helix chain 'A' and resid 1221 through 1231 removed outlier: 3.545A pdb=" N ASN A1229 " --> pdb=" O MET A1225 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A1231 " --> pdb=" O LEU A1227 " (cutoff:3.500A) 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: 3.795A pdb=" N ASP A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A1249 " --> pdb=" O THR A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1268 removed outlier: 4.279A pdb=" N GLU A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1293 Processing helix chain 'A' and resid 1293 through 1316 Proline residue: A1303 - end of helix removed outlier: 3.628A pdb=" N VAL A1308 " --> pdb=" O LEU A1304 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A1312 " --> pdb=" O VAL A1308 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1358 through 1376 removed outlier: 3.616A pdb=" N VAL A1371 " --> pdb=" O CYS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1392 removed outlier: 3.628A pdb=" N VAL A1384 " --> pdb=" O SER A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 4.017A 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 1442 through 1450 removed outlier: 4.352A pdb=" N PHE A1446 " --> pdb=" O PRO A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1463 Processing helix chain 'A' and resid 1479 through 1493 removed outlier: 3.542A pdb=" N VAL A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1493 " --> pdb=" O LEU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1503 Processing helix chain 'A' and resid 1513 through 1526 Processing helix chain 'A' and resid 1544 through 1555 Processing helix chain 'A' and resid 1560 through 1569 removed outlier: 3.652A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1611 Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1634 through 1641 removed outlier: 3.880A pdb=" N TRP A1641 " --> pdb=" O PHE A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 Processing helix chain 'A' and resid 1662 through 1672 Processing helix chain 'A' and resid 1674 through 1679 removed outlier: 3.586A pdb=" N THR A1677 " --> pdb=" O ARG A1674 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A1678 " --> pdb=" O LEU A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1697 Processing helix chain 'A' and resid 1706 through 1712 Processing helix chain 'A' and resid 1795 through 1814 removed outlier: 3.770A pdb=" N ILE A1806 " --> pdb=" O SER A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1828 Processing helix chain 'A' and resid 1829 through 1842 removed outlier: 3.768A pdb=" N LEU A1833 " --> pdb=" O VAL A1829 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A1840 " --> pdb=" O ILE A1836 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1863 Processing helix chain 'A' and resid 1883 through 1898 Processing helix chain 'A' and resid 1901 through 1914 removed outlier: 3.893A pdb=" N SER A1914 " --> pdb=" O ILE A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1930 through 1933 removed outlier: 3.960A pdb=" N SER A1933 " --> pdb=" O PRO A1930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1930 through 1933' Processing helix chain 'A' and resid 1934 through 1939 removed outlier: 3.854A pdb=" N PHE A1938 " --> pdb=" O ASN A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1964 removed outlier: 3.892A pdb=" N ARG A1947 " --> pdb=" O ASP A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1980 removed outlier: 4.105A pdb=" N TRP A1976 " --> pdb=" O GLN A1972 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1999 removed outlier: 3.723A pdb=" N VAL A1989 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2020 removed outlier: 3.548A pdb=" N GLU A2008 " --> pdb=" O SER A2004 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A2020 " --> pdb=" O ALA A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2039 removed outlier: 3.590A pdb=" N VAL A2025 " --> pdb=" O ASN A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2043 Processing helix chain 'A' and resid 2053 through 2067 removed outlier: 3.618A pdb=" N ARG A2062 " --> pdb=" O ALA A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2088 Proline residue: A2080 - end of helix Processing helix chain 'A' and resid 2094 through 2115 removed outlier: 3.543A pdb=" N LEU A2112 " --> pdb=" O ILE A2108 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS A2113 " --> pdb=" O ILE A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2136 removed outlier: 3.965A pdb=" N GLN A2126 " --> pdb=" O GLU A2122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A2127 " --> pdb=" O GLU A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2145 Processing helix chain 'A' and resid 2151 through 2159 removed outlier: 3.549A pdb=" N ILE A2155 " --> pdb=" O SER A2151 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A2156 " --> pdb=" O ALA A2152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A2157 " --> pdb=" O ALA A2153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A2159 " --> pdb=" O ILE A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2196 removed outlier: 4.145A pdb=" N VAL A2184 " --> pdb=" O SER A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2217 removed outlier: 3.692A pdb=" N GLU A2210 " --> pdb=" O ASP A2206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A2211 " --> pdb=" O GLN A2207 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A2212 " --> pdb=" O TRP A2208 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A2214 " --> pdb=" O GLU A2210 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A2215 " --> pdb=" O LEU A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2235 removed outlier: 3.760A pdb=" N ARG A2226 " --> pdb=" O SER A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2239 through 2260 removed outlier: 3.936A pdb=" N ILE A2243 " --> pdb=" O SER A2239 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A2259 " --> pdb=" O GLU A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2281 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: 4.749A pdb=" N PHE A2295 " --> pdb=" O HIS A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 removed outlier: 3.645A pdb=" N THR A2314 " --> pdb=" O TYR A2310 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A2315 " --> pdb=" O SER A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2328 through 2333 removed outlier: 4.148A pdb=" N ASP A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2334 through 2344 Processing helix chain 'A' and resid 2346 through 2358 removed outlier: 4.229A pdb=" N CYS A2350 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A2352 " --> pdb=" O TRP A2348 " (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: 3.853A pdb=" N VAL A2385 " --> pdb=" O SER A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2421 Processing helix chain 'A' and resid 2591 through 2609 removed outlier: 3.692A pdb=" N GLN A2595 " --> pdb=" O ASP A2591 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A2605 " --> pdb=" O VAL A2601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A2606 " --> pdb=" O LEU A2602 " (cutoff:3.500A) Processing helix chain 'A' and resid 2611 through 2629 removed outlier: 3.580A 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: 3.803A pdb=" N LEU A2640 " --> pdb=" O VAL A2636 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A2642 " --> pdb=" O ASN A2638 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A2643 " --> pdb=" O LEU A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2653 through 2670 Proline residue: A2659 - end of helix Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.611A pdb=" N GLN A2676 " --> pdb=" O SER A2673 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A2677 " --> pdb=" O PRO A2674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2673 through 2677' Processing helix chain 'A' and resid 2678 through 2679 No H-bonds generated for 'chain 'A' and resid 2678 through 2679' Processing helix chain 'A' and resid 2680 through 2685 removed outlier: 4.111A pdb=" N PHE A2685 " --> pdb=" O TYR A2681 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2722 Processing helix chain 'B' and resid 6 through 24 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.573A pdb=" N GLU B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 68 Processing helix chain 'B' and resid 72 through 97 Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.592A pdb=" N VAL B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 130 through 149 removed outlier: 4.031A pdb=" N LEU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 removed outlier: 3.730A pdb=" N LEU B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.931A pdb=" N GLU B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 201 Processing helix chain 'B' and resid 205 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.633A pdb=" N TYR B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 257 removed outlier: 3.661A pdb=" N ALA B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 277 Proline residue: B 268 - end of helix removed outlier: 3.693A pdb=" N CYS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 removed outlier: 4.109A pdb=" N ASP B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 309 removed outlier: 4.023A pdb=" N LYS B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 331 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 338 through 350 removed outlier: 4.113A pdb=" N VAL B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 391 through 399 removed outlier: 4.147A pdb=" N CYS B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.679A pdb=" N HIS B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.592A pdb=" N CYS B 434 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 487 through 503 removed outlier: 4.079A pdb=" N TYR B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.511A pdb=" N ALA B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 566 through 588 Processing helix chain 'B' and resid 592 through 615 Processing helix chain 'B' and resid 677 through 696 Processing helix chain 'B' and resid 699 through 721 removed outlier: 3.809A pdb=" N ARG B 711 " --> pdb=" O MET B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 732 removed outlier: 3.663A pdb=" N LEU B 731 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 732 " --> pdb=" O HIS B 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 728 through 732' Processing helix chain 'B' and resid 734 through 745 Processing helix chain 'B' and resid 751 through 765 Processing helix chain 'B' and resid 770 through 793 Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 890 through 904 Processing helix chain 'B' and resid 907 through 923 removed outlier: 3.945A pdb=" N GLN B 912 " --> pdb=" O LYS B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 945 removed outlier: 3.745A pdb=" N LEU B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 973 Processing helix chain 'B' and resid 979 through 986 removed outlier: 4.196A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1003 removed outlier: 3.756A pdb=" N MET B 992 " --> pdb=" O ILE B 988 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B1003 " --> pdb=" O VAL B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1025 Processing helix chain 'B' and resid 1034 through 1048 Processing helix chain 'B' and resid 1062 through 1080 removed outlier: 3.769A pdb=" N SER B1078 " --> pdb=" O GLU B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1119 Processing helix chain 'B' and resid 1135 through 1156 removed outlier: 3.526A pdb=" N LEU B1147 " --> pdb=" O HIS B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1165 removed outlier: 3.880A pdb=" N ILE B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1170 removed outlier: 3.695A pdb=" N TYR B1169 " --> pdb=" O GLY B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1189 Processing helix chain 'B' and resid 1221 through 1229 removed outlier: 4.389A pdb=" N ASN B1229 " --> pdb=" O MET B1225 " (cutoff:3.500A) 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 1247 removed outlier: 3.784A pdb=" N ARG B1241 " --> pdb=" O ASP B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1252 through 1267 removed outlier: 3.582A pdb=" N LEU B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1310 removed outlier: 6.257A pdb=" N THR B1295 " --> pdb=" O VAL B1291 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR B1296 " --> pdb=" O TYR B1292 " (cutoff:3.500A) Proline residue: B1303 - end of helix removed outlier: 3.520A pdb=" N ILE B1307 " --> pdb=" O PRO B1303 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1353 Processing helix chain 'B' and resid 1354 through 1357 Processing helix chain 'B' and resid 1358 through 1376 removed outlier: 3.574A pdb=" N GLN B1374 " --> pdb=" O GLN B1370 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG B1375 " --> pdb=" O VAL B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 3.618A pdb=" N VAL B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B1391 " --> pdb=" O ALA B1387 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1392 " --> pdb=" O MET B1388 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1399 removed outlier: 3.710A pdb=" N ALA B1396 " --> pdb=" O PHE B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1431 removed outlier: 3.540A pdb=" N LEU B1420 " --> pdb=" O ARG B1416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B1423 " --> pdb=" O LYS B1419 " (cutoff:3.500A) Processing helix chain 'B' and resid 1440 through 1442 No H-bonds generated for 'chain 'B' and resid 1440 through 1442' Processing helix chain 'B' and resid 1443 through 1448 Processing helix chain 'B' and resid 1450 through 1462 removed outlier: 3.695A pdb=" N ALA B1454 " --> pdb=" O ASN B1450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1461 " --> pdb=" O PHE B1457 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B1462 " --> pdb=" O PHE B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1492 Processing helix chain 'B' and resid 1514 through 1519 Processing helix chain 'B' and resid 1519 through 1525 Processing helix chain 'B' and resid 1567 through 1570 Processing helix chain 'B' and resid 1590 through 1592 No H-bonds generated for 'chain 'B' and resid 1590 through 1592' Processing helix chain 'B' and resid 1595 through 1611 removed outlier: 3.863A pdb=" N LYS B1611 " --> pdb=" O LEU B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1628 through 1632 removed outlier: 3.563A pdb=" N ARG B1632 " --> pdb=" O PRO B1629 " (cutoff:3.500A) Processing helix chain 'B' and resid 1634 through 1641 removed outlier: 3.548A pdb=" N LYS B1640 " --> pdb=" O ASP B1636 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP B1641 " --> pdb=" O PHE B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 Processing helix chain 'B' and resid 1662 through 1672 Processing helix chain 'B' and resid 1674 through 1678 removed outlier: 3.713A pdb=" N THR B1677 " --> pdb=" O ARG B1674 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY B1678 " --> pdb=" O LEU B1675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1674 through 1678' Processing helix chain 'B' and resid 1692 through 1697 removed outlier: 3.705A pdb=" N HIS B1697 " --> pdb=" O LEU B1694 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1712 Processing helix chain 'B' and resid 1795 through 1812 removed outlier: 3.708A pdb=" N LEU B1812 " --> pdb=" O THR B1808 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1842 removed outlier: 4.263A pdb=" N GLY B1842 " --> pdb=" O LEU B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1864 removed outlier: 3.586A pdb=" N ARG B1849 " --> pdb=" O ASP B1845 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B1854 " --> pdb=" O SER B1850 " (cutoff:3.500A) Processing helix chain 'B' and resid 1883 through 1898 Processing helix chain 'B' and resid 1901 through 1914 removed outlier: 4.023A pdb=" N GLU B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B1914 " --> pdb=" O ILE B1910 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1929 removed outlier: 3.770A pdb=" N LEU B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1930 through 1933 removed outlier: 3.779A pdb=" N SER B1933 " --> pdb=" O PRO B1930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1930 through 1933' Processing helix chain 'B' and resid 1934 through 1939 removed outlier: 3.580A pdb=" N PHE B1938 " --> pdb=" O ASN B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1944 through 1964 Processing helix chain 'B' and resid 1967 through 1975 Processing helix chain 'B' and resid 1975 through 1980 Processing helix chain 'B' and resid 1985 through 1999 removed outlier: 3.781A pdb=" N SER B1992 " --> pdb=" O VAL B1988 " (cutoff:3.500A) Processing helix chain 'B' and resid 2004 through 2021 removed outlier: 4.020A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2039 Processing helix chain 'B' and resid 2040 through 2042 No H-bonds generated for 'chain 'B' and resid 2040 through 2042' Processing helix chain 'B' and resid 2053 through 2067 Processing helix chain 'B' and resid 2078 through 2089 removed outlier: 3.631A pdb=" N LEU B2082 " --> pdb=" O HIS B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2114 Processing helix chain 'B' and resid 2121 through 2136 Processing helix chain 'B' and resid 2137 through 2144 Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.603A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B2157 " --> pdb=" O ALA B2153 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2199 removed outlier: 3.767A pdb=" N LEU B2181 " --> pdb=" O ALA B2177 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP B2198 " --> pdb=" O ALA B2194 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B2199 " --> pdb=" O CYS B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 removed outlier: 3.811A 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 Processing helix chain 'B' and resid 2263 through 2281 Processing helix chain 'B' and resid 2289 through 2303 removed outlier: 4.760A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2334 through 2343 removed outlier: 3.743A pdb=" N VAL B2338 " --> pdb=" O SER B2334 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B2339 " --> pdb=" O PRO B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.800A pdb=" N CYS B2350 " --> pdb=" O LEU B2346 " (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: 3.741A pdb=" N VAL B2385 " --> pdb=" O SER B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2414 through 2423 removed outlier: 4.182A pdb=" N THR B2423 " --> pdb=" O ALA B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2609 removed outlier: 3.505A pdb=" N LEU B2602 " --> pdb=" O LEU B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2611 through 2629 removed outlier: 3.872A pdb=" N GLU B2624 " --> pdb=" O GLU B2620 " (cutoff:3.500A) Processing helix chain 'B' and resid 2632 through 2639 removed outlier: 4.781A pdb=" N ASN B2638 " --> pdb=" O VAL B2635 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B2639 " --> pdb=" O VAL B2636 " (cutoff:3.500A) Processing helix chain 'B' and resid 2640 through 2651 removed outlier: 3.513A pdb=" N ILE B2644 " --> pdb=" O LEU B2640 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B2645 " --> pdb=" O ASP B2641 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2670 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2673 through 2677 removed outlier: 4.100A pdb=" N GLN B2676 " --> pdb=" O SER B2673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B2677 " --> pdb=" O PRO B2674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2673 through 2677' Processing helix chain 'B' and resid 2680 through 2684 Processing helix chain 'B' and resid 2706 through 2722 Processing sheet with id=AA1, first strand: chain 'A' and resid 945 through 947 removed outlier: 3.581A pdb=" N SER A 947 " --> pdb=" O GLN A 950 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1573 through 1577 removed outlier: 3.884A pdb=" N ILE A1584 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL A1621 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A1585 " --> pdb=" O VAL A1621 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP A1623 " --> pdb=" O PHE A1585 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A1587 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR A1618 " --> pdb=" O ALA A1655 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N TYR A1657 " --> pdb=" O TYR A1618 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A1620 " --> pdb=" O TYR A1657 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR A1659 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A1622 " --> pdb=" O TYR A1659 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A1686 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL A1656 " --> pdb=" O VAL A1686 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A1688 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A1658 " --> pdb=" O ILE A1688 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1759 through 1763 removed outlier: 6.275A pdb=" N THR A1730 " --> pdb=" O LEU A1723 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1723 " --> pdb=" O THR A1730 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A1732 " --> pdb=" O ASN A1721 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN A1721 " --> pdb=" O VAL A1732 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A1790 " --> pdb=" O LEU A1725 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1749 through 1751 Processing sheet with id=AA5, first strand: chain 'B' and resid 1572 through 1577 removed outlier: 4.188A pdb=" N ILE B1584 " --> pdb=" O ALA B1575 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B1621 " --> pdb=" O PRO B1583 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B1585 " --> pdb=" O VAL B1621 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP B1623 " --> pdb=" O PHE B1585 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B1587 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B1618 " --> pdb=" O VAL B1653 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B1655 " --> pdb=" O TYR B1618 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B1686 " --> pdb=" O SER B1654 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B1656 " --> pdb=" O VAL B1686 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B1688 " --> pdb=" O VAL B1656 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B1658 " --> pdb=" O ILE B1688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1759 through 1763 removed outlier: 6.234A pdb=" N ILE B1734 " --> pdb=" O HIS B1720 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N HIS B1720 " --> pdb=" O ILE B1734 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1736 " --> pdb=" O VAL B1718 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B1718 " --> pdb=" O VAL B1736 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B1790 " --> pdb=" O LEU B1725 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR B1787 " --> pdb=" O ILE B1782 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE B1782 " --> pdb=" O THR B1787 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLN B1777 " --> pdb=" O LEU B1772 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B1772 " --> pdb=" O GLN B1777 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR B1779 " --> pdb=" O ILE B1770 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE B1770 " --> pdb=" O THR B1779 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1781 " --> pdb=" O GLU B1768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1749 through 1751 2253 hydrogen bonds defined for protein. 6624 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: 9.87 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 11649 1.35 - 1.50: 9703 1.50 - 1.65: 15276 1.65 - 1.79: 162 1.79 - 1.94: 198 Bond restraints: 36988 Sorted by residual: bond pdb=" PG GSP A2901 " pdb=" S1G GSP A2901 " ideal model delta sigma weight residual 1.700 1.943 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" CA SER A1540 " pdb=" CB SER A1540 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.54e-02 4.22e+03 1.45e+01 bond pdb=" C ARG B1441 " pdb=" N PRO B1442 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.19e-02 7.06e+03 1.25e+01 bond pdb=" CA SER A1545 " pdb=" CB SER A1545 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.56e-02 4.11e+03 1.22e+01 bond pdb=" C PRO A1527 " pdb=" O PRO A1527 " ideal model delta sigma weight residual 1.240 1.205 0.036 1.12e-02 7.97e+03 1.03e+01 ... (remaining 36983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 49073 3.02 - 6.05: 887 6.05 - 9.07: 151 9.07 - 12.09: 30 12.09 - 15.11: 6 Bond angle restraints: 50147 Sorted by residual: angle pdb=" N PRO A1527 " pdb=" CA PRO A1527 " pdb=" C PRO A1527 " ideal model delta sigma weight residual 110.70 98.15 12.55 1.22e+00 6.72e-01 1.06e+02 angle pdb=" N LYS A1517 " pdb=" CA LYS A1517 " pdb=" C LYS A1517 " ideal model delta sigma weight residual 111.28 104.73 6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" C ASN A1542 " pdb=" CA ASN A1542 " pdb=" CB ASN A1542 " ideal model delta sigma weight residual 110.37 120.13 -9.76 1.64e+00 3.72e-01 3.55e+01 angle pdb=" C PRO A1514 " pdb=" CA PRO A1514 " pdb=" CB PRO A1514 " ideal model delta sigma weight residual 113.06 104.03 9.03 1.59e+00 3.96e-01 3.23e+01 angle pdb=" N LYS A1062 " pdb=" CA LYS A1062 " pdb=" C LYS A1062 " ideal model delta sigma weight residual 111.71 105.34 6.37 1.15e+00 7.56e-01 3.07e+01 ... (remaining 50142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 21735 29.97 - 59.94: 608 59.94 - 89.91: 62 89.91 - 119.89: 2 119.89 - 149.86: 1 Dihedral angle restraints: 22408 sinusoidal: 8972 harmonic: 13436 Sorted by residual: dihedral pdb=" CA ASP B2705 " pdb=" C ASP B2705 " pdb=" N TYR B2706 " pdb=" CA TYR B2706 " ideal model delta harmonic sigma weight residual 180.00 -140.45 -39.55 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA ASP B1248 " pdb=" C ASP B1248 " pdb=" N SER B1249 " pdb=" CA SER B1249 " ideal model delta harmonic sigma weight residual 180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" O3B GSP A2901 " pdb=" O3A GSP A2901 " pdb=" PB GSP A2901 " pdb=" PA GSP A2901 " ideal model delta sinusoidal sigma weight residual 93.55 -56.31 149.86 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 22405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5001 0.072 - 0.143: 768 0.143 - 0.215: 72 0.215 - 0.287: 19 0.287 - 0.358: 9 Chirality restraints: 5869 Sorted by residual: chirality pdb=" CB ILE B 237 " pdb=" CA ILE B 237 " pdb=" CG1 ILE B 237 " pdb=" CG2 ILE B 237 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA VAL A1061 " pdb=" N VAL A1061 " pdb=" C VAL A1061 " pdb=" CB VAL A1061 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA TYR A 235 " pdb=" N TYR A 235 " pdb=" C TYR A 235 " pdb=" CB TYR A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 5866 not shown) Planarity restraints: 6299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B2705 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C ASP B2705 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP B2705 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR B2706 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1048 " -0.027 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP B1048 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B1048 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B1048 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1048 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1048 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B1048 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2633 " -0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A2634 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A2634 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A2634 " -0.050 5.00e-02 4.00e+02 ... (remaining 6296 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3435 2.74 - 3.28: 38995 3.28 - 3.82: 62222 3.82 - 4.36: 72499 4.36 - 4.90: 119117 Nonbonded interactions: 296268 Sorted by model distance: nonbonded pdb=" O MET A2010 " pdb=" OG1 THR A2013 " model vdw 2.201 3.040 nonbonded pdb=" O MET A2064 " pdb=" OG SER A2068 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG A 385 " pdb=" O LEU A 423 " model vdw 2.219 3.120 nonbonded pdb=" O LEU A1340 " pdb=" OG1 THR A1343 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 80 " pdb=" OE2 GLU B 133 " model vdw 2.247 3.040 ... (remaining 296263 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 1050 or (resid 1061 through 1062 and (name N or \ name CA or name C or name O or name CB )) or resid 1063 through 1190 or resid 12 \ 20 through 1224 or (resid 1225 and (name N or name CA or name C or name O or nam \ e CB or name CG or name SD )) or resid 1226 through 1228 or (resid 1229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1230 through 1262 or ( \ resid 1263 and (name N or name CA or name C or name O or name CB )) or resid 126 \ 4 through 1273 or (resid 1274 and (name N or name CA or name C or name O or name \ CB )) or resid 1275 through 1373 or (resid 1374 and (name N or name CA or name \ C or name O or name CB )) or resid 1375 through 1464 or resid 1487 or (resid 148 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1489 through \ 1492 or (resid 1493 and (name N or name CA or name C or name O or name CB )) or \ resid 1494 or (resid 1495 through 1496 and (name N or name CA or name C or name \ O or name CB )) or resid 1497 through 1501 or resid 1513 through 1514 or (resid \ 1515 and (name N or name CA or name C or name O or name CB )) or resid 1516 thr \ ough 1520 or (resid 1521 through 1523 and (name N or name CA or name C or name O \ or name CB )) or resid 1524 through 1525 or (resid 1567 and (name N or name CA \ or name C or name O or name CB )) or resid 1568 or (resid 1569 and (name N or na \ me CA or name C or name O or name CB )) or resid 1570 through 1816 or resid 1829 \ through 2723)) selection = (chain 'B' and (resid 5 through 1271 or (resid 1272 and (name N or name CA or na \ me C or name O or name CB )) or resid 1273 through 1332 or (resid 1333 and (name \ N or name CA or name C or name O or name CB )) or resid 1334 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: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.160 Set scattering table: 0.140 Process input model: 34.580 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 0.243 36988 Z= 0.279 Angle : 1.024 15.113 50147 Z= 0.558 Chirality : 0.054 0.358 5869 Planarity : 0.007 0.090 6299 Dihedral : 13.988 149.857 13614 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 0.27 % Allowed : 0.64 % Favored : 99.09 % Cbeta Deviations : 0.05 % 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: -0.62 (0.12), residues: 4493 helix: -0.06 (0.09), residues: 3005 sheet: -0.74 (0.44), residues: 114 loop : -0.89 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 764 TYR 0.029 0.002 TYR A1659 PHE 0.040 0.003 PHE B1993 TRP 0.066 0.003 TRP B1048 HIS 0.008 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00574 (36988) covalent geometry : angle 1.02444 (50147) hydrogen bonds : bond 0.15602 ( 2253) hydrogen bonds : angle 6.28489 ( 6624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 GLU cc_start: 0.8261 (tp30) cc_final: 0.7814 (tp30) REVERT: A 1342 MET cc_start: 0.8758 (tpp) cc_final: 0.8415 (tpp) REVERT: A 1440 MET cc_start: 0.8750 (mmp) cc_final: 0.8308 (mmm) REVERT: A 1518 MET cc_start: 0.9327 (ppp) cc_final: 0.8972 (ppp) REVERT: A 1816 ASP cc_start: 0.8212 (p0) cc_final: 0.7981 (p0) REVERT: A 1968 TYR cc_start: 0.7861 (t80) cc_final: 0.7347 (t80) REVERT: A 1972 GLN cc_start: 0.8275 (mt0) cc_final: 0.7978 (mt0) REVERT: A 2012 ASP cc_start: 0.8510 (m-30) cc_final: 0.8244 (t70) REVERT: A 2192 MET cc_start: 0.8671 (ttt) cc_final: 0.7658 (tpp) REVERT: A 2196 MET cc_start: 0.4581 (mmm) cc_final: 0.3345 (mmm) REVERT: A 2295 PHE cc_start: 0.8806 (t80) cc_final: 0.8565 (t80) REVERT: A 2296 TRP cc_start: 0.7741 (m100) cc_final: 0.6528 (m100) REVERT: A 2310 TYR cc_start: 0.8716 (t80) cc_final: 0.8416 (t80) REVERT: A 2340 MET cc_start: 0.3306 (mmm) cc_final: 0.2925 (mmm) REVERT: B 496 MET cc_start: 0.9586 (mmp) cc_final: 0.9154 (mmm) REVERT: B 840 MET cc_start: 0.7938 (mmt) cc_final: 0.7621 (mmm) REVERT: B 895 MET cc_start: 0.9556 (mmm) cc_final: 0.9290 (mtm) REVERT: B 1005 MET cc_start: 0.9144 (mpp) cc_final: 0.8767 (mpp) REVERT: B 1022 MET cc_start: 0.9718 (ppp) cc_final: 0.9222 (ppp) REVERT: B 1041 MET cc_start: 0.9658 (mmp) cc_final: 0.9132 (mmm) REVERT: B 1180 MET cc_start: 0.9388 (mmm) cc_final: 0.9097 (mmm) REVERT: B 2064 MET cc_start: 0.9168 (mmm) cc_final: 0.8726 (mtp) outliers start: 11 outliers final: 6 residues processed: 261 average time/residue: 0.1975 time to fit residues: 89.7049 Evaluate side-chains 203 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 0.0040 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 697 ASN A 756 GLN A1039 ASN ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2102 HIS ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS B 128 ASN B 148 ASN B 697 ASN B 734 ASN ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 HIS ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2051 HIS B2319 GLN B2352 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.098722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072399 restraints weight = 238122.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073211 restraints weight = 179180.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.073432 restraints weight = 101246.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073565 restraints weight = 109764.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.074008 restraints weight = 88375.754| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36988 Z= 0.132 Angle : 0.641 10.404 50147 Z= 0.328 Chirality : 0.040 0.195 5869 Planarity : 0.004 0.070 6299 Dihedral : 6.215 142.484 4844 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 0.59 % Allowed : 5.88 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.40 (0.12), residues: 4493 helix: 0.78 (0.09), residues: 3077 sheet: -0.90 (0.44), residues: 113 loop : -0.67 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1204 TYR 0.034 0.001 TYR B2706 PHE 0.017 0.001 PHE A1275 TRP 0.023 0.001 TRP B1048 HIS 0.008 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00267 (36988) covalent geometry : angle 0.64091 (50147) hydrogen bonds : bond 0.04628 ( 2253) hydrogen bonds : angle 4.69860 ( 6624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.181 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 349 MET cc_start: 0.8271 (tpp) cc_final: 0.7207 (tpp) REVERT: A 775 GLU cc_start: 0.8355 (tp30) cc_final: 0.7890 (tp30) REVERT: A 1022 MET cc_start: 0.8894 (tmm) cc_final: 0.8565 (tmm) REVERT: A 1149 MET cc_start: 0.8850 (mmm) cc_final: 0.8461 (mmm) REVERT: A 1180 MET cc_start: 0.9009 (mmm) cc_final: 0.8564 (tmm) REVERT: A 1342 MET cc_start: 0.8941 (tpp) cc_final: 0.8574 (tpp) REVERT: A 1397 ILE cc_start: 0.9406 (mm) cc_final: 0.9095 (tt) REVERT: A 1440 MET cc_start: 0.8836 (mmp) cc_final: 0.8314 (mmp) REVERT: A 1518 MET cc_start: 0.9264 (ppp) cc_final: 0.8869 (ppp) REVERT: A 1816 ASP cc_start: 0.8657 (p0) cc_final: 0.8404 (p0) REVERT: A 1926 GLU cc_start: 0.8199 (tp30) cc_final: 0.7760 (tp30) REVERT: A 1968 TYR cc_start: 0.8198 (t80) cc_final: 0.7499 (t80) REVERT: A 1972 GLN cc_start: 0.8465 (mt0) cc_final: 0.7940 (mt0) REVERT: A 2012 ASP cc_start: 0.8491 (m-30) cc_final: 0.8243 (t70) REVERT: A 2066 MET cc_start: 0.7520 (mmt) cc_final: 0.7239 (mmt) REVERT: A 2196 MET cc_start: 0.4197 (mmm) cc_final: 0.3881 (mmm) REVERT: A 2295 PHE cc_start: 0.8753 (t80) cc_final: 0.8481 (t80) REVERT: A 2296 TRP cc_start: 0.7433 (m100) cc_final: 0.6281 (m100) REVERT: A 2310 TYR cc_start: 0.8591 (t80) cc_final: 0.8153 (t80) REVERT: A 2340 MET cc_start: 0.2792 (mmm) cc_final: 0.2468 (mmm) REVERT: B 108 MET cc_start: 0.9680 (mmm) cc_final: 0.9428 (mpp) REVERT: B 119 HIS cc_start: 0.8168 (t-90) cc_final: 0.7804 (t70) REVERT: B 374 ASP cc_start: 0.9504 (t0) cc_final: 0.9275 (p0) REVERT: B 376 MET cc_start: 0.9652 (mpp) cc_final: 0.9146 (mpp) REVERT: B 496 MET cc_start: 0.9574 (mmp) cc_final: 0.9308 (mmm) REVERT: B 707 MET cc_start: 0.9225 (ttt) cc_final: 0.8901 (mmm) REVERT: B 739 MET cc_start: 0.9482 (tpp) cc_final: 0.9249 (mmm) REVERT: B 968 MET cc_start: 0.9877 (mmt) cc_final: 0.9585 (mmm) REVERT: B 1005 MET cc_start: 0.9011 (mpp) cc_final: 0.8643 (mpp) REVERT: B 1022 MET cc_start: 0.9658 (ppp) cc_final: 0.9238 (ppp) REVERT: B 1023 MET cc_start: 0.8949 (mmm) cc_final: 0.8513 (mmm) REVERT: B 1041 MET cc_start: 0.9612 (mmp) cc_final: 0.8957 (mmm) REVERT: B 1180 MET cc_start: 0.9456 (mmm) cc_final: 0.9153 (mmm) REVERT: B 2064 MET cc_start: 0.8965 (mmm) cc_final: 0.8541 (mtt) REVERT: B 2353 MET cc_start: 0.9355 (mtm) cc_final: 0.8965 (mtp) outliers start: 24 outliers final: 10 residues processed: 255 average time/residue: 0.1953 time to fit residues: 86.6460 Evaluate side-chains 214 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 230 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 182 optimal weight: 0.1980 chunk 217 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 353 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 352 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 HIS ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2319 GLN ** B2364 ASN ** 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 = 0.4192 r_free = 0.4192 target = 0.097796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.070092 restraints weight = 216719.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067713 restraints weight = 140008.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.068363 restraints weight = 103055.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068094 restraints weight = 86289.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.068001 restraints weight = 82398.701| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36988 Z= 0.162 Angle : 0.619 9.466 50147 Z= 0.317 Chirality : 0.040 0.212 5869 Planarity : 0.004 0.069 6299 Dihedral : 5.771 139.650 4840 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 0.96 % Allowed : 8.70 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4493 helix: 1.15 (0.09), residues: 3100 sheet: -0.98 (0.44), residues: 120 loop : -0.58 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1204 TYR 0.031 0.001 TYR B2706 PHE 0.018 0.001 PHE B1905 TRP 0.032 0.001 TRP A1314 HIS 0.006 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00346 (36988) covalent geometry : angle 0.61880 (50147) hydrogen bonds : bond 0.04219 ( 2253) hydrogen bonds : angle 4.54627 ( 6624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 1.338 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 236 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: A 349 MET cc_start: 0.8236 (tpp) cc_final: 0.7239 (tpp) REVERT: A 707 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: A 760 MET cc_start: 0.9108 (mmt) cc_final: 0.8352 (mmt) REVERT: A 775 GLU cc_start: 0.8501 (tp30) cc_final: 0.8022 (tp30) REVERT: A 1149 MET cc_start: 0.8936 (mmm) cc_final: 0.8432 (mmm) REVERT: A 1180 MET cc_start: 0.9267 (mmm) cc_final: 0.8603 (tmm) REVERT: A 1342 MET cc_start: 0.9009 (tpp) cc_final: 0.8654 (tpp) REVERT: A 1440 MET cc_start: 0.8909 (mmp) cc_final: 0.8357 (mmp) REVERT: A 1518 MET cc_start: 0.9195 (ppp) cc_final: 0.8770 (ppp) REVERT: A 1791 PHE cc_start: 0.7533 (m-80) cc_final: 0.7182 (m-80) REVERT: A 1816 ASP cc_start: 0.8588 (p0) cc_final: 0.8336 (p0) REVERT: A 1926 GLU cc_start: 0.8495 (tp30) cc_final: 0.8067 (tp30) REVERT: A 2104 LEU cc_start: 0.9418 (tt) cc_final: 0.9185 (pp) REVERT: A 2196 MET cc_start: 0.4624 (mmm) cc_final: 0.4315 (mmm) REVERT: A 2295 PHE cc_start: 0.9026 (t80) cc_final: 0.8784 (t80) REVERT: A 2296 TRP cc_start: 0.7875 (m100) cc_final: 0.6620 (m100) REVERT: A 2310 TYR cc_start: 0.8944 (t80) cc_final: 0.8557 (t80) REVERT: A 2340 MET cc_start: 0.3882 (mmm) cc_final: 0.3459 (mmm) REVERT: B 119 HIS cc_start: 0.8161 (t-90) cc_final: 0.7862 (t-170) REVERT: B 376 MET cc_start: 0.9533 (mpp) cc_final: 0.9193 (mpp) REVERT: B 496 MET cc_start: 0.9537 (mmp) cc_final: 0.9264 (mmm) REVERT: B 707 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8812 (mmm) REVERT: B 739 MET cc_start: 0.9500 (tpp) cc_final: 0.9207 (mmm) REVERT: B 760 MET cc_start: 0.6500 (mmt) cc_final: 0.6218 (mmt) REVERT: B 968 MET cc_start: 0.9875 (mmt) cc_final: 0.9504 (mmm) REVERT: B 1005 MET cc_start: 0.8991 (mpp) cc_final: 0.8614 (mpp) REVERT: B 1022 MET cc_start: 0.9653 (ppp) cc_final: 0.9169 (ppp) REVERT: B 1023 MET cc_start: 0.9118 (mmm) cc_final: 0.8625 (mmm) REVERT: B 1041 MET cc_start: 0.9614 (mmp) cc_final: 0.9008 (mmm) REVERT: B 1180 MET cc_start: 0.9385 (mmm) cc_final: 0.9126 (mmm) REVERT: B 1927 TYR cc_start: 0.8837 (p90) cc_final: 0.8536 (p90) REVERT: B 2064 MET cc_start: 0.9104 (mmm) cc_final: 0.8867 (mtt) outliers start: 39 outliers final: 15 residues processed: 248 average time/residue: 0.1923 time to fit residues: 83.4574 Evaluate side-chains 224 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1780 LEU Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 253 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 380 optimal weight: 0.3980 chunk 357 optimal weight: 40.0000 chunk 267 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 147 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 GLN ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2688 ASN B 310 HIS ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.097529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.073798 restraints weight = 239385.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071387 restraints weight = 149423.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.071586 restraints weight = 131775.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.071481 restraints weight = 125721.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071870 restraints weight = 109292.957| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36988 Z= 0.137 Angle : 0.599 9.406 50147 Z= 0.303 Chirality : 0.039 0.198 5869 Planarity : 0.004 0.069 6299 Dihedral : 5.494 130.367 4840 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.13 % Allowed : 10.38 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.15 (0.13), residues: 4493 helix: 1.39 (0.09), residues: 3086 sheet: -0.93 (0.42), residues: 128 loop : -0.50 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1204 TYR 0.028 0.001 TYR B2706 PHE 0.035 0.001 PHE B 71 TRP 0.033 0.001 TRP A1314 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00293 (36988) covalent geometry : angle 0.59871 (50147) hydrogen bonds : bond 0.03907 ( 2253) hydrogen bonds : angle 4.39989 ( 6624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: A 349 MET cc_start: 0.8352 (tpp) cc_final: 0.7358 (tpp) REVERT: A 442 MET cc_start: 0.8704 (ttp) cc_final: 0.8290 (ttp) REVERT: A 760 MET cc_start: 0.9111 (mmt) cc_final: 0.8569 (mmt) REVERT: A 775 GLU cc_start: 0.8688 (tp30) cc_final: 0.8190 (tp30) REVERT: A 968 MET cc_start: 0.8838 (mpp) cc_final: 0.8435 (mpp) REVERT: A 1149 MET cc_start: 0.8900 (mmm) cc_final: 0.8516 (mmm) REVERT: A 1180 MET cc_start: 0.8988 (mmm) cc_final: 0.8505 (mmm) REVERT: A 1215 MET cc_start: 0.9065 (tpt) cc_final: 0.8845 (tpp) REVERT: A 1342 MET cc_start: 0.9077 (tpp) cc_final: 0.8708 (tpp) REVERT: A 1440 MET cc_start: 0.8809 (mmp) cc_final: 0.8364 (mmp) REVERT: A 1518 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8797 (ppp) REVERT: A 1791 PHE cc_start: 0.7509 (m-80) cc_final: 0.7060 (m-80) REVERT: A 1816 ASP cc_start: 0.8824 (p0) cc_final: 0.8595 (p0) REVERT: A 1926 GLU cc_start: 0.8334 (tp30) cc_final: 0.7893 (tp30) REVERT: A 1968 TYR cc_start: 0.8643 (t80) cc_final: 0.8251 (t80) REVERT: A 2012 ASP cc_start: 0.8520 (m-30) cc_final: 0.8263 (m-30) REVERT: A 2196 MET cc_start: 0.4735 (mmm) cc_final: 0.4521 (mmm) REVERT: A 2295 PHE cc_start: 0.8816 (t80) cc_final: 0.8479 (t80) REVERT: A 2296 TRP cc_start: 0.7663 (m100) cc_final: 0.6543 (m100) REVERT: A 2309 LEU cc_start: 0.8643 (mt) cc_final: 0.8332 (mt) REVERT: A 2310 TYR cc_start: 0.8721 (t80) cc_final: 0.8475 (t80) REVERT: A 2340 MET cc_start: 0.3367 (mmm) cc_final: 0.2988 (mmm) REVERT: B 108 MET cc_start: 0.9710 (mmm) cc_final: 0.9424 (ppp) REVERT: B 119 HIS cc_start: 0.8121 (t-90) cc_final: 0.7775 (t-170) REVERT: B 374 ASP cc_start: 0.9534 (p0) cc_final: 0.9258 (t0) REVERT: B 376 MET cc_start: 0.9591 (mpp) cc_final: 0.9236 (mpp) REVERT: B 496 MET cc_start: 0.9646 (mmp) cc_final: 0.9333 (mmm) REVERT: B 707 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8748 (mmm) REVERT: B 715 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9287 (mp0) REVERT: B 739 MET cc_start: 0.9472 (tpp) cc_final: 0.9183 (mmm) REVERT: B 760 MET cc_start: 0.6669 (mmt) cc_final: 0.6371 (mmt) REVERT: B 968 MET cc_start: 0.9861 (mmt) cc_final: 0.9501 (mmm) REVERT: B 1005 MET cc_start: 0.8963 (mpp) cc_final: 0.8613 (mpp) REVERT: B 1022 MET cc_start: 0.9693 (ppp) cc_final: 0.9238 (ppp) REVERT: B 1023 MET cc_start: 0.9104 (mmm) cc_final: 0.8648 (mmm) REVERT: B 1041 MET cc_start: 0.9652 (mmp) cc_final: 0.9022 (mmm) REVERT: B 1102 LEU cc_start: 0.9189 (mt) cc_final: 0.8820 (tp) REVERT: B 1180 MET cc_start: 0.9439 (mmm) cc_final: 0.9171 (mmm) REVERT: B 1260 MET cc_start: -0.2862 (pmm) cc_final: -0.4490 (mtm) REVERT: B 1927 TYR cc_start: 0.8785 (p90) cc_final: 0.8438 (p90) REVERT: B 2064 MET cc_start: 0.9014 (mmm) cc_final: 0.8813 (mtt) outliers start: 46 outliers final: 23 residues processed: 258 average time/residue: 0.1988 time to fit residues: 89.5692 Evaluate side-chains 238 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 431 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 233 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A2021 ASN A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1430 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.097892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072582 restraints weight = 238467.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073731 restraints weight = 152095.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072953 restraints weight = 98983.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073186 restraints weight = 104748.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.073409 restraints weight = 80645.935| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36988 Z= 0.115 Angle : 0.593 13.564 50147 Z= 0.294 Chirality : 0.039 0.342 5869 Planarity : 0.004 0.068 6299 Dihedral : 5.235 116.877 4839 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 11.41 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.38 (0.13), residues: 4493 helix: 1.58 (0.09), residues: 3086 sheet: -0.86 (0.43), residues: 128 loop : -0.44 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1204 TYR 0.027 0.001 TYR B2706 PHE 0.018 0.001 PHE A1389 TRP 0.033 0.001 TRP A1314 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00243 (36988) covalent geometry : angle 0.59292 (50147) hydrogen bonds : bond 0.03675 ( 2253) hydrogen bonds : angle 4.25075 ( 6624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9275 (ppp) cc_final: 0.9041 (ppp) REVERT: A 236 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8314 (mp10) REVERT: A 349 MET cc_start: 0.8234 (tpp) cc_final: 0.7251 (tpp) REVERT: A 694 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8918 (m-10) REVERT: A 775 GLU cc_start: 0.8357 (tp30) cc_final: 0.7894 (tp30) REVERT: A 968 MET cc_start: 0.8749 (mpp) cc_final: 0.8392 (mpp) REVERT: A 1149 MET cc_start: 0.8875 (mmm) cc_final: 0.8520 (mmm) REVERT: A 1180 MET cc_start: 0.9078 (mmm) cc_final: 0.8301 (mmm) REVERT: A 1215 MET cc_start: 0.8938 (tpt) cc_final: 0.8727 (tpp) REVERT: A 1342 MET cc_start: 0.9054 (tpp) cc_final: 0.8678 (tpp) REVERT: A 1440 MET cc_start: 0.8825 (mmp) cc_final: 0.8324 (mmp) REVERT: A 1816 ASP cc_start: 0.8551 (p0) cc_final: 0.8320 (p0) REVERT: A 1926 GLU cc_start: 0.8304 (tp30) cc_final: 0.7911 (tp30) REVERT: A 1965 LYS cc_start: 0.8562 (tppt) cc_final: 0.8346 (tppt) REVERT: A 1968 TYR cc_start: 0.8436 (t80) cc_final: 0.8021 (t80) REVERT: A 2012 ASP cc_start: 0.8345 (m-30) cc_final: 0.8067 (m-30) REVERT: A 2196 MET cc_start: 0.4972 (mmm) cc_final: 0.4725 (mmm) REVERT: A 2295 PHE cc_start: 0.8510 (t80) cc_final: 0.8217 (t80) REVERT: A 2296 TRP cc_start: 0.7436 (m100) cc_final: 0.6324 (m100) REVERT: A 2340 MET cc_start: 0.3090 (mmm) cc_final: 0.2746 (mmm) REVERT: B 108 MET cc_start: 0.9661 (mmm) cc_final: 0.9391 (ppp) REVERT: B 374 ASP cc_start: 0.9494 (p0) cc_final: 0.9211 (t0) REVERT: B 376 MET cc_start: 0.9617 (mpp) cc_final: 0.9220 (mpp) REVERT: B 496 MET cc_start: 0.9618 (mmp) cc_final: 0.9300 (mmm) REVERT: B 577 MET cc_start: 0.9651 (tpp) cc_final: 0.9373 (tpt) REVERT: B 707 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8819 (mmm) REVERT: B 715 GLU cc_start: 0.9533 (OUTLIER) cc_final: 0.9304 (mp0) REVERT: B 739 MET cc_start: 0.9450 (tpp) cc_final: 0.9147 (mmm) REVERT: B 760 MET cc_start: 0.6728 (mmt) cc_final: 0.6447 (mmt) REVERT: B 968 MET cc_start: 0.9867 (mmt) cc_final: 0.9464 (mmm) REVERT: B 1005 MET cc_start: 0.8874 (mpp) cc_final: 0.8524 (mpp) REVERT: B 1022 MET cc_start: 0.9654 (ppp) cc_final: 0.9159 (ppp) REVERT: B 1023 MET cc_start: 0.9140 (mmm) cc_final: 0.8679 (mmm) REVERT: B 1035 MET cc_start: 0.8752 (pmm) cc_final: 0.8520 (mmt) REVERT: B 1041 MET cc_start: 0.9620 (mmp) cc_final: 0.8949 (mmm) REVERT: B 1102 LEU cc_start: 0.9186 (mt) cc_final: 0.8824 (tp) REVERT: B 1134 MET cc_start: 0.8671 (tpp) cc_final: 0.7887 (pmm) REVERT: B 1149 MET cc_start: 0.9321 (mmm) cc_final: 0.9113 (mmm) REVERT: B 1180 MET cc_start: 0.9398 (mmm) cc_final: 0.9143 (mmm) REVERT: B 1260 MET cc_start: -0.2402 (OUTLIER) cc_final: -0.4261 (mtm) REVERT: B 1927 TYR cc_start: 0.8768 (p90) cc_final: 0.8496 (p90) REVERT: B 2064 MET cc_start: 0.9052 (mmm) cc_final: 0.8653 (mtt) outliers start: 46 outliers final: 22 residues processed: 266 average time/residue: 0.1911 time to fit residues: 89.4220 Evaluate side-chains 245 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 694 PHE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2036 ILE Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1260 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 178 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 293 optimal weight: 0.5980 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 389 optimal weight: 0.0570 chunk 212 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068377 restraints weight = 241358.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069816 restraints weight = 111503.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070810 restraints weight = 70793.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070815 restraints weight = 51323.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070815 restraints weight = 51150.017| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36988 Z= 0.138 Angle : 0.611 11.913 50147 Z= 0.302 Chirality : 0.040 0.330 5869 Planarity : 0.004 0.067 6299 Dihedral : 5.050 99.307 4838 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.38 % Allowed : 12.20 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.13), residues: 4493 helix: 1.66 (0.09), residues: 3091 sheet: -0.75 (0.44), residues: 128 loop : -0.41 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1204 TYR 0.027 0.001 TYR B2706 PHE 0.016 0.001 PHE A 250 TRP 0.032 0.001 TRP A1314 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00299 (36988) covalent geometry : angle 0.61056 (50147) hydrogen bonds : bond 0.03663 ( 2253) hydrogen bonds : angle 4.24564 ( 6624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9236 (ppp) cc_final: 0.9009 (ppp) REVERT: A 236 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: A 349 MET cc_start: 0.8301 (tpp) cc_final: 0.7305 (tpp) REVERT: A 775 GLU cc_start: 0.8491 (tp30) cc_final: 0.7977 (tp30) REVERT: A 968 MET cc_start: 0.8830 (mpp) cc_final: 0.8398 (mpp) REVERT: A 1050 MET cc_start: 0.8065 (mmm) cc_final: 0.7602 (tpt) REVERT: A 1149 MET cc_start: 0.8938 (mmm) cc_final: 0.8653 (mmm) REVERT: A 1180 MET cc_start: 0.9129 (mmm) cc_final: 0.8851 (mmm) REVERT: A 1215 MET cc_start: 0.8873 (tpt) cc_final: 0.8652 (tpp) REVERT: A 1342 MET cc_start: 0.8907 (tpp) cc_final: 0.8466 (tpp) REVERT: A 1440 MET cc_start: 0.8828 (mmp) cc_final: 0.8245 (mmp) REVERT: A 1791 PHE cc_start: 0.7213 (m-80) cc_final: 0.6840 (m-80) REVERT: A 1816 ASP cc_start: 0.8144 (p0) cc_final: 0.7906 (p0) REVERT: A 1926 GLU cc_start: 0.8317 (tp30) cc_final: 0.7940 (tp30) REVERT: A 1956 LYS cc_start: 0.9525 (mppt) cc_final: 0.9293 (mmmm) REVERT: A 1968 TYR cc_start: 0.8522 (t80) cc_final: 0.8113 (t80) REVERT: A 2010 MET cc_start: 0.8417 (ppp) cc_final: 0.7936 (ppp) REVERT: A 2012 ASP cc_start: 0.8442 (m-30) cc_final: 0.8194 (m-30) REVERT: A 2104 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8909 (pp) REVERT: A 2196 MET cc_start: 0.5089 (mmm) cc_final: 0.4734 (mmm) REVERT: A 2295 PHE cc_start: 0.8645 (t80) cc_final: 0.8330 (t80) REVERT: A 2296 TRP cc_start: 0.7598 (m100) cc_final: 0.6331 (m100) REVERT: A 2309 LEU cc_start: 0.8514 (mt) cc_final: 0.8133 (mt) REVERT: A 2310 TYR cc_start: 0.9037 (t80) cc_final: 0.8662 (t80) REVERT: A 2340 MET cc_start: 0.3453 (mmm) cc_final: 0.3079 (mmm) REVERT: B 143 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8958 (t80) REVERT: B 301 ASP cc_start: 0.9231 (m-30) cc_final: 0.9004 (m-30) REVERT: B 496 MET cc_start: 0.9646 (mmp) cc_final: 0.9310 (mmm) REVERT: B 707 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8793 (mmm) REVERT: B 715 GLU cc_start: 0.9533 (OUTLIER) cc_final: 0.9305 (mp0) REVERT: B 739 MET cc_start: 0.9440 (tpp) cc_final: 0.9116 (mmm) REVERT: B 968 MET cc_start: 0.9874 (mmt) cc_final: 0.9456 (mmm) REVERT: B 1005 MET cc_start: 0.8684 (mpp) cc_final: 0.8352 (mpp) REVERT: B 1035 MET cc_start: 0.8663 (pmm) cc_final: 0.8343 (pmm) REVERT: B 1041 MET cc_start: 0.9614 (mmp) cc_final: 0.8932 (mmm) REVERT: B 1102 LEU cc_start: 0.9200 (mt) cc_final: 0.8840 (tp) REVERT: B 1180 MET cc_start: 0.9323 (mmm) cc_final: 0.9119 (mmm) REVERT: B 1927 TYR cc_start: 0.8890 (p90) cc_final: 0.8624 (p90) REVERT: B 2064 MET cc_start: 0.9055 (mmm) cc_final: 0.8680 (mtt) outliers start: 56 outliers final: 36 residues processed: 264 average time/residue: 0.1974 time to fit residues: 91.3283 Evaluate side-chains 255 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1871 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2036 ILE Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2384 ILE Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 2056 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 162 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 324 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 278 optimal weight: 0.0000 chunk 41 optimal weight: 0.0770 chunk 366 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 400 GLN ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.097730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.072447 restraints weight = 240928.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.072946 restraints weight = 156145.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072534 restraints weight = 109111.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073105 restraints weight = 97446.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.073055 restraints weight = 78739.736| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36988 Z= 0.115 Angle : 0.606 14.998 50147 Z= 0.297 Chirality : 0.039 0.316 5869 Planarity : 0.004 0.066 6299 Dihedral : 4.884 87.647 4838 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 1.48 % Allowed : 13.03 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.13), residues: 4493 helix: 1.74 (0.09), residues: 3093 sheet: -0.60 (0.45), residues: 126 loop : -0.42 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1204 TYR 0.027 0.001 TYR B2706 PHE 0.038 0.001 PHE B 71 TRP 0.035 0.001 TRP A1314 HIS 0.007 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00248 (36988) covalent geometry : angle 0.60648 (50147) hydrogen bonds : bond 0.03524 ( 2253) hydrogen bonds : angle 4.15578 ( 6624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 226 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9295 (ppp) cc_final: 0.9082 (ppp) REVERT: A 236 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: A 349 MET cc_start: 0.8209 (tpp) cc_final: 0.7193 (tpp) REVERT: A 775 GLU cc_start: 0.8339 (tp30) cc_final: 0.7872 (tp30) REVERT: A 968 MET cc_start: 0.8865 (mpp) cc_final: 0.8563 (mpp) REVERT: A 1005 MET cc_start: 0.8113 (tmm) cc_final: 0.7888 (tmm) REVERT: A 1149 MET cc_start: 0.8898 (mmm) cc_final: 0.8649 (mmm) REVERT: A 1180 MET cc_start: 0.9150 (mmm) cc_final: 0.8821 (mmm) REVERT: A 1215 MET cc_start: 0.9012 (tpt) cc_final: 0.8794 (tpp) REVERT: A 1342 MET cc_start: 0.9086 (tpp) cc_final: 0.8716 (tpp) REVERT: A 1440 MET cc_start: 0.8810 (mmp) cc_final: 0.8349 (mmp) REVERT: A 1791 PHE cc_start: 0.7303 (m-80) cc_final: 0.6922 (m-80) REVERT: A 1816 ASP cc_start: 0.8580 (p0) cc_final: 0.8347 (p0) REVERT: A 1926 GLU cc_start: 0.8360 (tp30) cc_final: 0.7946 (tp30) REVERT: A 1956 LYS cc_start: 0.9428 (mppt) cc_final: 0.8862 (mttm) REVERT: A 1968 TYR cc_start: 0.8424 (t80) cc_final: 0.8092 (t80) REVERT: A 2010 MET cc_start: 0.8355 (ppp) cc_final: 0.7972 (ppp) REVERT: A 2012 ASP cc_start: 0.8334 (m-30) cc_final: 0.8054 (m-30) REVERT: A 2196 MET cc_start: 0.5102 (mmm) cc_final: 0.4732 (mmm) REVERT: A 2295 PHE cc_start: 0.8536 (t80) cc_final: 0.8248 (t80) REVERT: A 2296 TRP cc_start: 0.7427 (m100) cc_final: 0.6254 (m100) REVERT: A 2309 LEU cc_start: 0.8403 (mt) cc_final: 0.8027 (mt) REVERT: A 2310 TYR cc_start: 0.8866 (t80) cc_final: 0.8552 (t80) REVERT: A 2340 MET cc_start: 0.3228 (mmm) cc_final: 0.2933 (mmm) REVERT: B 108 MET cc_start: 0.9667 (mmm) cc_final: 0.9382 (ppp) REVERT: B 119 HIS cc_start: 0.8404 (t-90) cc_final: 0.8166 (t-170) REVERT: B 143 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8943 (t80) REVERT: B 496 MET cc_start: 0.9650 (mmp) cc_final: 0.9330 (mmm) REVERT: B 501 HIS cc_start: 0.9143 (t-170) cc_final: 0.8937 (m170) REVERT: B 707 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8764 (mmm) REVERT: B 715 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9296 (mp0) REVERT: B 739 MET cc_start: 0.9471 (tpp) cc_final: 0.9144 (mmm) REVERT: B 968 MET cc_start: 0.9867 (mmt) cc_final: 0.9539 (mmm) REVERT: B 1005 MET cc_start: 0.8902 (mpp) cc_final: 0.8556 (mpp) REVERT: B 1022 MET cc_start: 0.9604 (ppp) cc_final: 0.9030 (ppp) REVERT: B 1023 MET cc_start: 0.9089 (mmm) cc_final: 0.8668 (mmm) REVERT: B 1041 MET cc_start: 0.9665 (mmp) cc_final: 0.9007 (mmm) REVERT: B 1102 LEU cc_start: 0.9215 (mt) cc_final: 0.8856 (tp) REVERT: B 1134 MET cc_start: 0.8646 (tpp) cc_final: 0.7979 (pmm) REVERT: B 1149 MET cc_start: 0.8838 (mmp) cc_final: 0.8551 (mmp) REVERT: B 1180 MET cc_start: 0.9396 (mmm) cc_final: 0.9140 (mmm) REVERT: B 1260 MET cc_start: -0.2723 (pmm) cc_final: -0.4682 (mtt) REVERT: B 1927 TYR cc_start: 0.8779 (p90) cc_final: 0.8564 (p90) REVERT: B 2064 MET cc_start: 0.9013 (mmm) cc_final: 0.8656 (mtt) outliers start: 60 outliers final: 38 residues processed: 270 average time/residue: 0.1959 time to fit residues: 92.7182 Evaluate side-chains 252 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 2056 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 91 optimal weight: 0.9990 chunk 450 optimal weight: 0.9980 chunk 297 optimal weight: 20.0000 chunk 289 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 384 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2051 HIS ** B2364 ASN ** 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 = 0.4193 r_free = 0.4193 target = 0.097651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.068910 restraints weight = 216526.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.067948 restraints weight = 137444.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067850 restraints weight = 95447.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.068113 restraints weight = 75738.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.068074 restraints weight = 64551.314| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36988 Z= 0.132 Angle : 0.620 14.950 50147 Z= 0.304 Chirality : 0.039 0.307 5869 Planarity : 0.004 0.066 6299 Dihedral : 4.768 84.051 4838 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.30 % Allowed : 13.55 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.13), residues: 4493 helix: 1.77 (0.10), residues: 3100 sheet: -0.58 (0.44), residues: 126 loop : -0.40 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1204 TYR 0.027 0.001 TYR B2706 PHE 0.017 0.001 PHE B1110 TRP 0.038 0.001 TRP A1314 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00285 (36988) covalent geometry : angle 0.61958 (50147) hydrogen bonds : bond 0.03527 ( 2253) hydrogen bonds : angle 4.17104 ( 6624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.441 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 108 MET cc_start: 0.9196 (ppp) cc_final: 0.8967 (ppp) REVERT: A 236 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8277 (mp10) REVERT: A 349 MET cc_start: 0.8179 (tpp) cc_final: 0.7188 (tpp) REVERT: A 775 GLU cc_start: 0.8533 (tp30) cc_final: 0.8028 (tp30) REVERT: A 968 MET cc_start: 0.8913 (mpp) cc_final: 0.8580 (mpp) REVERT: A 1149 MET cc_start: 0.8947 (mmm) cc_final: 0.8727 (mmm) REVERT: A 1180 MET cc_start: 0.9140 (mmm) cc_final: 0.8783 (mmm) REVERT: A 1215 MET cc_start: 0.9058 (tpt) cc_final: 0.8816 (tpp) REVERT: A 1342 MET cc_start: 0.9050 (tpp) cc_final: 0.8643 (tpp) REVERT: A 1440 MET cc_start: 0.8829 (mmp) cc_final: 0.8247 (mmp) REVERT: A 1791 PHE cc_start: 0.7331 (m-80) cc_final: 0.7000 (m-80) REVERT: A 1816 ASP cc_start: 0.8491 (p0) cc_final: 0.8250 (p0) REVERT: A 1926 GLU cc_start: 0.8516 (tp30) cc_final: 0.8077 (tp30) REVERT: A 1956 LYS cc_start: 0.9452 (mppt) cc_final: 0.9247 (mmmm) REVERT: A 1968 TYR cc_start: 0.8521 (t80) cc_final: 0.8217 (t80) REVERT: A 2010 MET cc_start: 0.8297 (ppp) cc_final: 0.7929 (ppp) REVERT: A 2012 ASP cc_start: 0.8468 (m-30) cc_final: 0.8202 (m-30) REVERT: A 2196 MET cc_start: 0.5185 (mmm) cc_final: 0.4945 (mmm) REVERT: A 2295 PHE cc_start: 0.8846 (t80) cc_final: 0.8553 (t80) REVERT: A 2296 TRP cc_start: 0.7817 (m100) cc_final: 0.6448 (m100) REVERT: A 2309 LEU cc_start: 0.8530 (mt) cc_final: 0.8214 (mt) REVERT: A 2310 TYR cc_start: 0.9152 (t80) cc_final: 0.8748 (t80) REVERT: A 2340 MET cc_start: 0.3963 (mmm) cc_final: 0.3600 (mmm) REVERT: B 108 MET cc_start: 0.9670 (mmm) cc_final: 0.9393 (ppp) REVERT: B 143 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8909 (t80) REVERT: B 376 MET cc_start: 0.9555 (mpp) cc_final: 0.9271 (mpp) REVERT: B 496 MET cc_start: 0.9675 (mmp) cc_final: 0.9337 (mmm) REVERT: B 501 HIS cc_start: 0.9240 (t-170) cc_final: 0.8930 (m170) REVERT: B 577 MET cc_start: 0.9656 (tpp) cc_final: 0.9429 (tpt) REVERT: B 707 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8693 (mmm) REVERT: B 715 GLU cc_start: 0.9513 (OUTLIER) cc_final: 0.9299 (mp0) REVERT: B 739 MET cc_start: 0.9483 (tpp) cc_final: 0.9161 (mmm) REVERT: B 760 MET cc_start: 0.6473 (mmt) cc_final: 0.5998 (mmt) REVERT: B 968 MET cc_start: 0.9877 (mmt) cc_final: 0.9543 (mmm) REVERT: B 1005 MET cc_start: 0.8813 (mpp) cc_final: 0.8492 (mpp) REVERT: B 1022 MET cc_start: 0.9592 (ppp) cc_final: 0.8883 (ppp) REVERT: B 1023 MET cc_start: 0.9154 (mmm) cc_final: 0.8755 (mmm) REVERT: B 1041 MET cc_start: 0.9663 (mmp) cc_final: 0.9038 (mmm) REVERT: B 1102 LEU cc_start: 0.9136 (mt) cc_final: 0.8771 (tp) REVERT: B 1134 MET cc_start: 0.8640 (tpp) cc_final: 0.7736 (pmm) REVERT: B 1180 MET cc_start: 0.9289 (mmm) cc_final: 0.9064 (mmm) REVERT: B 1260 MET cc_start: -0.2215 (pmm) cc_final: -0.3734 (mtt) REVERT: B 1927 TYR cc_start: 0.8881 (p90) cc_final: 0.8674 (p90) REVERT: B 2064 MET cc_start: 0.9060 (mmm) cc_final: 0.8705 (mtt) outliers start: 53 outliers final: 37 residues processed: 259 average time/residue: 0.1957 time to fit residues: 89.3919 Evaluate side-chains 254 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 2056 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 61 optimal weight: 5.9990 chunk 357 optimal weight: 30.0000 chunk 314 optimal weight: 3.9990 chunk 395 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 442 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 417 optimal weight: 2.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.097477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.068711 restraints weight = 217262.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067871 restraints weight = 138258.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067695 restraints weight = 94211.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.068111 restraints weight = 75902.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.068091 restraints weight = 63743.985| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36988 Z= 0.138 Angle : 0.631 15.926 50147 Z= 0.310 Chirality : 0.039 0.287 5869 Planarity : 0.004 0.066 6299 Dihedral : 4.697 76.756 4838 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 1.20 % Allowed : 13.70 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.13), residues: 4493 helix: 1.79 (0.09), residues: 3096 sheet: -0.55 (0.45), residues: 126 loop : -0.37 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1204 TYR 0.026 0.001 TYR B2706 PHE 0.040 0.001 PHE B 71 TRP 0.041 0.001 TRP A1314 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00298 (36988) covalent geometry : angle 0.63144 (50147) hydrogen bonds : bond 0.03528 ( 2253) hydrogen bonds : angle 4.19705 ( 6624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.235 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 108 MET cc_start: 0.9197 (ppp) cc_final: 0.8903 (ppp) REVERT: A 236 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: A 349 MET cc_start: 0.8158 (tpp) cc_final: 0.7180 (tpp) REVERT: A 775 GLU cc_start: 0.8465 (tp30) cc_final: 0.7969 (tp30) REVERT: A 968 MET cc_start: 0.8917 (mpp) cc_final: 0.8584 (mpp) REVERT: A 1180 MET cc_start: 0.9142 (mmm) cc_final: 0.8774 (mmm) REVERT: A 1215 MET cc_start: 0.9073 (tpt) cc_final: 0.8831 (tpp) REVERT: A 1260 MET cc_start: 0.8953 (mmm) cc_final: 0.8702 (mmm) REVERT: A 1342 MET cc_start: 0.9035 (tpp) cc_final: 0.8642 (tpp) REVERT: A 1421 MET cc_start: 0.9321 (mmm) cc_final: 0.9000 (mmm) REVERT: A 1440 MET cc_start: 0.8837 (mmp) cc_final: 0.8253 (mmp) REVERT: A 1816 ASP cc_start: 0.8460 (p0) cc_final: 0.8215 (p0) REVERT: A 1926 GLU cc_start: 0.8523 (tp30) cc_final: 0.8043 (tp30) REVERT: A 1968 TYR cc_start: 0.8489 (t80) cc_final: 0.8277 (t80) REVERT: A 2010 MET cc_start: 0.8261 (ppp) cc_final: 0.7973 (ppp) REVERT: A 2012 ASP cc_start: 0.8479 (m-30) cc_final: 0.8209 (m-30) REVERT: A 2196 MET cc_start: 0.5283 (mmm) cc_final: 0.5034 (mmm) REVERT: A 2295 PHE cc_start: 0.8833 (t80) cc_final: 0.8554 (t80) REVERT: A 2296 TRP cc_start: 0.7828 (m100) cc_final: 0.6456 (m100) REVERT: A 2309 LEU cc_start: 0.8550 (mt) cc_final: 0.8254 (mt) REVERT: A 2310 TYR cc_start: 0.9124 (t80) cc_final: 0.8712 (t80) REVERT: A 2340 MET cc_start: 0.3986 (mmm) cc_final: 0.3708 (mmm) REVERT: A 2353 MET cc_start: 0.6875 (ttt) cc_final: 0.6516 (mtp) REVERT: B 108 MET cc_start: 0.9657 (mmm) cc_final: 0.9403 (ppp) REVERT: B 143 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8895 (t80) REVERT: B 376 MET cc_start: 0.9559 (mpp) cc_final: 0.9267 (mpp) REVERT: B 496 MET cc_start: 0.9656 (mmp) cc_final: 0.9353 (mmm) REVERT: B 546 MET cc_start: 0.8888 (tpt) cc_final: 0.8524 (tpt) REVERT: B 577 MET cc_start: 0.9644 (tpp) cc_final: 0.9390 (tpt) REVERT: B 707 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: B 715 GLU cc_start: 0.9513 (OUTLIER) cc_final: 0.9295 (mp0) REVERT: B 739 MET cc_start: 0.9471 (tpp) cc_final: 0.9147 (mmm) REVERT: B 760 MET cc_start: 0.6492 (mmt) cc_final: 0.5947 (mmt) REVERT: B 1005 MET cc_start: 0.8830 (mpp) cc_final: 0.8514 (mpp) REVERT: B 1022 MET cc_start: 0.9566 (ppp) cc_final: 0.9100 (ppp) REVERT: B 1023 MET cc_start: 0.9171 (mmm) cc_final: 0.8724 (mmm) REVERT: B 1041 MET cc_start: 0.9667 (mmp) cc_final: 0.9069 (mmm) REVERT: B 1050 MET cc_start: 0.8933 (mmm) cc_final: 0.8700 (mmp) REVERT: B 1102 LEU cc_start: 0.9147 (mt) cc_final: 0.8781 (tp) REVERT: B 1134 MET cc_start: 0.8669 (tpp) cc_final: 0.7718 (pmm) REVERT: B 1180 MET cc_start: 0.9312 (mmm) cc_final: 0.9102 (mmm) REVERT: B 1260 MET cc_start: -0.2076 (pmm) cc_final: -0.3623 (mtt) REVERT: B 1927 TYR cc_start: 0.8897 (p90) cc_final: 0.8682 (p90) REVERT: B 2064 MET cc_start: 0.9030 (mmm) cc_final: 0.8678 (mtt) outliers start: 49 outliers final: 40 residues processed: 250 average time/residue: 0.1895 time to fit residues: 83.4877 Evaluate side-chains 256 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 2056 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 429 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 361 optimal weight: 20.0000 chunk 289 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** 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 = 0.4175 r_free = 0.4175 target = 0.096845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.068097 restraints weight = 216108.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.066903 restraints weight = 134386.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066781 restraints weight = 101554.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067763 restraints weight = 80673.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.067296 restraints weight = 62914.952| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36988 Z= 0.175 Angle : 0.663 15.924 50147 Z= 0.327 Chirality : 0.040 0.273 5869 Planarity : 0.004 0.066 6299 Dihedral : 4.735 70.207 4838 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 1.18 % Allowed : 13.72 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.13), residues: 4493 helix: 1.74 (0.09), residues: 3103 sheet: -0.56 (0.43), residues: 132 loop : -0.37 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1204 TYR 0.025 0.001 TYR B2706 PHE 0.019 0.001 PHE B1993 TRP 0.043 0.001 TRP A1314 HIS 0.008 0.001 HIS B2051 Details of bonding type rmsd covalent geometry : bond 0.00379 (36988) covalent geometry : angle 0.66266 (50147) hydrogen bonds : bond 0.03701 ( 2253) hydrogen bonds : angle 4.28397 ( 6624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 1.486 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 236 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: A 349 MET cc_start: 0.8109 (tpp) cc_final: 0.7237 (tpp) REVERT: A 707 MET cc_start: 0.8964 (ttp) cc_final: 0.7911 (tmm) REVERT: A 747 MET cc_start: 0.9009 (pmm) cc_final: 0.8712 (pmm) REVERT: A 775 GLU cc_start: 0.8671 (tp30) cc_final: 0.8139 (tp30) REVERT: A 968 MET cc_start: 0.8885 (mpp) cc_final: 0.8575 (mpp) REVERT: A 1149 MET cc_start: 0.8919 (mmm) cc_final: 0.8651 (mmm) REVERT: A 1180 MET cc_start: 0.9134 (mmm) cc_final: 0.8790 (mmm) REVERT: A 1215 MET cc_start: 0.9044 (tpt) cc_final: 0.8812 (tpp) REVERT: A 1342 MET cc_start: 0.9026 (tpp) cc_final: 0.8614 (tpp) REVERT: A 1440 MET cc_start: 0.8871 (mmp) cc_final: 0.8268 (mmp) REVERT: A 1816 ASP cc_start: 0.8441 (p0) cc_final: 0.8191 (p0) REVERT: A 1926 GLU cc_start: 0.8452 (tp30) cc_final: 0.7986 (tp30) REVERT: A 1968 TYR cc_start: 0.8509 (t80) cc_final: 0.8261 (t80) REVERT: A 2010 MET cc_start: 0.8167 (ppp) cc_final: 0.7896 (ppp) REVERT: A 2012 ASP cc_start: 0.8302 (m-30) cc_final: 0.8056 (m-30) REVERT: A 2196 MET cc_start: 0.5303 (mmm) cc_final: 0.5023 (mmm) REVERT: A 2295 PHE cc_start: 0.8801 (t80) cc_final: 0.8486 (t80) REVERT: A 2296 TRP cc_start: 0.7831 (m100) cc_final: 0.6435 (m100) REVERT: A 2309 LEU cc_start: 0.8608 (mt) cc_final: 0.8321 (mt) REVERT: A 2310 TYR cc_start: 0.9107 (t80) cc_final: 0.8672 (t80) REVERT: A 2340 MET cc_start: 0.4076 (mmm) cc_final: 0.3771 (mmm) REVERT: B 143 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8869 (t80) REVERT: B 376 MET cc_start: 0.9558 (mpp) cc_final: 0.9262 (mpp) REVERT: B 496 MET cc_start: 0.9670 (mmp) cc_final: 0.9364 (mmm) REVERT: B 707 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8674 (mmm) REVERT: B 715 GLU cc_start: 0.9514 (OUTLIER) cc_final: 0.9297 (mp0) REVERT: B 739 MET cc_start: 0.9469 (tpp) cc_final: 0.9150 (mmm) REVERT: B 760 MET cc_start: 0.6501 (mmt) cc_final: 0.5951 (mmt) REVERT: B 1005 MET cc_start: 0.8805 (mpp) cc_final: 0.8489 (mpp) REVERT: B 1022 MET cc_start: 0.9555 (ppp) cc_final: 0.9064 (ppp) REVERT: B 1023 MET cc_start: 0.9193 (mmm) cc_final: 0.8744 (mmm) REVERT: B 1041 MET cc_start: 0.9675 (mmp) cc_final: 0.9156 (mmm) REVERT: B 1050 MET cc_start: 0.8863 (mmm) cc_final: 0.8597 (mmp) REVERT: B 1102 LEU cc_start: 0.9168 (mt) cc_final: 0.8833 (tp) REVERT: B 1180 MET cc_start: 0.9270 (mmm) cc_final: 0.9042 (mmm) REVERT: B 1260 MET cc_start: -0.1858 (pmm) cc_final: -0.3365 (mtt) REVERT: B 2064 MET cc_start: 0.9060 (mmm) cc_final: 0.8840 (mtt) outliers start: 48 outliers final: 38 residues processed: 245 average time/residue: 0.2081 time to fit residues: 88.4210 Evaluate side-chains 250 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1928 MET Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 2056 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 307 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 380 optimal weight: 8.9990 chunk 349 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 450 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** 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 = 0.4181 r_free = 0.4181 target = 0.097087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068536 restraints weight = 216684.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066940 restraints weight = 165612.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.066852 restraints weight = 119646.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066951 restraints weight = 86242.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067348 restraints weight = 70052.358| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36988 Z= 0.150 Angle : 0.655 16.237 50147 Z= 0.320 Chirality : 0.040 0.260 5869 Planarity : 0.004 0.065 6299 Dihedral : 4.687 63.325 4838 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 1.08 % Allowed : 13.92 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 4493 helix: 1.77 (0.09), residues: 3098 sheet: -0.53 (0.43), residues: 130 loop : -0.34 (0.19), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1204 TYR 0.026 0.001 TYR B2706 PHE 0.037 0.001 PHE B 71 TRP 0.040 0.001 TRP A1314 HIS 0.006 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00326 (36988) covalent geometry : angle 0.65471 (50147) hydrogen bonds : bond 0.03587 ( 2253) hydrogen bonds : angle 4.23360 ( 6624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7858.57 seconds wall clock time: 136 minutes 6.76 seconds (8166.76 seconds total)