Starting phenix.real_space_refine on Sat Mar 7 06:03:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.map" model { file = "/net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z88_14546/03_2026/7z88_14546.cif" } resolution = 3.33 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= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 52 5.49 5 S 227 5.16 5 Cl 1 4.86 5 C 24682 2.51 5 N 6575 2.21 5 O 7216 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 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: 38754 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3599, 28443 Classifications: {'peptide': 3599} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 153, 'TRANS': 3444} Chain breaks: 21 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 33, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 7, 'PHE:plan': 2, 'TYR:plan': 4, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 258 Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5274 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'1IX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.72, per 1000 atoms: 0.20 Number of scatterers: 38754 At special positions: 0 Unit cell: (131.704, 179.952, 225.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 227 16.00 P 52 15.00 F 1 9.00 O 7216 8.00 N 6575 7.00 C 24682 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: 3.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9112 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 11 sheets defined 61.6% alpha, 3.5% beta 14 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.700A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 79 through 96 removed outlier: 3.919A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 4.346A pdb=" N VAL A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.858A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 216 through 232 Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.815A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 288 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.641A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.713A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.863A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.711A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 472 through 491 removed outlier: 4.479A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.583A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 749 through 758 removed outlier: 3.593A pdb=" N ALA A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 779 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 828 through 837 removed outlier: 3.621A pdb=" N THR A 837 " --> pdb=" O HIS A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.542A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.667A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 945 removed outlier: 3.898A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.944A pdb=" N TYR A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.039A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1018 Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.616A pdb=" N ARG A1026 " --> pdb=" O ASP A1022 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1074 through 1086 Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1104 through 1114 Processing helix chain 'A' and resid 1118 through 1121 Processing helix chain 'A' and resid 1122 through 1145 removed outlier: 3.925A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 removed outlier: 3.678A pdb=" N HIS A1175 " --> pdb=" O TRP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1215 removed outlier: 3.528A pdb=" N TRP A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 4.004A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1272 Processing helix chain 'A' and resid 1277 through 1282 Processing helix chain 'A' and resid 1283 through 1287 removed outlier: 4.063A pdb=" N ALA A1286 " --> pdb=" O GLY A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1300 Processing helix chain 'A' and resid 1325 through 1350 removed outlier: 3.959A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1359 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 3.606A pdb=" N VAL A1371 " --> pdb=" O HIS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.508A pdb=" N ILE A1382 " --> pdb=" O PRO A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1409 removed outlier: 3.541A pdb=" N ALA A1393 " --> pdb=" O VAL A1389 " (cutoff:3.500A) Proline residue: A1396 - end of helix removed outlier: 3.740A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A1409 " --> pdb=" O ALA A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1423 removed outlier: 4.186A pdb=" N GLU A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1432 removed outlier: 3.634A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1461 removed outlier: 3.817A pdb=" N ASP A1444 " --> pdb=" O ASP A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1491 removed outlier: 3.949A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1521 Processing helix chain 'A' and resid 1524 through 1534 Processing helix chain 'A' and resid 1556 through 1564 removed outlier: 3.802A pdb=" N TYR A1560 " --> pdb=" O GLY A1556 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1577 through 1585 removed outlier: 4.270A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 Processing helix chain 'A' and resid 1613 through 1625 removed outlier: 3.579A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1656 Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 3.877A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1693 removed outlier: 3.662A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1700 Processing helix chain 'A' and resid 1703 through 1722 Processing helix chain 'A' and resid 1735 through 1753 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1787 Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1822 removed outlier: 3.742A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 removed outlier: 3.744A pdb=" N LEU A1827 " --> pdb=" O SER A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1852 removed outlier: 5.121A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1884 Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1909 through 1921 removed outlier: 3.591A pdb=" N LYS A1913 " --> pdb=" O ASN A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1953 Processing helix chain 'A' and resid 1960 through 1965 removed outlier: 4.145A pdb=" N GLY A1964 " --> pdb=" O LYS A1960 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1965 " --> pdb=" O PHE A1961 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1960 through 1965' Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.799A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1976 through 1982 removed outlier: 3.789A pdb=" N ASN A1980 " --> pdb=" O LEU A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 2037 through 2046 removed outlier: 3.677A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2125 through 2135 removed outlier: 4.012A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.624A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2158 removed outlier: 3.673A pdb=" N ARG A2158 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 Processing helix chain 'A' and resid 2182 through 2196 Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2255 through 2261 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 4.079A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 3.913A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 3.901A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2354 removed outlier: 3.784A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2369 removed outlier: 3.681A pdb=" N PHE A2360 " --> pdb=" O MET A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2403 removed outlier: 4.177A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2424 Processing helix chain 'A' and resid 2428 through 2442 removed outlier: 3.698A pdb=" N MET A2442 " --> pdb=" O ILE A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2446 Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 3.646A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2483 removed outlier: 3.948A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2508 removed outlier: 4.897A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2527 Processing helix chain 'A' and resid 2536 through 2543 removed outlier: 3.845A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.054A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2798 Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2862 Processing helix chain 'A' and resid 2866 through 2870 removed outlier: 4.035A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 4.130A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2931 removed outlier: 4.636A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2941 Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.667A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2966 through 2977 Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.828A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3018 removed outlier: 4.256A pdb=" N SER A3018 " --> pdb=" O CYS A3014 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3056 Proline residue: A3042 - end of helix removed outlier: 3.638A pdb=" N GLY A3055 " --> pdb=" O LEU A3051 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A3056 " --> pdb=" O LEU A3052 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3068 removed outlier: 4.100A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3072 through 3082 removed outlier: 4.146A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3084 through 3093 Processing helix chain 'A' and resid 3095 through 3115 Processing helix chain 'A' and resid 3123 through 3145 removed outlier: 3.716A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) Processing helix chain 'A' and resid 3146 through 3152 removed outlier: 6.316A pdb=" N GLY A3149 " --> pdb=" O SER A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.698A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3251 through 3264 removed outlier: 4.344A pdb=" N LYS A3264 " --> pdb=" O LYS A3260 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3292 through 3302 removed outlier: 3.624A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3304 through 3309 removed outlier: 3.532A pdb=" N GLU A3309 " --> pdb=" O SER A3305 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3342 Processing helix chain 'A' and resid 3354 through 3362 removed outlier: 4.189A pdb=" N ARG A3358 " --> pdb=" O ASP A3354 " (cutoff:3.500A) Processing helix chain 'A' and resid 3372 through 3391 Processing helix chain 'A' and resid 3407 through 3428 Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 4.797A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3463 removed outlier: 4.049A pdb=" N LEU A3463 " --> pdb=" O GLU A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 4.095A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3489 removed outlier: 3.556A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 4.051A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A3505 " --> pdb=" O HIS A3501 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A3506 " --> pdb=" O MET A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3510 through 3514 Processing helix chain 'A' and resid 3515 through 3525 removed outlier: 3.825A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3535 through 3540 Processing helix chain 'A' and resid 3547 through 3563 Processing helix chain 'A' and resid 3567 through 3579 removed outlier: 3.523A pdb=" N SER A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3596 Processing helix chain 'A' and resid 3604 through 3615 removed outlier: 4.382A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3627 removed outlier: 4.050A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3630 through 3637 Processing helix chain 'A' and resid 3641 through 3650 removed outlier: 3.634A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3674 Processing helix chain 'A' and resid 3680 through 3683 removed outlier: 3.762A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3680 through 3683' Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3778 through 3784 removed outlier: 3.651A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.527A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3848 Processing helix chain 'A' and resid 3853 through 3859 Processing helix chain 'A' and resid 3863 through 3878 removed outlier: 3.908A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3890 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.908A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3964 through 3972 removed outlier: 4.167A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A3972 " --> pdb=" O ILE A3968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4040 through 4050 Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 removed outlier: 3.545A pdb=" N GLU A4125 " --> pdb=" O GLU A4122 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 3.855A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.584A pdb=" N ILE B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.975A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.652A pdb=" N THR B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.800A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 392 removed outlier: 3.509A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 removed outlier: 4.080A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 521 through 530 removed outlier: 4.151A pdb=" N VAL B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 217 through 223 removed outlier: 3.719A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.716A pdb=" N PHE C 356 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.219A pdb=" N VAL C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP C 386 " --> pdb=" O HIS C 382 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.527A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.571A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 596 through 605 Processing helix chain 'C' and resid 610 through 626 Processing helix chain 'C' and resid 628 through 649 Processing helix chain 'C' and resid 652 through 669 Processing helix chain 'C' and resid 671 through 682 removed outlier: 3.873A pdb=" N ASP C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3736 through 3738 removed outlier: 6.638A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.540A pdb=" N ARG B 165 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 367 through 370 removed outlier: 8.677A pdb=" N LEU B 345 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 260 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 347 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS B 262 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY B 349 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 346 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 297 through 303 removed outlier: 3.977A pdb=" N CYS C 296 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 301 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 290 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.813A pdb=" N ALA C 8 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA C 55 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 133 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 135 " --> pdb=" O CYS C 13 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 341 removed outlier: 4.040A pdb=" N PHE C 340 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 252 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 262 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 365 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 364 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 315 through 316 removed outlier: 3.893A pdb=" N ASP C 319 " --> pdb=" O TYR C 316 " (cutoff:3.500A) 1950 hydrogen bonds defined for protein. 5733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 12.96 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12162 1.34 - 1.46: 8810 1.46 - 1.59: 18203 1.59 - 1.71: 102 1.71 - 1.83: 359 Bond restraints: 39636 Sorted by residual: bond pdb=" C11 1IX A4201 " pdb="CL1 1IX A4201 " ideal model delta sigma weight residual 1.728 1.833 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C24 1IX A4201 " pdb=" N26 1IX A4201 " ideal model delta sigma weight residual 1.371 1.475 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C12 1IX A4201 " pdb=" C13 1IX A4201 " ideal model delta sigma weight residual 1.379 1.471 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C14 1IX A4201 " pdb=" C16 1IX A4201 " ideal model delta sigma weight residual 1.480 1.565 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C ASP A2289 " pdb=" N PRO A2290 " ideal model delta sigma weight residual 1.331 1.365 -0.033 7.90e-03 1.60e+04 1.76e+01 ... (remaining 39631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 52871 2.96 - 5.91: 819 5.91 - 8.87: 89 8.87 - 11.82: 14 11.82 - 14.78: 4 Bond angle restraints: 53797 Sorted by residual: angle pdb=" C SER A2547 " pdb=" N PRO A2548 " pdb=" CA PRO A2548 " ideal model delta sigma weight residual 119.84 134.62 -14.78 1.25e+00 6.40e-01 1.40e+02 angle pdb=" N VAL A 407 " pdb=" CA VAL A 407 " pdb=" C VAL A 407 " ideal model delta sigma weight residual 113.53 107.38 6.15 9.80e-01 1.04e+00 3.94e+01 angle pdb=" N ARG A3965 " pdb=" CA ARG A3965 " pdb=" C ARG A3965 " ideal model delta sigma weight residual 111.33 118.64 -7.31 1.21e+00 6.83e-01 3.65e+01 angle pdb=" N VAL A 976 " pdb=" CA VAL A 976 " pdb=" C VAL A 976 " ideal model delta sigma weight residual 110.62 115.78 -5.16 1.02e+00 9.61e-01 2.56e+01 angle pdb=" C LEU A1639 " pdb=" N GLU A1640 " pdb=" CA GLU A1640 " ideal model delta sigma weight residual 122.08 129.68 -7.60 1.53e+00 4.27e-01 2.47e+01 ... (remaining 53792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 22706 28.04 - 56.08: 1224 56.08 - 84.12: 122 84.12 - 112.17: 10 112.17 - 140.21: 2 Dihedral angle restraints: 24064 sinusoidal: 10096 harmonic: 13968 Sorted by residual: dihedral pdb=" CA PRO A1020 " pdb=" C PRO A1020 " pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA ARG A3462 " pdb=" C ARG A3462 " pdb=" N LEU A3463 " pdb=" CA LEU A3463 " 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=" CA ARG B 252 " pdb=" C ARG B 252 " pdb=" N LYS B 253 " pdb=" CA LYS B 253 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 ... (remaining 24061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5095 0.063 - 0.127: 918 0.127 - 0.190: 105 0.190 - 0.253: 12 0.253 - 0.317: 5 Chirality restraints: 6135 Sorted by residual: chirality pdb=" CG LEU A3005 " pdb=" CB LEU A3005 " pdb=" CD1 LEU A3005 " pdb=" CD2 LEU A3005 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA TYR A3531 " pdb=" N TYR A3531 " pdb=" C TYR A3531 " pdb=" CB TYR A3531 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 6132 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A4055 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A4056 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A4056 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A4056 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 634 " -0.063 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO A 635 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 635 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 635 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A4005 " 0.025 2.00e-02 2.50e+03 2.89e-02 1.47e+01 pdb=" CG PHE A4005 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A4005 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A4005 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A4005 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A4005 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A4005 " 0.003 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1861 2.71 - 3.26: 42046 3.26 - 3.80: 64141 3.80 - 4.35: 82673 4.35 - 4.90: 130876 Nonbonded interactions: 321597 Sorted by model distance: nonbonded pdb=" OE1 GLU A3478 " pdb=" OG1 THR A3479 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP B 505 " pdb=" OH TYR C 333 " model vdw 2.195 3.040 nonbonded pdb=" O GLU A1769 " pdb=" NH2 ARG A1822 " model vdw 2.203 3.120 nonbonded pdb=" O CYS A 931 " pdb=" OH TYR A 984 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A3828 " pdb=" OE1 GLU A4125 " model vdw 2.215 3.040 ... (remaining 321592 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 42.630 Find NCS groups from input model: 0.210 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 39636 Z= 0.236 Angle : 0.917 14.776 53797 Z= 0.500 Chirality : 0.050 0.317 6135 Planarity : 0.006 0.111 6660 Dihedral : 16.275 140.207 14952 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.29 % Favored : 88.62 % Rotamer: Outliers : 0.19 % Allowed : 0.55 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.26 (0.11), residues: 4694 helix: -1.29 (0.09), residues: 2710 sheet: -2.56 (0.32), residues: 212 loop : -3.47 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 517 TYR 0.032 0.002 TYR A3531 PHE 0.067 0.002 PHE A4005 TRP 0.037 0.003 TRP A 300 HIS 0.021 0.002 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00524 (39636) covalent geometry : angle 0.91681 (53797) hydrogen bonds : bond 0.14395 ( 1985) hydrogen bonds : angle 6.71940 ( 5803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 690 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 PHE cc_start: 0.5882 (t80) cc_final: 0.5428 (t80) REVERT: A 321 LYS cc_start: 0.6074 (ttmt) cc_final: 0.5680 (mttp) REVERT: A 343 GLU cc_start: 0.4615 (pt0) cc_final: 0.4388 (pt0) REVERT: A 862 LEU cc_start: 0.7500 (pp) cc_final: 0.7057 (pp) REVERT: A 901 MET cc_start: 0.6048 (ptm) cc_final: 0.5536 (ttp) REVERT: A 976 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6438 (t) REVERT: A 1136 ARG cc_start: 0.6700 (mtt90) cc_final: 0.6208 (mtt180) REVERT: A 1382 ILE cc_start: 0.8100 (pt) cc_final: 0.7792 (pt) REVERT: A 1592 MET cc_start: 0.6560 (mmm) cc_final: 0.6139 (mmm) REVERT: A 2087 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6284 (mm-30) REVERT: A 2439 ILE cc_start: 0.8634 (tt) cc_final: 0.8387 (tt) REVERT: A 2540 LEU cc_start: 0.7379 (mm) cc_final: 0.7171 (mm) REVERT: A 2935 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 3729 MET cc_start: 0.7473 (ppp) cc_final: 0.6989 (ppp) REVERT: A 3808 ASN cc_start: 0.6896 (m-40) cc_final: 0.6490 (m-40) REVERT: A 3885 ARG cc_start: 0.6168 (mtm-85) cc_final: 0.5948 (mtm-85) REVERT: A 4046 TYR cc_start: 0.6117 (m-10) cc_final: 0.5805 (m-10) REVERT: A 4062 ASP cc_start: 0.6067 (m-30) cc_final: 0.5407 (m-30) REVERT: B 204 HIS cc_start: 0.4749 (t-90) cc_final: 0.4200 (t-90) REVERT: B 328 ILE cc_start: 0.8402 (tp) cc_final: 0.8166 (tp) REVERT: B 493 LEU cc_start: 0.8255 (tp) cc_final: 0.7929 (tt) REVERT: C 428 GLU cc_start: 0.6464 (tt0) cc_final: 0.6106 (tt0) REVERT: C 514 ASN cc_start: 0.5980 (m-40) cc_final: 0.5401 (m-40) outliers start: 8 outliers final: 2 residues processed: 697 average time/residue: 0.2399 time to fit residues: 271.4425 Evaluate side-chains 589 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 586 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 4090 ARG Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN A2432 GLN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3074 GLN ** A3251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3660 ASN A3743 HIS A3924 HIS A4115 ASN B 158 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 350 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.233748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.200207 restraints weight = 43181.270| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.95 r_work: 0.3847 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39636 Z= 0.170 Angle : 0.773 11.070 53797 Z= 0.396 Chirality : 0.046 0.236 6135 Planarity : 0.005 0.071 6660 Dihedral : 12.584 141.214 5664 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.26 % Rotamer: Outliers : 1.13 % Allowed : 10.18 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -2.45 (0.12), residues: 4694 helix: -0.59 (0.10), residues: 2760 sheet: -2.26 (0.33), residues: 200 loop : -3.25 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 290 TYR 0.021 0.002 TYR A2412 PHE 0.036 0.002 PHE A2260 TRP 0.021 0.002 TRP A1633 HIS 0.015 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00390 (39636) covalent geometry : angle 0.77309 (53797) hydrogen bonds : bond 0.04657 ( 1985) hydrogen bonds : angle 5.17453 ( 5803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 649 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6895 (ttpp) REVERT: A 294 PHE cc_start: 0.6266 (t80) cc_final: 0.5716 (t80) REVERT: A 321 LYS cc_start: 0.6178 (ttmt) cc_final: 0.5852 (mttm) REVERT: A 326 MET cc_start: 0.6051 (ttp) cc_final: 0.5843 (ttp) REVERT: A 384 MET cc_start: 0.6102 (mtt) cc_final: 0.5784 (mtp) REVERT: A 628 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5769 (mp0) REVERT: A 770 LEU cc_start: 0.8205 (mm) cc_final: 0.7497 (mt) REVERT: A 853 ILE cc_start: 0.8144 (mt) cc_final: 0.7659 (mm) REVERT: A 1038 LYS cc_start: 0.7056 (mtpp) cc_final: 0.6420 (mttm) REVERT: A 1066 LEU cc_start: 0.8497 (tp) cc_final: 0.7973 (mt) REVERT: A 1136 ARG cc_start: 0.6531 (mtt90) cc_final: 0.5912 (mtt-85) REVERT: A 1273 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6714 (mm-30) REVERT: A 1382 ILE cc_start: 0.8328 (pt) cc_final: 0.8044 (pt) REVERT: A 1592 MET cc_start: 0.6720 (mmm) cc_final: 0.6002 (mmm) REVERT: A 1760 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: A 1806 ARG cc_start: 0.5892 (tmt-80) cc_final: 0.5642 (ttp80) REVERT: A 1825 LEU cc_start: 0.7114 (mt) cc_final: 0.6673 (mt) REVERT: A 2042 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7339 (mp-120) REVERT: A 2085 MET cc_start: 0.2448 (OUTLIER) cc_final: 0.2239 (tpp) REVERT: A 2087 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 2331 MET cc_start: 0.8033 (mmt) cc_final: 0.7586 (tpt) REVERT: A 2439 ILE cc_start: 0.8564 (tt) cc_final: 0.8313 (tt) REVERT: A 3683 CYS cc_start: 0.6376 (OUTLIER) cc_final: 0.6172 (t) REVERT: A 3729 MET cc_start: 0.7387 (ppp) cc_final: 0.7017 (ppp) REVERT: A 3808 ASN cc_start: 0.7530 (m-40) cc_final: 0.7150 (m-40) REVERT: A 3820 MET cc_start: 0.7186 (ptm) cc_final: 0.6958 (ptp) REVERT: A 4062 ASP cc_start: 0.6145 (m-30) cc_final: 0.5792 (m-30) REVERT: B 102 ILE cc_start: 0.7445 (mm) cc_final: 0.7123 (mm) REVERT: B 204 HIS cc_start: 0.5057 (t-90) cc_final: 0.4359 (t-90) REVERT: B 514 MET cc_start: 0.3577 (mpp) cc_final: 0.2736 (mpt) REVERT: C 271 ARG cc_start: 0.6350 (ttm-80) cc_final: 0.5938 (mtm180) REVERT: C 514 ASN cc_start: 0.5987 (m-40) cc_final: 0.5500 (m-40) outliers start: 47 outliers final: 27 residues processed: 662 average time/residue: 0.2229 time to fit residues: 240.6690 Evaluate side-chains 624 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 592 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2243 GLU Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3683 CYS Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 439 optimal weight: 0.0070 chunk 148 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 370 optimal weight: 0.8980 chunk 243 optimal weight: 0.5980 chunk 392 optimal weight: 0.9980 chunk 247 optimal weight: 0.0770 chunk 136 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 399 optimal weight: 0.0670 chunk 411 optimal weight: 0.7980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN A1754 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3251 ASN A3924 HIS B 132 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.236640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.204087 restraints weight = 42945.661| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.95 r_work: 0.3880 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39636 Z= 0.140 Angle : 0.698 12.405 53797 Z= 0.358 Chirality : 0.043 0.220 6135 Planarity : 0.005 0.077 6660 Dihedral : 12.345 142.070 5659 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.57 % Favored : 90.37 % Rotamer: Outliers : 1.98 % Allowed : 13.87 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.95 (0.12), residues: 4694 helix: -0.16 (0.10), residues: 2764 sheet: -1.94 (0.36), residues: 191 loop : -3.10 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1136 TYR 0.022 0.001 TYR A1675 PHE 0.029 0.001 PHE A2260 TRP 0.016 0.001 TRP A1633 HIS 0.011 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00315 (39636) covalent geometry : angle 0.69820 (53797) hydrogen bonds : bond 0.04037 ( 1985) hydrogen bonds : angle 4.80521 ( 5803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 640 time to evaluate : 1.268 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 96 MET cc_start: 0.5222 (ppp) cc_final: 0.4982 (mtt) REVERT: A 321 LYS cc_start: 0.5880 (ttmt) cc_final: 0.5533 (mttp) REVERT: A 384 MET cc_start: 0.6104 (mtt) cc_final: 0.5733 (mtp) REVERT: A 396 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6193 (p90) REVERT: A 628 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: A 754 MET cc_start: 0.7410 (ttm) cc_final: 0.6990 (tpp) REVERT: A 762 TYR cc_start: 0.7831 (t80) cc_final: 0.7629 (t80) REVERT: A 770 LEU cc_start: 0.8271 (mm) cc_final: 0.7528 (mt) REVERT: A 853 ILE cc_start: 0.8034 (mt) cc_final: 0.7539 (mm) REVERT: A 868 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7883 (mttp) REVERT: A 870 LEU cc_start: 0.7527 (tt) cc_final: 0.7283 (tt) REVERT: A 1066 LEU cc_start: 0.8405 (tp) cc_final: 0.7872 (mt) REVERT: A 1106 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5750 (tt) REVERT: A 1136 ARG cc_start: 0.6380 (mtt90) cc_final: 0.5846 (mtt-85) REVERT: A 1382 ILE cc_start: 0.8331 (pt) cc_final: 0.8002 (pt) REVERT: A 1592 MET cc_start: 0.6651 (mmm) cc_final: 0.5969 (mmm) REVERT: A 1760 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: A 1802 TYR cc_start: 0.7105 (t80) cc_final: 0.6689 (t80) REVERT: A 1825 LEU cc_start: 0.7087 (mt) cc_final: 0.6683 (mt) REVERT: A 1880 MET cc_start: 0.6226 (mpp) cc_final: 0.5735 (mpp) REVERT: A 2085 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.2321 (tpp) REVERT: A 2087 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6967 (mm-30) REVERT: A 2220 MET cc_start: 0.7699 (mtt) cc_final: 0.7358 (mtt) REVERT: A 2331 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7349 (tpt) REVERT: A 2439 ILE cc_start: 0.8648 (tt) cc_final: 0.8233 (tt) REVERT: A 3708 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.4327 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7545 (m-40) cc_final: 0.7225 (m-40) REVERT: A 3885 ARG cc_start: 0.6909 (mtm-85) cc_final: 0.6704 (mtm-85) REVERT: B 217 TYR cc_start: 0.3395 (OUTLIER) cc_final: 0.2332 (m-10) REVERT: B 294 GLU cc_start: 0.6289 (tp30) cc_final: 0.5977 (tp30) REVERT: B 514 MET cc_start: 0.4483 (OUTLIER) cc_final: 0.3688 (mpt) REVERT: C 514 ASN cc_start: 0.5786 (m110) cc_final: 0.5279 (m-40) REVERT: C 516 LEU cc_start: 0.6902 (mt) cc_final: 0.6433 (mt) outliers start: 82 outliers final: 35 residues processed: 680 average time/residue: 0.2293 time to fit residues: 255.5957 Evaluate side-chains 643 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 599 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2243 GLU Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 54 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 327 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 393 optimal weight: 0.1980 chunk 277 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3924 HIS B 132 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.234139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.202218 restraints weight = 42930.827| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.79 r_work: 0.3899 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39636 Z= 0.162 Angle : 0.700 11.996 53797 Z= 0.358 Chirality : 0.044 0.228 6135 Planarity : 0.005 0.064 6660 Dihedral : 12.330 142.439 5659 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.40 % Favored : 89.54 % Rotamer: Outliers : 3.02 % Allowed : 16.04 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.80 (0.12), residues: 4694 helix: -0.08 (0.10), residues: 2777 sheet: -1.89 (0.36), residues: 194 loop : -3.00 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 187 TYR 0.027 0.002 TYR C 416 PHE 0.031 0.002 PHE A2260 TRP 0.018 0.001 TRP A1633 HIS 0.011 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00378 (39636) covalent geometry : angle 0.70019 (53797) hydrogen bonds : bond 0.04014 ( 1985) hydrogen bonds : angle 4.73246 ( 5803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 613 time to evaluate : 1.444 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 282 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: A 321 LYS cc_start: 0.6066 (ttmt) cc_final: 0.5585 (mttp) REVERT: A 396 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6478 (p90) REVERT: A 628 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: A 754 MET cc_start: 0.7501 (ttm) cc_final: 0.7080 (tpp) REVERT: A 853 ILE cc_start: 0.8104 (mt) cc_final: 0.7632 (mm) REVERT: A 868 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7916 (mttm) REVERT: A 870 LEU cc_start: 0.7640 (tt) cc_final: 0.7415 (tt) REVERT: A 961 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6953 (mt) REVERT: A 1066 LEU cc_start: 0.8464 (tp) cc_final: 0.7949 (mt) REVERT: A 1106 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5623 (tt) REVERT: A 1136 ARG cc_start: 0.6406 (mtt90) cc_final: 0.6180 (mtt180) REVERT: A 1382 ILE cc_start: 0.8316 (pt) cc_final: 0.7978 (pt) REVERT: A 1428 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6100 (mp) REVERT: A 1592 MET cc_start: 0.6732 (mmm) cc_final: 0.5931 (mmm) REVERT: A 1754 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: A 1760 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: A 1802 TYR cc_start: 0.6971 (t80) cc_final: 0.6503 (t80) REVERT: A 1825 LEU cc_start: 0.7526 (mt) cc_final: 0.7322 (mt) REVERT: A 1878 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5751 (t0) REVERT: A 2042 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7132 (mp-120) REVERT: A 2085 MET cc_start: 0.2926 (OUTLIER) cc_final: 0.2078 (pmm) REVERT: A 2220 MET cc_start: 0.7583 (mtt) cc_final: 0.7286 (mtt) REVERT: A 2331 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: A 2439 ILE cc_start: 0.8666 (tt) cc_final: 0.8271 (tt) REVERT: A 2576 MET cc_start: 0.3169 (mmt) cc_final: 0.2905 (tpp) REVERT: A 3414 MET cc_start: 0.4774 (mmp) cc_final: 0.4420 (mmp) REVERT: A 3683 CYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5924 (t) REVERT: A 3708 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.4375 (mmt-90) REVERT: A 3729 MET cc_start: 0.7447 (ppp) cc_final: 0.7189 (ptp) REVERT: A 3808 ASN cc_start: 0.7482 (m-40) cc_final: 0.7205 (m-40) REVERT: A 3885 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6632 (mtm-85) REVERT: B 50 GLU cc_start: 0.6504 (tp30) cc_final: 0.6163 (pt0) REVERT: B 102 ILE cc_start: 0.7042 (mm) cc_final: 0.6793 (mm) REVERT: B 217 TYR cc_start: 0.3584 (OUTLIER) cc_final: 0.2653 (m-10) REVERT: B 281 LEU cc_start: 0.7216 (pt) cc_final: 0.6096 (mt) REVERT: B 294 GLU cc_start: 0.6422 (tp30) cc_final: 0.6103 (tp30) REVERT: B 514 MET cc_start: 0.4623 (OUTLIER) cc_final: 0.3946 (mpt) REVERT: C 514 ASN cc_start: 0.6128 (m110) cc_final: 0.5569 (m-40) REVERT: C 516 LEU cc_start: 0.6893 (mt) cc_final: 0.6531 (mt) outliers start: 125 outliers final: 67 residues processed: 681 average time/residue: 0.2412 time to fit residues: 269.4915 Evaluate side-chains 669 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 586 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1754 GLN Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3683 CYS Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 460 optimal weight: 0.2980 chunk 352 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 406 optimal weight: 0.3980 chunk 218 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 283 optimal weight: 0.0670 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.237797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.205503 restraints weight = 42850.988| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.92 r_work: 0.3894 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39636 Z= 0.132 Angle : 0.673 11.503 53797 Z= 0.343 Chirality : 0.042 0.246 6135 Planarity : 0.005 0.062 6660 Dihedral : 12.219 143.239 5659 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.33 % Favored : 90.63 % Rotamer: Outliers : 2.94 % Allowed : 17.49 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.62 (0.12), residues: 4694 helix: 0.07 (0.10), residues: 2781 sheet: -1.72 (0.35), residues: 194 loop : -2.96 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 187 TYR 0.027 0.001 TYR C 416 PHE 0.026 0.001 PHE A2809 TRP 0.014 0.001 TRP A1633 HIS 0.009 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00301 (39636) covalent geometry : angle 0.67323 (53797) hydrogen bonds : bond 0.03724 ( 1985) hydrogen bonds : angle 4.59891 ( 5803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 629 time to evaluate : 1.391 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 282 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: A 321 LYS cc_start: 0.6064 (ttmt) cc_final: 0.5609 (mttp) REVERT: A 396 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6562 (p90) REVERT: A 628 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: A 853 ILE cc_start: 0.8073 (mt) cc_final: 0.7603 (mm) REVERT: A 868 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7868 (mttp) REVERT: A 883 TYR cc_start: 0.6574 (m-80) cc_final: 0.5847 (m-10) REVERT: A 961 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6945 (mt) REVERT: A 1038 LYS cc_start: 0.6955 (mtpp) cc_final: 0.6266 (mttm) REVERT: A 1066 LEU cc_start: 0.8381 (tp) cc_final: 0.7935 (mt) REVERT: A 1136 ARG cc_start: 0.6539 (mtt90) cc_final: 0.6163 (mtt180) REVERT: A 1164 CYS cc_start: 0.6491 (OUTLIER) cc_final: 0.6235 (m) REVERT: A 1189 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: A 1382 ILE cc_start: 0.8290 (pt) cc_final: 0.7967 (pt) REVERT: A 1592 MET cc_start: 0.6660 (mmm) cc_final: 0.5951 (mmm) REVERT: A 1748 ASP cc_start: 0.5778 (t0) cc_final: 0.5366 (m-30) REVERT: A 1768 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.7099 (mtm180) REVERT: A 1825 LEU cc_start: 0.7471 (mt) cc_final: 0.7056 (mt) REVERT: A 1878 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5343 (t0) REVERT: A 2085 MET cc_start: 0.2832 (OUTLIER) cc_final: 0.2077 (pmm) REVERT: A 2087 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 2184 TYR cc_start: 0.5650 (p90) cc_final: 0.5430 (p90) REVERT: A 2220 MET cc_start: 0.7595 (mtt) cc_final: 0.7372 (mtt) REVERT: A 2331 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7466 (tpt) REVERT: A 2341 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4745 (pt) REVERT: A 3012 GLU cc_start: 0.4910 (pt0) cc_final: 0.4626 (pt0) REVERT: A 3708 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.4270 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7504 (m-40) cc_final: 0.7197 (m-40) REVERT: A 3883 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 3889 ARG cc_start: 0.7758 (tmt170) cc_final: 0.7094 (ttt-90) REVERT: B 50 GLU cc_start: 0.6537 (tp30) cc_final: 0.6116 (pt0) REVERT: B 102 ILE cc_start: 0.7247 (mm) cc_final: 0.6937 (mm) REVERT: B 217 TYR cc_start: 0.3326 (OUTLIER) cc_final: 0.2526 (m-10) REVERT: B 254 ARG cc_start: 0.6620 (ttp-170) cc_final: 0.6158 (ttp-170) REVERT: B 281 LEU cc_start: 0.7361 (pt) cc_final: 0.6302 (mt) REVERT: B 294 GLU cc_start: 0.6421 (tp30) cc_final: 0.6122 (tp30) REVERT: B 341 ASP cc_start: 0.7648 (t0) cc_final: 0.7342 (t0) REVERT: B 363 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7959 (ttm110) REVERT: B 514 MET cc_start: 0.4597 (OUTLIER) cc_final: 0.3892 (mpt) REVERT: C 43 GLN cc_start: 0.6059 (pt0) cc_final: 0.5785 (pt0) REVERT: C 514 ASN cc_start: 0.5753 (m110) cc_final: 0.5392 (m-40) outliers start: 122 outliers final: 77 residues processed: 697 average time/residue: 0.2477 time to fit residues: 281.0468 Evaluate side-chains 696 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 605 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2859 GLN Chi-restraints excluded: chain A residue 2942 ILE Chi-restraints excluded: chain A residue 3159 ARG Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3932 MET Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 356 optimal weight: 0.0670 chunk 101 optimal weight: 0.7980 chunk 386 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 237 optimal weight: 0.1980 chunk 290 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A1772 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3185 ASN A3924 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** 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 = 0.4433 r_free = 0.4433 target = 0.237267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.203473 restraints weight = 42799.351| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.97 r_work: 0.3877 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39636 Z= 0.136 Angle : 0.665 10.041 53797 Z= 0.339 Chirality : 0.042 0.214 6135 Planarity : 0.005 0.069 6660 Dihedral : 12.175 144.012 5659 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.59 % Favored : 90.39 % Rotamer: Outliers : 3.50 % Allowed : 18.17 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.49 (0.12), residues: 4694 helix: 0.18 (0.10), residues: 2774 sheet: -1.70 (0.35), residues: 195 loop : -2.90 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3289 TYR 0.025 0.001 TYR C 416 PHE 0.026 0.001 PHE A4005 TRP 0.012 0.001 TRP A1633 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00311 (39636) covalent geometry : angle 0.66528 (53797) hydrogen bonds : bond 0.03633 ( 1985) hydrogen bonds : angle 4.52471 ( 5803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 620 time to evaluate : 1.449 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 282 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: A 321 LYS cc_start: 0.6090 (ttmt) cc_final: 0.5766 (mttm) REVERT: A 396 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6471 (p90) REVERT: A 628 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: A 853 ILE cc_start: 0.8088 (mt) cc_final: 0.7621 (mm) REVERT: A 868 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7990 (mttm) REVERT: A 883 TYR cc_start: 0.6587 (m-80) cc_final: 0.5893 (m-10) REVERT: A 960 GLN cc_start: 0.7576 (mt0) cc_final: 0.7078 (mm110) REVERT: A 961 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7007 (mt) REVERT: A 1038 LYS cc_start: 0.6747 (mtpp) cc_final: 0.6066 (mttm) REVERT: A 1066 LEU cc_start: 0.8387 (tp) cc_final: 0.7950 (mt) REVERT: A 1106 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5677 (tt) REVERT: A 1136 ARG cc_start: 0.6664 (mtt90) cc_final: 0.6268 (mtt-85) REVERT: A 1164 CYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6509 (m) REVERT: A 1189 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 1382 ILE cc_start: 0.8342 (pt) cc_final: 0.8018 (pt) REVERT: A 1428 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6203 (mt) REVERT: A 1592 MET cc_start: 0.6728 (mmm) cc_final: 0.5962 (mmm) REVERT: A 1617 LYS cc_start: 0.7406 (mtpt) cc_final: 0.7168 (mmmt) REVERT: A 1748 ASP cc_start: 0.5739 (t0) cc_final: 0.5390 (m-30) REVERT: A 1825 LEU cc_start: 0.7675 (mt) cc_final: 0.7349 (mt) REVERT: A 1878 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5722 (t0) REVERT: A 2085 MET cc_start: 0.3208 (OUTLIER) cc_final: 0.2446 (pmm) REVERT: A 2220 MET cc_start: 0.7543 (mtt) cc_final: 0.7318 (mtt) REVERT: A 2331 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7441 (tpt) REVERT: A 2341 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4802 (pt) REVERT: A 2423 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7809 (t) REVERT: A 2576 MET cc_start: 0.3073 (mmt) cc_final: 0.2850 (tpp) REVERT: A 3178 ILE cc_start: 0.6128 (mp) cc_final: 0.5589 (mm) REVERT: A 3708 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.4258 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7442 (m-40) cc_final: 0.7165 (m-40) REVERT: A 3883 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7657 (tt) REVERT: A 3889 ARG cc_start: 0.7790 (tmt170) cc_final: 0.7232 (ttt-90) REVERT: B 50 GLU cc_start: 0.6630 (tp30) cc_final: 0.6198 (pt0) REVERT: B 102 ILE cc_start: 0.6783 (mm) cc_final: 0.6583 (mm) REVERT: B 217 TYR cc_start: 0.3467 (OUTLIER) cc_final: 0.2863 (m-10) REVERT: B 254 ARG cc_start: 0.6625 (ttp-170) cc_final: 0.6176 (ttp-170) REVERT: B 281 LEU cc_start: 0.7385 (pt) cc_final: 0.6349 (mt) REVERT: B 294 GLU cc_start: 0.6414 (tp30) cc_final: 0.6115 (tp30) REVERT: B 341 ASP cc_start: 0.7683 (t0) cc_final: 0.7439 (t0) REVERT: B 409 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6751 (t80) REVERT: B 514 MET cc_start: 0.4794 (OUTLIER) cc_final: 0.4082 (mpt) REVERT: C 514 ASN cc_start: 0.5878 (m110) cc_final: 0.5538 (m-40) outliers start: 145 outliers final: 93 residues processed: 708 average time/residue: 0.2400 time to fit residues: 280.3751 Evaluate side-chains 704 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 593 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2859 GLN Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 225 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 145 optimal weight: 0.0870 chunk 426 optimal weight: 10.0000 chunk 252 optimal weight: 0.0770 chunk 85 optimal weight: 0.7980 chunk 421 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 406 optimal weight: 0.7980 chunk 358 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1754 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2784 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** 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 = 0.4433 r_free = 0.4433 target = 0.237321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.204004 restraints weight = 42805.889| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.92 r_work: 0.3900 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39636 Z= 0.142 Angle : 0.674 10.470 53797 Z= 0.344 Chirality : 0.043 0.259 6135 Planarity : 0.005 0.063 6660 Dihedral : 12.145 144.164 5659 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.42 % Favored : 90.54 % Rotamer: Outliers : 3.59 % Allowed : 18.72 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.43 (0.12), residues: 4694 helix: 0.21 (0.10), residues: 2776 sheet: -1.65 (0.35), residues: 195 loop : -2.84 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3159 TYR 0.026 0.001 TYR C 416 PHE 0.025 0.001 PHE B 49 TRP 0.022 0.001 TRP A4127 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00330 (39636) covalent geometry : angle 0.67426 (53797) hydrogen bonds : bond 0.03660 ( 1985) hydrogen bonds : angle 4.51565 ( 5803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 605 time to evaluate : 1.300 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 282 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: A 321 LYS cc_start: 0.6108 (ttmt) cc_final: 0.5823 (mttm) REVERT: A 396 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6528 (p90) REVERT: A 628 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: A 632 GLU cc_start: 0.6883 (tt0) cc_final: 0.5809 (mm-30) REVERT: A 762 TYR cc_start: 0.7593 (t80) cc_final: 0.7377 (t80) REVERT: A 853 ILE cc_start: 0.8094 (mt) cc_final: 0.7629 (mm) REVERT: A 868 LYS cc_start: 0.8240 (mmtp) cc_final: 0.7965 (mttm) REVERT: A 883 TYR cc_start: 0.6552 (m-80) cc_final: 0.6046 (m-10) REVERT: A 960 GLN cc_start: 0.7530 (mt0) cc_final: 0.7051 (mm110) REVERT: A 961 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6975 (mt) REVERT: A 1038 LYS cc_start: 0.6764 (mtpp) cc_final: 0.6072 (mttm) REVERT: A 1066 LEU cc_start: 0.8385 (tp) cc_final: 0.7948 (mt) REVERT: A 1106 ILE cc_start: 0.5973 (OUTLIER) cc_final: 0.5653 (tt) REVERT: A 1136 ARG cc_start: 0.6677 (mtt90) cc_final: 0.6249 (mtt-85) REVERT: A 1189 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 1382 ILE cc_start: 0.8325 (pt) cc_final: 0.8008 (pt) REVERT: A 1428 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6246 (mt) REVERT: A 1592 MET cc_start: 0.6503 (mmm) cc_final: 0.5779 (mmm) REVERT: A 1617 LYS cc_start: 0.7367 (mtpt) cc_final: 0.7152 (mmmt) REVERT: A 1748 ASP cc_start: 0.5596 (t0) cc_final: 0.5270 (m-30) REVERT: A 1768 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.6660 (mtm180) REVERT: A 1825 LEU cc_start: 0.7726 (mt) cc_final: 0.7384 (mt) REVERT: A 1878 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5418 (t0) REVERT: A 2085 MET cc_start: 0.3004 (OUTLIER) cc_final: 0.2392 (pmm) REVERT: A 2331 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7386 (tpt) REVERT: A 2341 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5267 (pt) REVERT: A 2423 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (t) REVERT: A 2555 LEU cc_start: 0.7973 (mt) cc_final: 0.7299 (mt) REVERT: A 2576 MET cc_start: 0.3044 (mmt) cc_final: 0.2837 (tpp) REVERT: A 3178 ILE cc_start: 0.6128 (mp) cc_final: 0.5596 (mm) REVERT: A 3708 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.4296 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7351 (m-40) cc_final: 0.7118 (m-40) REVERT: A 3885 ARG cc_start: 0.6869 (ttp-170) cc_final: 0.6641 (mtm-85) REVERT: A 3889 ARG cc_start: 0.7580 (tmt170) cc_final: 0.7029 (ttt-90) REVERT: B 50 GLU cc_start: 0.6664 (tp30) cc_final: 0.6318 (pt0) REVERT: B 102 ILE cc_start: 0.6798 (mm) cc_final: 0.6538 (mm) REVERT: B 156 ASP cc_start: 0.6807 (m-30) cc_final: 0.6439 (m-30) REVERT: B 217 TYR cc_start: 0.3433 (OUTLIER) cc_final: 0.2856 (m-10) REVERT: B 254 ARG cc_start: 0.6605 (ttp-170) cc_final: 0.6184 (ttp-170) REVERT: B 281 LEU cc_start: 0.7387 (pt) cc_final: 0.6387 (mt) REVERT: B 294 GLU cc_start: 0.6403 (tp30) cc_final: 0.6144 (tp30) REVERT: B 341 ASP cc_start: 0.7593 (t0) cc_final: 0.7342 (t0) REVERT: B 363 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7963 (ttm110) REVERT: B 514 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.3868 (mpt) REVERT: C 514 ASN cc_start: 0.5729 (m110) cc_final: 0.5398 (m-40) outliers start: 149 outliers final: 104 residues processed: 687 average time/residue: 0.2403 time to fit residues: 271.6702 Evaluate side-chains 720 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 601 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2859 GLN Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3932 MET Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 248 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 371 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 387 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 GLN A3924 HIS B 101 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** 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 = 0.4417 r_free = 0.4417 target = 0.235407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.195505 restraints weight = 42559.396| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.51 r_work: 0.3764 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 39636 Z= 0.158 Angle : 0.691 12.988 53797 Z= 0.351 Chirality : 0.044 0.258 6135 Planarity : 0.005 0.062 6660 Dihedral : 12.154 144.196 5659 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 3.55 % Allowed : 19.13 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.44 (0.12), residues: 4694 helix: 0.18 (0.10), residues: 2781 sheet: -1.63 (0.36), residues: 195 loop : -2.81 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3159 TYR 0.026 0.002 TYR C 416 PHE 0.026 0.002 PHE A2260 TRP 0.036 0.002 TRP A4127 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00373 (39636) covalent geometry : angle 0.69096 (53797) hydrogen bonds : bond 0.03747 ( 1985) hydrogen bonds : angle 4.54212 ( 5803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 617 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6964 (tt0) cc_final: 0.6759 (tt0) REVERT: A 282 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: A 321 LYS cc_start: 0.6197 (ttmt) cc_final: 0.5784 (mttm) REVERT: A 396 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6589 (p90) REVERT: A 628 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5963 (mp0) REVERT: A 762 TYR cc_start: 0.7619 (t80) cc_final: 0.7401 (t80) REVERT: A 853 ILE cc_start: 0.8166 (mt) cc_final: 0.7700 (mm) REVERT: A 868 LYS cc_start: 0.8308 (mmtp) cc_final: 0.8005 (mttm) REVERT: A 883 TYR cc_start: 0.6747 (m-80) cc_final: 0.6114 (m-10) REVERT: A 960 GLN cc_start: 0.7593 (mt0) cc_final: 0.7118 (mm110) REVERT: A 961 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7045 (mt) REVERT: A 1038 LYS cc_start: 0.6811 (mtpp) cc_final: 0.6065 (mttm) REVERT: A 1066 LEU cc_start: 0.8430 (tp) cc_final: 0.7972 (mt) REVERT: A 1106 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5819 (tt) REVERT: A 1136 ARG cc_start: 0.6720 (mtt90) cc_final: 0.6227 (mtt-85) REVERT: A 1189 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: A 1382 ILE cc_start: 0.8343 (pt) cc_final: 0.8025 (pt) REVERT: A 1428 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6130 (mt) REVERT: A 1617 LYS cc_start: 0.7431 (mtpt) cc_final: 0.7169 (mmmt) REVERT: A 1748 ASP cc_start: 0.5807 (t0) cc_final: 0.5495 (m-30) REVERT: A 1768 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6855 (mtm180) REVERT: A 1825 LEU cc_start: 0.7735 (mt) cc_final: 0.7432 (mt) REVERT: A 1878 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6167 (t0) REVERT: A 2085 MET cc_start: 0.2928 (OUTLIER) cc_final: 0.2324 (pmm) REVERT: A 2220 MET cc_start: 0.7733 (mtt) cc_final: 0.7503 (mtt) REVERT: A 2254 ARG cc_start: 0.5494 (mtp-110) cc_final: 0.5126 (mtp-110) REVERT: A 2331 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: A 2347 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6526 (mttp) REVERT: A 2423 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7708 (t) REVERT: A 2452 ARG cc_start: 0.7542 (tpt170) cc_final: 0.7297 (tpt170) REVERT: A 3178 ILE cc_start: 0.6288 (mp) cc_final: 0.5691 (mm) REVERT: A 3708 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.4490 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7563 (m-40) cc_final: 0.7278 (m-40) REVERT: A 3889 ARG cc_start: 0.7635 (tmt170) cc_final: 0.7084 (ttp80) REVERT: A 4128 MET cc_start: 0.5162 (ttp) cc_final: 0.4954 (ttt) REVERT: B 50 GLU cc_start: 0.6752 (tp30) cc_final: 0.6180 (pt0) REVERT: B 156 ASP cc_start: 0.7105 (m-30) cc_final: 0.6715 (m-30) REVERT: B 217 TYR cc_start: 0.3567 (OUTLIER) cc_final: 0.3002 (m-10) REVERT: B 254 ARG cc_start: 0.6731 (ttp-170) cc_final: 0.6273 (ttp-170) REVERT: B 281 LEU cc_start: 0.7363 (pt) cc_final: 0.6411 (mt) REVERT: B 294 GLU cc_start: 0.6573 (tp30) cc_final: 0.6269 (tp30) REVERT: B 341 ASP cc_start: 0.7866 (t0) cc_final: 0.7573 (t0) REVERT: B 363 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7964 (ttm110) REVERT: B 514 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.3757 (mpt) REVERT: C 29 SER cc_start: 0.7060 (t) cc_final: 0.6786 (p) REVERT: C 150 ILE cc_start: 0.4289 (OUTLIER) cc_final: 0.4033 (pt) REVERT: C 479 THR cc_start: 0.7927 (p) cc_final: 0.7212 (t) REVERT: C 514 ASN cc_start: 0.5952 (m110) cc_final: 0.5620 (m-40) REVERT: C 633 MET cc_start: 0.7076 (mpp) cc_final: 0.6748 (mpp) outliers start: 147 outliers final: 111 residues processed: 701 average time/residue: 0.2546 time to fit residues: 296.5118 Evaluate side-chains 729 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 603 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1898 GLN Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3932 MET Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 168 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 425 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 395 optimal weight: 0.5980 chunk 259 optimal weight: 0.0570 chunk 442 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 474 optimal weight: 8.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.237274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.203488 restraints weight = 42763.059| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.91 r_work: 0.3896 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39636 Z= 0.139 Angle : 0.683 12.809 53797 Z= 0.346 Chirality : 0.043 0.276 6135 Planarity : 0.005 0.062 6660 Dihedral : 12.077 144.769 5659 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.46 % Favored : 90.52 % Rotamer: Outliers : 3.38 % Allowed : 19.52 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.34 (0.12), residues: 4694 helix: 0.26 (0.10), residues: 2786 sheet: -1.52 (0.36), residues: 193 loop : -2.77 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3159 TYR 0.023 0.001 TYR C 416 PHE 0.024 0.001 PHE A4005 TRP 0.035 0.001 TRP A4127 HIS 0.008 0.001 HIS A3924 Details of bonding type rmsd covalent geometry : bond 0.00324 (39636) covalent geometry : angle 0.68295 (53797) hydrogen bonds : bond 0.03600 ( 1985) hydrogen bonds : angle 4.47441 ( 5803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 605 time to evaluate : 1.354 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 138 PHE cc_start: 0.7276 (m-80) cc_final: 0.6860 (m-80) REVERT: A 159 GLU cc_start: 0.6766 (tt0) cc_final: 0.6541 (tt0) REVERT: A 282 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: A 321 LYS cc_start: 0.6168 (ttmt) cc_final: 0.5852 (mttm) REVERT: A 396 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6582 (p90) REVERT: A 583 LEU cc_start: 0.6988 (mt) cc_final: 0.6689 (mt) REVERT: A 628 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5904 (mp0) REVERT: A 762 TYR cc_start: 0.7560 (t80) cc_final: 0.7355 (t80) REVERT: A 853 ILE cc_start: 0.8105 (mt) cc_final: 0.7636 (mm) REVERT: A 868 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7918 (mttm) REVERT: A 883 TYR cc_start: 0.6696 (m-80) cc_final: 0.6074 (m-10) REVERT: A 960 GLN cc_start: 0.7504 (mt0) cc_final: 0.7096 (mm110) REVERT: A 961 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7041 (mt) REVERT: A 1038 LYS cc_start: 0.6727 (mtpp) cc_final: 0.6032 (mttm) REVERT: A 1106 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5667 (tt) REVERT: A 1136 ARG cc_start: 0.6685 (mtt90) cc_final: 0.6209 (mtt-85) REVERT: A 1189 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: A 1351 THR cc_start: 0.6979 (t) cc_final: 0.6733 (p) REVERT: A 1382 ILE cc_start: 0.8292 (pt) cc_final: 0.7963 (pt) REVERT: A 1428 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6157 (mt) REVERT: A 1592 MET cc_start: 0.6284 (mmm) cc_final: 0.5703 (mmm) REVERT: A 1748 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.5336 (m-30) REVERT: A 1768 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6751 (mtm180) REVERT: A 1825 LEU cc_start: 0.7694 (mt) cc_final: 0.7384 (mt) REVERT: A 2085 MET cc_start: 0.3077 (OUTLIER) cc_final: 0.2577 (pmm) REVERT: A 2220 MET cc_start: 0.7612 (mtt) cc_final: 0.7243 (mtt) REVERT: A 2331 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7556 (tpt) REVERT: A 2347 LYS cc_start: 0.6849 (mmtt) cc_final: 0.6409 (mttp) REVERT: A 2423 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7782 (t) REVERT: A 2452 ARG cc_start: 0.7388 (tpt170) cc_final: 0.7133 (tpt170) REVERT: A 3178 ILE cc_start: 0.6101 (mp) cc_final: 0.5541 (mm) REVERT: A 3708 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.4366 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7323 (m-40) cc_final: 0.7079 (m-40) REVERT: A 3889 ARG cc_start: 0.7602 (tmt170) cc_final: 0.7068 (ttt-90) REVERT: B 156 ASP cc_start: 0.6798 (m-30) cc_final: 0.6432 (m-30) REVERT: B 217 TYR cc_start: 0.3470 (OUTLIER) cc_final: 0.2941 (m-10) REVERT: B 254 ARG cc_start: 0.6587 (ttp-170) cc_final: 0.6123 (ttp-170) REVERT: B 281 LEU cc_start: 0.7273 (pt) cc_final: 0.6419 (mt) REVERT: B 294 GLU cc_start: 0.6362 (tp30) cc_final: 0.6064 (tp30) REVERT: B 341 ASP cc_start: 0.7706 (t0) cc_final: 0.7482 (t0) REVERT: B 363 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7916 (ttm110) REVERT: B 409 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 479 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6909 (mp0) REVERT: B 514 MET cc_start: 0.4258 (OUTLIER) cc_final: 0.3708 (mpt) REVERT: C 40 MET cc_start: 0.5184 (ttp) cc_final: 0.4637 (ptt) REVERT: C 150 ILE cc_start: 0.3660 (OUTLIER) cc_final: 0.3366 (pt) REVERT: C 479 THR cc_start: 0.7914 (p) cc_final: 0.7110 (t) REVERT: C 514 ASN cc_start: 0.5865 (m110) cc_final: 0.5555 (m-40) outliers start: 140 outliers final: 109 residues processed: 681 average time/residue: 0.2395 time to fit residues: 267.8996 Evaluate side-chains 719 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 594 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1748 ASP Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3932 MET Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 76 optimal weight: 0.9990 chunk 328 optimal weight: 0.6980 chunk 200 optimal weight: 0.0570 chunk 208 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 390 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 456 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 399 optimal weight: 0.9980 chunk 432 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A1457 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 GLN ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 670 GLN ** 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 = 0.4431 r_free = 0.4431 target = 0.237057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.204187 restraints weight = 42677.289| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.91 r_work: 0.3887 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 39636 Z= 0.143 Angle : 0.692 12.201 53797 Z= 0.350 Chirality : 0.043 0.304 6135 Planarity : 0.005 0.063 6660 Dihedral : 12.050 145.048 5659 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.43 % Rotamer: Outliers : 3.18 % Allowed : 19.73 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.33 (0.12), residues: 4694 helix: 0.26 (0.10), residues: 2790 sheet: -1.55 (0.36), residues: 195 loop : -2.75 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3289 TYR 0.024 0.001 TYR C 416 PHE 0.026 0.001 PHE A4005 TRP 0.039 0.001 TRP A4127 HIS 0.009 0.001 HIS A 935 Details of bonding type rmsd covalent geometry : bond 0.00335 (39636) covalent geometry : angle 0.69163 (53797) hydrogen bonds : bond 0.03638 ( 1985) hydrogen bonds : angle 4.47835 ( 5803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 602 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5175 (ppp) cc_final: 0.4664 (ttm) REVERT: A 159 GLU cc_start: 0.6826 (tt0) cc_final: 0.6473 (tt0) REVERT: A 282 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: A 321 LYS cc_start: 0.6185 (ttmt) cc_final: 0.5736 (mttm) REVERT: A 396 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6607 (p90) REVERT: A 583 LEU cc_start: 0.7018 (mt) cc_final: 0.6719 (mt) REVERT: A 628 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: A 762 TYR cc_start: 0.7548 (t80) cc_final: 0.7337 (t80) REVERT: A 853 ILE cc_start: 0.8116 (mt) cc_final: 0.7648 (mm) REVERT: A 868 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7890 (mttm) REVERT: A 883 TYR cc_start: 0.6716 (m-80) cc_final: 0.6108 (m-10) REVERT: A 961 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7057 (mt) REVERT: A 1038 LYS cc_start: 0.6734 (mtpp) cc_final: 0.6028 (mttm) REVERT: A 1106 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5734 (tt) REVERT: A 1136 ARG cc_start: 0.6674 (mtt90) cc_final: 0.6185 (mtt-85) REVERT: A 1189 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: A 1351 THR cc_start: 0.6909 (t) cc_final: 0.6683 (p) REVERT: A 1382 ILE cc_start: 0.8298 (pt) cc_final: 0.7984 (pt) REVERT: A 1428 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6196 (mt) REVERT: A 1457 GLN cc_start: 0.7613 (mt0) cc_final: 0.7315 (mt0) REVERT: A 1592 MET cc_start: 0.6786 (mmm) cc_final: 0.6062 (mmm) REVERT: A 1614 GLN cc_start: 0.6794 (pt0) cc_final: 0.6541 (mm110) REVERT: A 1768 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6733 (mtm180) REVERT: A 1825 LEU cc_start: 0.7717 (mt) cc_final: 0.7441 (mt) REVERT: A 2085 MET cc_start: 0.3002 (OUTLIER) cc_final: 0.2569 (pmm) REVERT: A 2220 MET cc_start: 0.7611 (mtt) cc_final: 0.7247 (mtt) REVERT: A 2254 ARG cc_start: 0.5200 (mtp-110) cc_final: 0.4858 (mtp-110) REVERT: A 2331 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7408 (tpt) REVERT: A 2423 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7694 (t) REVERT: A 2452 ARG cc_start: 0.7361 (tpt170) cc_final: 0.7087 (tpt170) REVERT: A 2555 LEU cc_start: 0.7936 (mt) cc_final: 0.7663 (mt) REVERT: A 2576 MET cc_start: 0.2778 (ttm) cc_final: 0.1409 (mtt) REVERT: A 3178 ILE cc_start: 0.6087 (mp) cc_final: 0.5532 (mm) REVERT: A 3326 GLN cc_start: 0.5567 (tp40) cc_final: 0.5320 (tm-30) REVERT: A 3654 MET cc_start: 0.1753 (ppp) cc_final: 0.1079 (ppp) REVERT: A 3708 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.4434 (mmt-90) REVERT: A 3808 ASN cc_start: 0.7317 (m-40) cc_final: 0.7090 (m-40) REVERT: A 3889 ARG cc_start: 0.7539 (tmt170) cc_final: 0.6975 (ttt-90) REVERT: B 156 ASP cc_start: 0.6761 (m-30) cc_final: 0.6394 (m-30) REVERT: B 217 TYR cc_start: 0.3580 (OUTLIER) cc_final: 0.3028 (m-10) REVERT: B 254 ARG cc_start: 0.6590 (ttp-170) cc_final: 0.6147 (ttp-170) REVERT: B 281 LEU cc_start: 0.7255 (pt) cc_final: 0.6403 (mt) REVERT: B 294 GLU cc_start: 0.6334 (tp30) cc_final: 0.6100 (tp30) REVERT: B 363 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7914 (ttm110) REVERT: B 409 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.7098 (t80) REVERT: B 479 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6947 (mp0) REVERT: B 514 MET cc_start: 0.4294 (OUTLIER) cc_final: 0.3756 (mpt) REVERT: C 40 MET cc_start: 0.5206 (ttp) cc_final: 0.4668 (ptt) REVERT: C 150 ILE cc_start: 0.3710 (OUTLIER) cc_final: 0.3343 (pt) REVERT: C 479 THR cc_start: 0.7906 (p) cc_final: 0.7134 (t) REVERT: C 514 ASN cc_start: 0.5895 (m-40) cc_final: 0.5540 (m-40) outliers start: 132 outliers final: 108 residues processed: 676 average time/residue: 0.2433 time to fit residues: 272.7278 Evaluate side-chains 721 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 598 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1898 GLN Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3932 MET Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 225 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 344 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A 990 GLN ** A1589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** 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 = 0.4432 r_free = 0.4432 target = 0.237096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.204636 restraints weight = 43000.091| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.89 r_work: 0.3879 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 39636 Z= 0.172 Angle : 0.765 59.177 53797 Z= 0.409 Chirality : 0.044 0.387 6135 Planarity : 0.005 0.063 6660 Dihedral : 12.055 145.010 5659 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.65 % Favored : 90.33 % Rotamer: Outliers : 3.14 % Allowed : 19.78 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -1.33 (0.12), residues: 4694 helix: 0.26 (0.10), residues: 2789 sheet: -1.54 (0.36), residues: 195 loop : -2.75 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3763 TYR 0.023 0.001 TYR C 416 PHE 0.032 0.001 PHE A4005 TRP 0.034 0.002 TRP A4127 HIS 0.010 0.001 HIS A 935 Details of bonding type rmsd covalent geometry : bond 0.00400 (39636) covalent geometry : angle 0.76546 (53797) hydrogen bonds : bond 0.03661 ( 1985) hydrogen bonds : angle 4.48147 ( 5803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8933.79 seconds wall clock time: 154 minutes 40.46 seconds (9280.46 seconds total)